BEGIN:VCALENDAR VERSION:2.0 PRODID:-//CERN//INDICO//EN BEGIN:VEVENT SUMMARY:Welcome DTSTART;VALUE=DATE-TIME:20220228T080000Z DTEND;VALUE=DATE-TIME:20220228T080500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-498@cern.ch DESCRIPTION:https://indico.unina.it/event/57/contributions/498/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/498/ END:VEVENT BEGIN:VEVENT SUMMARY:Colloquium scientifico: Dissecting temperature sensing and epigene tic switching using computational modelling and experiments DTSTART;VALUE=DATE-TIME:20220228T103000Z DTEND;VALUE=DATE-TIME:20220228T113000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-444@cern.ch DESCRIPTION:Speakers: Martin Howard (John Innes Centre\, UK)\nMy group is studying the mechanistic basis of epigenetic regulation in the Polycomb sy stem\, a vital epigenetic silencing pathway that is widely conserved from flies to plants to humans. We use the process of vernalization in plants i n our experiments\, which involves memory of winter cold to permit floweri ng only when winter has passed via quantitative epigenetic silencing of th e floral repressor FLC. Utilising this system has numerous advantages\, in cluding slow dynamics and the ability to read out mitotic heritability of expression states through clonal cell files in the roots. Using computatio nal modelling and experiments (including ChIP and fluorescent reporter ima ging)\, we have shown that FLC cold-induced silencing is essentially an al l-or-nothing (bistable) digital process. The quantitative nature of vernal ization is generated by digital chromatin-mediated FLC silencing in a subp opulation of cells whose number increases with the duration of cold. We ha ve further shown that Polycomb-based epigenetic memory is indeed stored lo cally in the chromatin (in cis) via a dual fluorescent labelling approach. I will also discuss how further predictions from the computational modell ing\, including opposing chromatin modification states and extra protein m emory storage elements\, are being investigated. I will also discuss the m echanisms by which long term fluctuating temperature signals are sensed be fore being converted into digital chromatin states for long term memory st orage.\n\nhttps://indico.unina.it/event/57/contributions/444/ LOCATION: URL:https://indico.unina.it/event/57/contributions/444/ END:VEVENT BEGIN:VEVENT SUMMARY:Mathematical modeling of induced hyperthermia problems DTSTART;VALUE=DATE-TIME:20220228T153000Z DTEND;VALUE=DATE-TIME:20220228T154000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-497@cern.ch DESCRIPTION:Speakers: Marcello Iasiello ()\nhttps://indico.unina.it/event/ 57/contributions/497/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/497/ END:VEVENT BEGIN:VEVENT SUMMARY:MULTI-OMICS SURVEILLANCE OF COVID-19 ALLOWS THE IDENTIFICATION OF CLINICALLY RELEVANT LINEAGES AND HOST TRANSCRIPTIONAL SIGNATURES DTSTART;VALUE=DATE-TIME:20220228T144000Z DTEND;VALUE=DATE-TIME:20220228T145000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-466@cern.ch DESCRIPTION:Speakers: Marcello Salvi ()\nGenomic surveillance of severe ac ute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only approach t o rapidly monitor and tackle emerging variants of concern (VOC) of the COV ID-19 pandemic. Such scrutiny is crucial to limit the spread of VOC that m ight escape the immune protection conferred by vaccination strategies. It is also becoming clear now that efficient genomic surveillance would requ ire monitoring of the host gene expression to identify prognostic biomarke rs of treatments efficacy and disease progression. Here we applied an inte grated workflow for RNA extracted from nasal swabs to obtain in parallel t he full genome of SARS-CoV-2 and transcriptome of host respiratory epithel ium\, altogether representing the majority of Italian processed genomic sa mples. We have matured and applied novel proof-of-principle approaches to prioritize possible gain-of-function mutations by leveraging patients' met adata and isolated patient-specific signatures of SARS-CoV-2 infection. Th e aforementioned goals have all been achieved in a cost-effective manner t hat does not require automation\, in an effort to allow any lab with a ben chtop sequencer and a limited budget to perform integrated genomic surveil lance on premises.\nOur approach extends the scope of SARS-CoV-2 genomic s urveillance\, as it allows for the examination of in-vivo samples characte rized by the predominance of degraded RNA molecules. This competence enabl es overcoming the limitation of in-vitro and single-cell studies\, such as model-specific variations and a small number of samples limit\, respectiv ely. Gene expression data from COVID-19 patients might have a pivotal role as a bridge between genomic data and translational medicine. On one hand\ , finding a gene signature that describes and defines the patient status a fter SARS-CoV-2 infection might support new variants surveillance and addr ess their pathogenic effect on the host. On the other hand\, it might be u sed to evaluate the efficacy of new treatments\, especially non vaccine-ba sed.\n\nhttps://indico.unina.it/event/57/contributions/466/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/466/ END:VEVENT BEGIN:VEVENT SUMMARY:TBD DTSTART;VALUE=DATE-TIME:20220228T171500Z DTEND;VALUE=DATE-TIME:20220228T172500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-495@cern.ch DESCRIPTION:Speakers: Simona Bianco ()\nhttps://indico.unina.it/event/57/c ontributions/495/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/495/ END:VEVENT BEGIN:VEVENT SUMMARY:TBD DTSTART;VALUE=DATE-TIME:20220228T151000Z DTEND;VALUE=DATE-TIME:20220228T152000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-494@cern.ch DESCRIPTION:Speakers: Mattia Conte ()\nhttps://indico.unina.it/event/57/co ntributions/494/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/494/ END:VEVENT BEGIN:VEVENT SUMMARY:The astrophysical side of exobiology: the search for habitable exo planets and life in the Galaxy DTSTART;VALUE=DATE-TIME:20220228T143000Z DTEND;VALUE=DATE-TIME:20220228T144000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-459@cern.ch DESCRIPTION:Speakers: Covone Giovanni (University Federico II)\nThe list o f known exoplanets is rapidly growing (almost 5000 at the moment)\, but we know only an handful of rocky planets in their circumstellar habitable zo ne. We propose a revision of the criteria for defining the habitable zone \, based on the updated knowledge of the role and diffusion of biometals\, and present updated results on the statistics of Earth-like planets in th e Galaxy.\n\nhttps://indico.unina.it/event/57/contributions/459/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/459/ END:VEVENT BEGIN:VEVENT SUMMARY:A fast variational algorithm to detect the clonal copy number subs tructure of tumors from single-cell data DTSTART;VALUE=DATE-TIME:20220228T141000Z DTEND;VALUE=DATE-TIME:20220228T142000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-471@cern.ch DESCRIPTION:Speakers: Antonio De Falco (University of Naples Federico II ( DIETI) & BIOGEM Institute of Molecular Biology and Genetics\, 83031 Arian o Irpino\, Italy)\nUnderstanding intratumor heterogeneity and the interact ions between tumor cells and the immune system is the critical step in the study of tumor growth and evolution. Typically in these studies a large n umber of unsorted cells from tumor biopsies are subject to Single-cell RNA sequencing (scRNA-seq) and then classified as malignant cells\, stromal c ells\, and immune cells.\n \n The distinction of malignant from non- malignant cells is a key step in the follow-up analysis of scRNA-seq tumor datasets. The basic idea to solve such a problem relies on estimating com mon copy number alterations that characterize aneuploidy cells. The copy n umber profiles are obtained by considering the gene expression profiles of each cell as a function of the genomic coordinates. \n \n The main drawback is that the clusters of reference non-malignant cells require man ual identification\, and recent work that tries to overcome this problem i s severely affected by a wrong identification of normal cells and\, simila rly to other methods\, was not designed to perform a complete automatic id entification of the clones\, reporting their breakpoints\, the specific an d shared alteration and a complete clonal deconvolution.\n \n We hav e developed Single CEll Variational ANeuploidy analysis (SCEVAN). It uses a multichannel segmentation algorithm that exploiting the assumption that all the cells in a given copy number clone share the same breakpoints. Th us\, the smoothed expression profile of every individual cell constitutes part of the evidence of the copy number profile in each subclone. SCEVAN e xploit a set of stromal and immune signatures and the fact that malignant cells often harbor aneuploid copy number events to automatically discrimin ate between transformed cells and micro-environment cells. Afterwards\, SC EVAN performs a complete downstream analysis to automatically identify tum or subclones\, classifying their specific and shared alterations up to a c lone phylogeny.\n \n We apply SCEVAN to several datasets encompassin g 106 samples and 93\,322 cells from different tumors types and technologi es. For which SCEVAN exhibits faster and more accurate performance against state-of-the-art methods. Clonal deconvolution extracted from scRNA-seq c an also be used to study tumor evolution\, for example in glioma tumors ha s allowed us to confirming that the heterogeneity of glioma subtypes is dr iven by the clonal architectures and to identify novel drivers of cellular states such as the Proliferative/Progenitor (PPR) subtype.\n \n SCE VAN is available in open source as an R package at the following address \\href{https://github.com/AntonioDeFalco/SCEVAN}{https://github.com/Anto nioDeFalco/SCEVAN}.\n\nhttps://indico.unina.it/event/57/contributions/471/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/471/ END:VEVENT BEGIN:VEVENT SUMMARY:High throughput automated data collection of rodents behavior via digital cages DTSTART;VALUE=DATE-TIME:20220228T134000Z DTEND;VALUE=DATE-TIME:20220228T135000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-453@cern.ch DESCRIPTION:Speakers: Livia D'Angelo (University of Naples Federico II)\nA utomatic analysis of rodent behavior has been receiving growing attention in recent years\, since rodents have been the reference species for many n euroscientific studies. In parallel\, a number of technologies have been d eveloped in a bid to automate the data interpretation. Thanks to the Digit al Ventilated Cage (DVC by Tecniplast)\, a system relying on the detection of animal activity via the generation of tiny electromagnetic fields\, we have recently obtained an unbiased understanding of in-cage spontaneous m ouse behavior and longitudinally tracked locomotor activity in the two sex es of three non-genetically altered mouse strains during a 24-h period for two months. The recorded locomotor activity of the three mice strains was analysed by relying on different and commonly used circadian metrics (i.e .\, day and night activity\, diurnal activity\, responses to lights-on and lights-off phases\, acrophase and activity onset and regularity disruptio n index) to capture key behavioral responses. We compared the 24-h spontan eous locomotor activity of the mice and extrapolated key aspects of the da y and night activity patterns for each strain. All analysed metrics clearl y show significant differences in the circadian activity of the three sele cted strains\, identifying key differences characterizing strain-specific spontaneous locomotor patterns during the 24-h period. The behavioral diff erences were also analysed by an unsupervised machine learning approach. E ach strain corresponded to a cluster\, and notably the repeated and longit udinal measurements of all circadian metrics confirmed that data referring to cages housing each strain were included in a specific cluster. A furth er analysis is in progress to identify the spatial pattern of in-cage reco rded spontaneous locomotor activity of the same mice strains. \n\nFuochi e t al. 2021. Phenotyping spontaneous locomotor activity in inbred and outbr ed mouse strains by using Digital Ventilated Cages. Lab Anim (NY) 50(8):21 5-223. doi: 10.1038/s41684-021-00793-0.\n\nhttps://indico.unina.it/event/5 7/contributions/453/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/453/ END:VEVENT BEGIN:VEVENT SUMMARY:Dr.ssa Valeria Fascione\, Assessore alla Ricerca Regione Campania DTSTART;VALUE=DATE-TIME:20220228T083500Z DTEND;VALUE=DATE-TIME:20220228T084500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-493@cern.ch DESCRIPTION:https://indico.unina.it/event/57/contributions/493/ LOCATION: URL:https://indico.unina.it/event/57/contributions/493/ END:VEVENT BEGIN:VEVENT SUMMARY:Prof. Matteo Lorito\, Rettore Università di Napoli Federico II DTSTART;VALUE=DATE-TIME:20220228T082500Z DTEND;VALUE=DATE-TIME:20220228T083500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-492@cern.ch DESCRIPTION:https://indico.unina.it/event/57/contributions/492/ LOCATION: URL:https://indico.unina.it/event/57/contributions/492/ END:VEVENT BEGIN:VEVENT SUMMARY:Prof. Luca Lista\, Direttore INFN Sezione di Napoli DTSTART;VALUE=DATE-TIME:20220228T081500Z DTEND;VALUE=DATE-TIME:20220228T082500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-491@cern.ch DESCRIPTION:https://indico.unina.it/event/57/contributions/491/ LOCATION: URL:https://indico.unina.it/event/57/contributions/491/ END:VEVENT BEGIN:VEVENT SUMMARY:Prof. Gennaro Miele\, Direttore Dip.to di Fisica Federico II DTSTART;VALUE=DATE-TIME:20220228T080500Z DTEND;VALUE=DATE-TIME:20220228T081500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-490@cern.ch DESCRIPTION:https://indico.unina.it/event/57/contributions/490/ LOCATION: URL:https://indico.unina.it/event/57/contributions/490/ END:VEVENT BEGIN:VEVENT SUMMARY:La TFdA\, la didattica e la terza missione (Prof. Barbara Majello) DTSTART;VALUE=DATE-TIME:20220228T093000Z DTEND;VALUE=DATE-TIME:20220228T094000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-483@cern.ch DESCRIPTION:https://indico.unina.it/event/57/contributions/483/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/483/ END:VEVENT BEGIN:VEVENT SUMMARY:La TFdA\, i Dottorati e l'alta formazione (Prof. Michele Ceccarell i) DTSTART;VALUE=DATE-TIME:20220228T092000Z DTEND;VALUE=DATE-TIME:20220228T093000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-482@cern.ch DESCRIPTION:https://indico.unina.it/event/57/contributions/482/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/482/ END:VEVENT BEGIN:VEVENT SUMMARY:La ricerca scientifica nella TFdA e le sue applicazioni (Prof. Die go Di Bernardo) DTSTART;VALUE=DATE-TIME:20220228T091000Z DTEND;VALUE=DATE-TIME:20220228T092000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-481@cern.ch DESCRIPTION:https://indico.unina.it/event/57/contributions/481/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/481/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduzione Generale (Prof. Tommaso Russo) DTSTART;VALUE=DATE-TIME:20220228T090000Z DTEND;VALUE=DATE-TIME:20220228T091000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-480@cern.ch DESCRIPTION:https://indico.unina.it/event/57/contributions/480/ LOCATION: URL:https://indico.unina.it/event/57/contributions/480/ END:VEVENT BEGIN:VEVENT SUMMARY:Development of mathematical and statistical models for biological processes DTSTART;VALUE=DATE-TIME:20220228T145000Z DTEND;VALUE=DATE-TIME:20220228T150000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-479@cern.ch DESCRIPTION:Speakers: Fabrizio Cartenì ()\n**Abstract:**\n\nResearch acti vities carried out at the Dept. of Agricultural Sciences involve: i) the d evelopment of process-based mechanistic models for the quantitative analys is of biological systems using several approaches such as Ordinary and Par tial Differential Equations (ODE and PDE) and Individual-Based (IBM). In t his context we work on the integration of different approaches to simulate the temporal and spatial dynamics at different scales\; ii) the use of Sy stem Dynamic models (ODE) to simulate the growth of microbial cultures mai nly driven by metabolic fluxes. PDE models have been used to simulate the emergence of vegetation patterns simulating plant-soil interactions and\, with a similar approach\, the differentiation of vascular tissues in plant s\; iii) the implementation of hybrid modeling aiming at integrating conti nuous approaches (ODE\, PDE) within an IBM framework. Such models have bee n proposed and applied at ecological scale to simulate the formation of ve getation patterns and at tissue/organ scale to simulate xylogenesis and wo und closure in plants. The hybrid modeling approach has the big advantage of simulating complex systems as sets of different modules\, which can be implemented in different mathematical approaches most appropriate to rende r the subsystem under consideration\; iv) the implementation of pest model s in a geospatial framework including cyberinfrastructures to enhance mode l development and exploitation. There is a strong connection with the data management part\, since climate\, environmental and pest parameters geosp atial data (cubes) support the deployment and the geospatial usage of the model.\n\n**Recent publications:**\n\n - Cartenì\, F.\, Giannino\, F.\, S chweingruber\, F. H.\, & Mazzoleni\, S. (2014). Modelling the development and arrangement of the primary vascular structure in plants. Annals of Bot any\, 114(4)\, 619–627.\n - Cartenì\, F.\, Deslauriers\, A.\, Rossi\, S .\, Morin\, H.\, De Micco\, V.\, Mazzoleni\, S.\, & Giannino\, F. (2018). The Physiological Mechanisms Behind the Earlywood-To-Latewood Transition: A Process-Based Modeling Approach. Frontiers in Plant Science\, 9\, 1053.\ n - Carteni\, F.\, Occhicone\, A.\, Giannino\, F.\, Vincenot\, C. E.\, de Alteriis\, E.\, Palomba\, E.\, & Mazzoleni\, S. (2020). A General Process- Based Model for Describing the Metabolic Shift in Microbial Cell Cultures. Frontiers in Microbiology\, 11\, 521368.\n - Caputo\, B.\, Langella\, G.\ , Petrella\, V.\, Virgillito\, C.\, Manica\, M.\, Filipponi\, F.\, Varone\ , M.\, Primo\, P.\, Puggioli\, A.\, Bellini\, R.\, D’Antonio\, C.\, Iesu \, L.\, Tullo\, L.\, Rizzo\, C.\, Longobardi\, A.\, Sollazzo\, G.\, Perrot ta\, M. M.\, Fabozzi\, M.\, Palmieri\, F.\, … Salvemini\, M. (2021). Aed es albopictus bionomics data collection by citizen participation on Procid a Island\, a promising Mediterranean site for the assessment of innovative and community-based integrated pest management methods. PLoS Neglected Tr opical Diseases\, 15(9)\, e0009698.\n - Giannino\, F.\, Hay Mele\, B.\, De Micco\, V.\, Toraldo\, G.\, Mazzoleni\, S.\, & Cartenì\, F. (undefined 2 019). An Individual Based Model of Wound Closure in Plant Stems. IEEE Acce ss\, 7\, 65821–65827.\n - Marasco\, A.\, Iuorio\, A.\, Cartení\, F.\, B onanomi\, G.\, Tartakovsky\, D. M.\, Mazzoleni\, S.\, & Giannino\, F. (201 4). Vegetation pattern formation due to interactions between water availab ility and toxicity in plant-soil feedback. Bulletin of Mathematical Biolog y\, 76(11)\, 2866–2883.\n - Martino\, R.\, Nicolazzo\, M.\, & Langella\, G. (2019). A full integrated system for agroclimatic and pest monitoring at farm and landscape scales in Campania Region. IOP Conference Series. Ea rth and Environmental Science\, 275(1)\, 012007.\n - Terribile\, F.\, Bonf ante\, A.\, D’Antonio\, A.\, De Mascellis\, R.\, De Michele\, C.\, Lange lla\, G.\, Manna\, P.\, Mileti\, F. A.\, Vingiani\, S.\, & Basile\, A. (20 17). A geospatial decision support system for supporting quality viticultu re at the landscape scale. Computers and Electronics in Agriculture\, 140\ , 88–102.\n - Vincenot\, C. E.\, Carteni\, F.\, Mazzoleni\, S.\, Rietker k\, M.\, & Giannino\, F. (2016). Spatial Self-Organization of Vegetation S ubject to Climatic Stress-Insights from a System Dynamics-Individual-Based Hybrid Model. Frontiers in Plant Science\, 7\, 636.\n\nhttps://indico.uni na.it/event/57/contributions/479/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/479/ END:VEVENT BEGIN:VEVENT SUMMARY:Triplex-Peptide Nucleic Acid (PNA) biological systems investigated through advanced computational methods DTSTART;VALUE=DATE-TIME:20220228T161500Z DTEND;VALUE=DATE-TIME:20220228T162500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-478@cern.ch DESCRIPTION:Speakers: Antonio Lupia (Department of Pharmacy\, University F ederico II of Naples)\nPeptide Nucleic Acids (PNAs)\, introduced by Nielse n et al. in 1991\, are synthetic DNA/RNA analogues and represent a promisi ng tool for gene modulation in anticancer treatment[1]. In the PNA structu re\, repetitive N-2-aminoethyl-glycine units replace the traditional sugar -phosphate DNA backbone\, and the polyamide chain is connected to nucleoba se covalently via carboxymethyl spacer. Thanks to their uncharged peptidyl backbone and resistance towards chemical and enzymatic degradation\, PNAs can form hybrid complexes with complementary DNA or RNA strands [2-3]. In this view\, advanced computational methods based on both conventional and accelerated Molecular Dynamics (cMD and aMD\, respectively) simulations w ere helpful to accurately elucidate the atomistic structural organisation of two differently protonated PNAs structures wrapped into triplex DNA/PNA . In particular\, aMD allowed us to improve the conformational space sampl ing by reducing energy barriers separating different states of a system\, thus observing atomistic details about the conformational changes of the t wo triplex systems. In fact\, although the mechanistic aspects for the for mation of PNA-DNA triplexes are known\, detailed structural information on the PNA-DNA heterotriplexes are still missing. Our findings are in agreem ent with experimental data and lay the foundation for a further developmen t of novel PNAs in anticancer therapy.\n\n\n[1] Nielsen\, P.E.\, Egholm\, M.\, Berg\, R.H.\, Buchardt\, O.\, 1991. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254\, 1497–1500.\n\n[2] Verona\, M. D. et al. Focus on PNA Flexibility a nd RNA Binding using Molecular Dynamics and Metadynamics. Sci. Rep. 7\, 42 799\;\n\n[3] Zarrilli\, F.\; Amato\, F.\; Morgillo\, C.M.\; Pinto\, B.\; S antarpia\, G.\; Borbone\, N.\; D’Errico\, S.\; Catalanotti\, B.\; Piccia lli\, G.\; Castaldo\, G.\; Oliviero\, G. Peptide Nucleic Acids as miRNA Ta rget Protectors for the Treatment of Cystic Fibrosis. Molecules 2017\, 22\ , 1144.\n\nhttps://indico.unina.it/event/57/contributions/478/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/478/ END:VEVENT BEGIN:VEVENT SUMMARY:Transport Phenomena in Biological Systems: Mathematical models of Cancer Invasion. DTSTART;VALUE=DATE-TIME:20220228T162500Z DTEND;VALUE=DATE-TIME:20220228T163500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-477@cern.ch DESCRIPTION:Speakers: ROSALIA FERRARO (Università degli Studi di Napoli F ederico II)\nIn recent years\, mathematical models are providing fundament al support in cancer research. By accounting for various biological and ph ysical processes\, these models can reveal insights into the dynamics of t umour growth and invasiveness\, thereby allowing the development of pharma cological strategies to control tumour proliferation and invasion. The use of these tools is becoming increasingly widespread in the clinical field\ , predicting in some cases with a very high precision both the course of t he specific patient and his response to therapies. \nCellular automata are simplified\, discrete mechanistic models where a cell population evolves autonomously in time according to pre-defined rules that capture elementar y biological processes\, such as cell proliferation\, cell motility\, and cell-cell interactions. In our work\, a new in silico model able to mimic some of the peculiar characteristics of tumour cells\, such as fast prolif eration\, high cell motility\, impaired cell adhesion\, and elevated sensi tivity to chemotactic stimuli is proposed. The goal of this research\, run in collaboration with Houston Methodist Academic Institute\, is to invest igate tumour growth and invasiveness and its response to specific pharmaco logical treatments. In particular\, tumoral cell motility and invasiveness are investigated mimicking the evolution of cell tissues in 2D and 3D mod els. Numerical predictions are validated by direct comparison with experim ental data developed in-vitro. 2D cell monolayer (Wound Healing) and 3D sp heroids in Extracellular Matrix scaffold have been monitored by Time Lapse microscopy to obtain quantitative measurement of dynamic evolution in in vivo mimicking conditions.\n\nhttps://indico.unina.it/event/57/contributio ns/477/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/477/ END:VEVENT BEGIN:VEVENT SUMMARY:Structural investigation of the ubiquitylation effects on the huma n Bardet-Biedl Syndrome (BBS) complex through Coarse-Grained Molecular Dyn amics simulations DTSTART;VALUE=DATE-TIME:20220228T140000Z DTEND;VALUE=DATE-TIME:20220228T141000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-476@cern.ch DESCRIPTION:Speakers: Federica Moraca (Department of Pharmacy University “Federico II” of Naples)\nBardet-Biedl syndrome (BBS) is a ciliopathy genetic disorder characterized in most cases by obesity\, polydactyly\, re nal dystrophy and cystic kidneys. BBS is strictly related to the hetero-oc tameric protein complex named as BBSome. The recruitment of BBSome into ci lia membranes is mediated by the binding with the GTP binding protein ARL6 \, which binds at the interface between the BBS1 and BBS7 subunit of BBSom e [1]. Specifically\, the ARL6 binding occurs only in the active state of BBSome\, characterized by an open conformation bewteen the BBS1 and BBS7 β-propeller subunits [2]\, while in absence of ARL6 (apo form)\, BBS1 is arranged in a more closed conformation. Additionally\, the most promising structural and functional properties\, are exerted by the BBSome core comp lex formed by the BBS1\, 4\, 8\, 9 and 18 subunits\, with the latter havin g remarkable stabilizing effect on the complex [3]. Experimental data\, re vealed the ubiquitination at K143 residue of BBS1 by the E3 ligase praja2 positively regulates the binding to ARL6\, but a detailed structural mecha nism of action is still unknown\, probably because of the large size of th e system\, which requires long-time scale simulations. We have undertaken this challenge using microseconds-long Coarse-Grained Molecular Dynamics ( CG-MD) simulations on both the homology models of the human sequence of BB Some (wt-hBBSome) and the K143 monoubiquitinated form (Ub-hBBSome)\, follo wed by essential motion analyses. The CG description\, in fact\, allows bu ilding a simplified representation of systems\, resulting in the possibili ty to increase the orders of magnitude in the simulated time and length sc ales. Our advanced computational approach provided structural insights for the comprehension of the Ubiquitin (Ub) role on the BBSome subunits\, rep resenting a valuable therapeutic approach for ciliopathy disorders. \n\n 1. Yang S.\; Bahl K.\; Chou H.T et al. eLife 2020\;9:e55954\n2. Klink U.B. \; Gatsogiannis C.\; Hofnagel O. et al. eLife 2020\;9:e53910\n3. Klink U.B .\; Zent\, E.\; Juneja P. et al. eLife 2017\;6:e27434.\n\nhttps://indico.u nina.it/event/57/contributions/476/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/476/ END:VEVENT BEGIN:VEVENT SUMMARY:Design of a miniaturized iron-sulfur protein DTSTART;VALUE=DATE-TIME:20220228T170500Z DTEND;VALUE=DATE-TIME:20220228T171500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-475@cern.ch DESCRIPTION:Speakers: Marco Chino (Department of Chemical Sciences\, Unive rsity of Naples "Federico II")\nComputational protein design has collected many successes in recent years\,1\,2 however de novo proteins with a tetr athiolate mononuclear metal site have never been characterized both in str ucture and function. In this case\, the selection of the first and second sphere of the iron center able to purposely induce a chosen redox potentia l is still a difficult task3. Besides in repurposed natural scaffolds or i n small cyclic peptide moieties4\, de novo proteins featuring tetrathiolat e metal clusters have never been structurally characterized before. We pre sent\, for the first time\, the structural and functional features of a fu lly designed FeS4 protein and its cognate Zn adduct\, namely METPsc. Inspi red by natural rubredoxins\, this miniaturized protein does not hold any s equence correlation to the known congeners\, as assessed by BLASTP. Striki ngly\, METPsc 28-long sequence stores all the information required to fold around the metal in a tetrahedral geometry and to function as an electron -transfer protein\, as confirmed by crystallography\, UV-Vis and EPR spect roscopy\, and cyclic voltammetry. Finally\, we exploited its terminal elec tron acceptor properties in an artificial electron chain triggered by visi ble light. Its applicability in optoelectronics and light-harvesting biode vices is being explored.\n\n1. F. Pirro\, N. Schmidt\, J. Lincoff\, Z. X. Widel\, N. F. Polizzi\, L. Liu\, M. J. Therien\, M. Grabe\, M. Chino\, A. Lombardi\, W. F. DeGrado\, *Proc. Natl. Acad. Sci.* **2020**\, *117*\, 332 46–33253.\n2. S. La Gatta\, L. Leone\, O. Maglio\, M. De Fenza\, F. Nast ri\, V. Pavone\, M. Chino\, A. Lombardi\, *Molecules* **2021**\, *26*\, 52 21.\n3. E. N. Mirts\, A. Bhagi-Damodaran\, Y. Lu\, *Acc. Chem. Res.* **201 9**\, *52*\, 935–944.\n4. F. Nastri\, D. D’Alonzo\, L. Leone\, G. Zamb rano\, V. Pavone\, A. Lombardi\, *Trends Biochem. Sci.* **2019**\, *44*\, 1022–1040.\n\nhttps://indico.unina.it/event/57/contributions/475/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/475/ END:VEVENT BEGIN:VEVENT SUMMARY:Genomic Medicine applications for diagnosis and discovery in rare diseases DTSTART;VALUE=DATE-TIME:20220228T152000Z DTEND;VALUE=DATE-TIME:20220228T153000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-474@cern.ch DESCRIPTION:Speakers: Michele Pinelli (Department of Molecular Medicine an d Medical Biotechnology)\nGenomic Medicine (GM) is an interdisciplinary me dical specialty\, whose goal is applying genomic information to clinics an d research. Genome data\, such as those generated by microarray (MA) and n ext generation sequencing (NGS)\, are natively digital and thus well suite d for computational analysis and sharing. Nonetheless\, their volume and c omplexity require ad hoc computational approaches and bioinformatics infra structures. Commercial and academic organizations have developed several t ools for common diagnostic purposes\; however\, more complex analyses are still poorly covered. \n\nSince our activity is dedicated to patients with rare diseases who manifest complex phenotypes and undergo multiple genomi c assays\, we have to assemble ad-hoc custom analytical pipelines. \n\nWe developed genePryor\, a prioritization tool for NGS variants. genePryor is aimed to quickly identify known pathogenic variants\, as well as highligh t potential new disease-causing genes and variants. genePryor integrates i nformation from multiple public and user-provided sources\, considers inhe ritance analysis on multiple pedigrees of variable complexity\, and integr ates results from MA and NGS. genePryor has been used to analyze data from the Telethon Undiagnosed Disease Program (TUDP - about 1800 WES)\, contri buting to the high diagnostic yield of the program\, with about 50% conclu sive diagnoses and novel genetic diseases identified. Planned improvements regard integrating tools to automatically match patient-gene phenotypes\, considering non-Mendelian patterns of inheritance (like digeny)\, improvi ng identification of variants with potential regulatory effects.\n\nTo stu dy copy number variants (CNV) with a potential positional effect\, we chal lenged the hypothesis that CNV may affect gene expression and determine a clinical phenotype by altering the genomic region between disease-genes an d their enhancers. We studied 1900 CNVs from the cytogenetic units of Fede rico II and identified 27 CNVs located in gene-enhancer intervals. After m anual curation\, we found a consistent match between the gene and the pati ent phenotypes for a deletion located in the locus of Sonic Hedgehog (SHH) gene carried by a patient with a complex phenotype. For this CNV\, the St rings-and-Binders model supported a slight reduction of gene-enhancer inte ractions\, consistent with a potential positional effect of the variant. W e plan to repeat the analysis on data from public repositories to verify t he generalizability of our hypothesis and to refine the workflow. \n\nPine lli\, M.\, Terrone\, G.\, Troglio\, F.\, Squeo\, G. M.\, Cappuccio\, G.\, Imperati\, F.\, Pignataro\, P.\, Genesio\, R.\, Nitch\, L.\, Del Giudice\, E.\, Merla\, G.\, Testa\, G.\, & Brunetti-Pierri\, N. (2020). A small 7q1 1.23 microduplication involving GTF2I in a family with intellectual disabi lity. *Clinical Genetics* \n\nHaijes\, H. A.\, Koster\, M. J. E.\, Rehmann \, H.\, Li\, D.\, Hakonarson\, H.\, Cappuccio\, G.\, Hancarova\, M.\, Leha lle\, D.\, Reardon\, W.\, Schaefer\, G. B.\, Lehman\, A.\, van de Laar\, I . M. B. H.\, Tesselaar\, C. D.\, Turner\, C.\, Goldenberg\, A.\, Patrier\, S.\, Thevenon\, J.\, Pinelli\, M.\, Brunetti-Pierri\, N.\, … van Hassel t\, P. M. (2019). De Novo Heterozygous POLR2A Variants Cause a Neurodevelo pmental Syndrome with Profound Infantile-Onset Hypotonia. *The American Jo urnal of Human Genetics* \n\nGoldmann\, J. M.\, Wong\, W. S. W.\, Pinelli\ , M.\, Farrah\, T.\, Bodian\, D.\, Stittrich\, A. B.\, Glusman\, G.\, Viss ers\, L. E. L. M.\, Hoischen\, A.\, Roach\, J. C.\, Vockley\, J. G.\, Velt man\, J. A.\, Solomon\, B. D.\, Gilissen\, C.\, & Niederhuber\, J. E. (201 6). Parent-of-origin-specific signatures of de novo mutations. *Nature Gen etics*\n\nhttps://indico.unina.it/event/57/contributions/474/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/474/ END:VEVENT BEGIN:VEVENT SUMMARY:Development and management of databases for geospatial application s\, plant and food sciences\, and marine biology DTSTART;VALUE=DATE-TIME:20220228T173500Z DTEND;VALUE=DATE-TIME:20220228T174500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-473@cern.ch DESCRIPTION:Speakers: Maria Ercolano ()\n**Abstract:**\n\nWe present some of the research lines carried out at the Dept. of Agricultural Sciences ai ming at developing databases for multiple purposes: i) management of geosp atial data\, both vector and raster data models using widespread (postgreS QL+Postgis\, GeoServer) and cutting edge (rasdaman) technologies. Data oth er than geospatial can be stored according to reference standards. Common data include: soil\, vegetation\, pest\, climate\, environment\, hydrology \, and so forth. In the Mascabruno building there is a data center with ~2 00TB of HDD storage and 8 cores rasdaman enterprise license\; ii) with the pressure of feeding an ever growing population and meeting new environme ntal challenges\, future economies and societies will be depending on sust ainable crop production and protection. Through the use of natural plant s timulants\, hormones\, and other nutrients\, research is aiming to improve the efficiency\, the physiological\, and the molecular mechanisms behind these trending supports. We are involved in the development of the Sustain able Crop Production Atlas (SCPA) framework to comprehensively annotate an d disseminate the knowledge involving new ways for sustainable crop produc tion\; iii) PRGdb is a web accessible open-source database that represents the first repository providing a comprehensive overview of pathogen recep tor genes (PRGs) in plants. The database collects information on isolated and predicted pathogen receptor genes (PRG) and tools for facilitating the ir analysis. In the latest version (PRGdb 4.0) a robust prediction tool fo r PRG genes\, named DRAGO 3\, based on HMM and BLAST search is available. Furthermore\, the inferred cross-link between genomic and phenotypic infor mation allows access to a large body of information to find answers to sev eral biological questions.\nIn addition\, the Department contributes on th e implementation of Omics and Metaomics resources in Plant Genomics\, Heal th\, Food Sciences and Nutrigenomics\, and in Marine Biology contributing to EU projects and to European Infrastructures like EMBRC\, ELIXIR\, EMSO and to the European open sciences-life initiatives.\n\n**Recent publicatio ns:**\n\n - Ambrosino\, L.\, Colantuono\, C.\, Monticolo\, F.\, Chiusano\, M.L. (2018) Bioinformatics resources for plant genomics: opportunities an d bottlenecks in the-omics era. Current Issues in Molecular Biology\, 27(1 )\, 71–88.\n - Bancheri\, M.\, Fusco\, F.\, Torre\, D. D.\, Terribile\, F.\, Manna\, P.\, Langella\, G.\, De Vita\, P.\, Allocca\, V.\, Loishandl- Weisz\, H.\, Hermann\, T.\, De Michele\, C.\, Coppola\, A.\, Mileti\, F. A .\, & Basile\, A. (2022). The pesticide fate tool for groundwater vulnerab ility assessment within the geospatial decision support system LandSupport . The Science of the Total Environment\, 807(Pt 1)\, 150793.\n - Bostan\, H\, Chiusano\, M.L. (2015) NexGenEx-Tom: a gene expression platform to inv estigate the functionalities of the tomato genome\, BMC plant biology\, 15 (1)\, 1–13.\n - Calle García\, J.\, Guadagno\, A.\, Paytuvi-Gallart\, A .\, Saera-Vila\, A.\, Amoroso\, C. G.\, D’Esposito\, D.\, Andolfo\, G.\, Aiese Cigliano\, R.\, Sanseverino\, W.\, & Ercolano\, M. R. (2022). PRGdb 4.0: an updated database dedicated to genes involved in plant disease res istance process. Nucleic Acids Research\, 50(D1)\, D1483–D1490.\n - Lang ella\, G.\, Basile\, A.\, Giannecchini\, S.\, Moccia\, F. D.\, Mileti\, F. A.\, Munafó\, M.\, Pinto\, F.\, & Terribile\, F. (2020). Soil Monitor: a n internet platform to challenge soil sealing in Italy. Land Degradation & Development\, 31(18)\, 2883–2900.\n - Monticolo\, F.\, Palomba\, E.\, D e Santis\, R.\, Assentato\, L.\, Triscino\, V.\, Langella\, M. C.\, Lanzot ti\, V.\, & Chiusano\, M. L. (2020). anti-HCoV: A web resource to collect natural compounds against human coronaviruses. Trends in Food Science & Te chnology\, 106\, 1–11.\n - Plant Cell Atlas Consortium\, Jha\, S. G.\, B orowsky\, A. T.\, Cole\, B. J.\, Fahlgren\, N.\, Farmer\, A.\, Huang\, S.- S. C.\, Karia\, P.\, Libault\, M.\, Provart\, N. J.\, Rice\, S. L.\, Saura -Sanchez\, M.\, Agarwal\, P.\, Ahkami\, A. H.\, Anderton\, C. R.\, Briggs\ , S. P.\, Brophy\, J. A.\, Denolf\, P.\, Di Costanzo\, L. F.\, … Rhee\, S. Y. (2021). Vision\, challenges and opportunities for a Plant Cell Atlas . eLife\, 10. https://doi.org/10.7554/eLife.66877.\n - Tangherlini\, M.\, Miralto\, M.\, Colantuono\, C.\, Sangiovanni\, M.\, Dell’ Anno\, A.\, Co rinaldesi\, C.\, Danovaro\, R.\, & Chiusano\, M. L. (2018). GLOSSary: the GLobal Ocean 16S subunit web accessible resource. BMC Bioinformatics\, 19( Suppl 15)\, 443.\n - Osuna-Cruz\, C. M.\, Paytuvi-Gallart\, A.\, Di Donato \, A.\, Sundesha\, V.\, Andolfo\, G.\, Aiese Cigliano\, R.\, Sanseverino\, W.\, & Ercolano\, M. R. (2018). PRGdb 3.0: a comprehensive platform for p rediction and analysis of plant disease resistance genes. Nucleic Acids Re search\, 46(D1)\, D1197–D1201.\n\nhttps://indico.unina.it/event/57/contr ibutions/473/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/473/ END:VEVENT BEGIN:VEVENT SUMMARY:Multi-omics analyses for plant genetics\, food sciences\, and micr obiome studies DTSTART;VALUE=DATE-TIME:20220228T115000Z DTEND;VALUE=DATE-TIME:20220228T120000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-472@cern.ch DESCRIPTION:Speakers: Nunzio D'Agostino ()\n**Abstract:**\n\nHigh-throughp ut techniques and experiments enable researchers to investigate complex bi ological processes through large-scale analysis of omics data. The growth of big omics data entails continuous computational challenges in the colle ction\, management\, analysis and interpretation (mining) of data\, as wel l as in their sharing\, visualization\, storage and integration to obtain emerging information necessary to understand the biology of complex system s (systems biology). Indeed\, It is imperative to undertake an integrative approach that combines multi-omics data to highlight the interrelationshi ps of different classes of biomolecules and their functions\, and to inves tigate the biological system as a whole (holistic approach).\n\nWe present some of the research activities carried out at the Dept. of Agricultural Sciences with the aim of developing computational tools and applying multi -omics data analysis strategies for multiple purposes. The spread of incre asingly efficient methods for the sequencing of DNA (genomics and metageno mics) and RNA (transcriptomics) and of NGS-based genotyping techniques all owed to (i) explore the “sequence space”\; (ii) investigate genome str ucture and organization\; (iii) characterize gene function and gene expres sion patterns\; (iv) study food and human microbiomes\, with particular f ocus on large-scale analyses performed at strain-level resolution\; (v) pr ovide high-resolution profiling of nucleotide variation within germplasm c ollections (population genomics)\; (vi) discover loci that are associated with key agronomic traits via genome-wide association studies\; (vii) stud y molecular mechanisms involved in plant-microbe interaction.\n\n**Recent publications:**\n\n - Andolfo\, G.\, Schuster\, C.\, Gharsa\, H. B.\, Ruoc co\, M.\, & Leclerque\, A. (2021). Genomic analysis of the nomenclatural t ype strain of the nematode-associated entomopathogenic bacterium Providenc ia vermicola. BMC Genomics\, 22(1)\, 708.\n - Chiusano\, M. L.\, Incerti\, G.\, Colantuono\, C.\, Termolino\, P.\, Palomba\, E.\, Monticolo\, F.\, B envenuto\, G.\, Foscari\, A.\, Esposito\, A.\, Marti\, L.\, de Lorenzo\, G .\, Vega-Muñoz\, I.\, Heil\, M.\, Carteni\, F.\, Bonanomi\, G.\, & Mazzol eni\, S. (2021). Arabidopsis thaliana Response to Extracellular DNA: Self Versus Nonself Exposure. Plants\, 10(8). https://doi.org/10.3390/plants100 81744.\n - Cigliano\, R. A.\, Aversano\, R.\, Di Matteo\, A.\, Palombieri\ , S.\, Termolino\, P.\, Angelini\, C.\, Bostan\, H.\, Cammareri\, M.\, Con siglio\, F. M.\, Ragione\, F. D.\, Paparo\, R.\, Valkov\, V. T.\, Vitiello \, A.\, Carputo\, D.\, Chiusano\, M. L.\, D’Esposito\, M.\, Grandillo\, S.\, Matarazzo\, M. R.\, Frusciante\, L.\, … Conicella\, C. (2022). Mult i-omics data integration provides insights into the post-harvest biology o f a long shelf-life tomato landrace. Horticulture Research. https://doi.or g/10.1093/hr/uhab042.\n - De Filippis\, F.\, Pasolli\, E.\, & Ercolini\, D . (2020). Newly Explored Faecalibacterium Diversity Is Connected to Age\, Lifestyle\, Geography\, and Disease. Current Biology: CB\, 30(24)\, 4932 –4943.e4.\n - De Filippis\, F.\, Paparo\, L.\, Nocerino\, R.\, Della Gat ta\, G.\, Carucci\, L.\, Russo\, R.\, Pasolli\, E.\, Ercolini\, D.\, & Ber ni Canani\, R. (2021). Specific gut microbiome signatures and the associat ed pro-inflamatory functions are linked to pediatric allergy and acquisiti on of immune tolerance. Nature Communications\, 12(1)\, 5958.\n - De Palma \, M.\, Salzano\, M.\, Villano\, C.\, Aversano\, R.\, Lorito\, M.\, Ruocco \, M.\, Docimo\, T.\, Piccinelli\, A. L.\, D’Agostino\, N.\, & Tucci\, M . (2019). Transcriptome reprogramming\, epigenetic modifications and alter native splicing orchestrate the tomato root response to the beneficial fun gus Trichoderma harzianum. Horticulture Research\, 6\, 5.\n - Monticolo\, F.\, & Chiusano\, M. L. (2021). Computational Approaches for Cancer-Fighti ng: From Gene Expression to Functional Foods. Cancers\, 13(16). https://do i.org/10.3390/cancers13164207.\n - Monticolo\, F.\, Palomba\, E.\, & Chius ano\, M. L. (2021). Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae. Cell Death Discovery\, 7(1)\, 17.\n - Palmieri\, D.\, Vitale\, S.\, Lima\, G.\, Di Pietro\, A.\, & Turrà\, D. ( 2020). A bacterial endophyte exploits chemotropism of a fungal pathogen fo r plant colonization. Nature Communications\, 11(1)\, 5264.\n - Pasolli\, E.\, Asnicar\, F.\, Manara\, S.\, Zolfo\, M.\, Karcher\, N.\, Armanini\, F .\, Beghini\, F.\, Manghi\, P.\, Tett\, A.\, Ghensi\, P.\, Collado\, M. C. \, Rice\, B. L.\, DuLong\, C.\, Morgan\, X. C.\, Golden\, C. D.\, Quince\, C.\, Huttenhower\, C.\, & Segata\, N. (2019). Extensive Unexplored Human Microbiome Diversity Revealed by Over 150\,000 Genomes from Metagenomes Sp anning Age\, Geography\, and Lifestyle. Cell\, 176(3)\, 649–662.e20.\n - Pasolli\, E.\, De Filippis\, F.\, Mauriello\, I. E.\, Cumbo\, F.\, Walsh\ , A. M.\, Leech\, J.\, Cotter\, P. D.\, Segata\, N.\, & Ercolini\, D. (202 0). Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nature Communications\, 11(1)\, 2610.\n - Pavan\, S.\, Delvento\, C.\, Ricciardi\, L.\, Lotti\, C.\, Ciani\, E.\, & D’Ago stino\, N. (2020). Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies . Frontiers in Genetics\, 11\, 447.\n - Vitale\, S.\, Di Pietro\, A.\, & T urrà\, D. (2019). Autocrine pheromone signalling regulates community beha viour in the fungal pathogen Fusarium oxysporum. Nature Microbiology\, 4(9 )\, 1443–1449.\n - Zotti\, M.\, De Filippis\, F.\, Cesarano\, G.\, Ercol ini\, D.\, Tesei\, G.\, Allegrezza\, M.\, Giannino\, F.\, Mazzoleni\, S.\, & Bonanomi\, G. (2020). One ring to rule them all: an ecosystem engineer fungus fosters plant and microbial diversity in a Mediterranean grassland. The New Phytologist\, 227(3)\, 884–898.\n\nhttps://indico.unina.it/even t/57/contributions/472/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/472/ END:VEVENT BEGIN:VEVENT SUMMARY:PROTEOMICS INVESTIGATION TO UNVEIL MOLECULAR DETAILS OF CELLULAR P ROCESSES DTSTART;VALUE=DATE-TIME:20220228T165500Z DTEND;VALUE=DATE-TIME:20220228T170500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-470@cern.ch DESCRIPTION:Speakers: FLORA COZZOLINO (Dipartimento di Scienze Chimiche\, Università di Napoli “Federico II”\, Complesso Universitario di Monte Sant'Angelo\, Via Cintia 4\, 80125\, Napoli\, Italy\; e CEINGE Biotecnolo gie Avanzate s.c.a r.l.\, Via G. Salvatore 486\, 80145\, Napoli\, Italy)\, Vittoria Monaco (Dipartimento di Scienze Chimiche\, Università di Napoli “Federico II”\, Complesso Universitario di Monte Sant'Angelo\, Via Ci ntia 4\, 80125\, Napoli\, Italy\; e CEINGE Biotecnologie Avanzate s.c.a r. l.\, Via G. Salvatore 486\, 80145\, Napoli\, Italy)\, Monti Maria (Dipart imento di Scienze Chimiche\, Università di Napoli “Federico II”\, Com plesso Universitario di Monte Sant'Angelo\, Via Cintia 4\, 80125\, Napoli\ , Italy\; e CEINGE Biotecnologie Avanzate s.c.a r.l.\, Via G. Salvatore 48 6\, 80145\, Napoli\, Italy)\nThe "Omics Sciences" have revolutionized mode rn biology. To date\, there is no scientific field\, from medicine to envi ronmental sciences\, passing through biochemistry and pharmacology that do es not resort to these sciences for the study of complex biological system s.\nProteomics among these fields aims to study the entire set of constitu tive proteins of a tissue\, an organism in specific moment with the ambiti ous prospect of correlating this ‘molecular snapshot’ to the observed phenotype.\nFrom the conception of proteomics as a large-scale evolution o f the chemistry and biochemistry of proteins\, we have gradually come to t he definition of a science that has revolutionized the central dogma of bi ology highlighting how every metabolic and functional process is the resul t of a complex network of nonlinear interactions between genes\, transcrip ts and proteins.\nThe bursting success of Proteomics and all other “Omic s Sciences” has been possible in the last decade thanks to the strong te chnological push supported by the development of powerful bioinformatics t ools that allow the qualitative and quantitative analysis of mass spectrom etry data\, together with functional analysis and correlation of the genes \, transcripts\, proteins or metabolites to reconstruct the appropriate re lationship networks. \nIn the field of Proteomics investigation\, two main application areas have been taken off: functional proteomics\, which aims to define the molecular mechanisms underlying biological processes of int erest through to the identification of in vivo protein-protein interaction (PPI) [1]\; differential proteomics\, addressed to the comparison of prot ein expression profiles in multiple biological conditions\, e. g. wild typ e vs mutant or vs pharmacologically treated\, etc\, in order to define the biological processes affected by the specific treatment or condition. Dif ferent methodologies have been developed to carry out the qualitative-quan titative analyses of the protein content in samples using both labelled an d label-free approaches. [2]\nAmong many application fields\, both these a pproaches are also largely employed in the investigation of a biological p rocess\, both in physiological and pathological conditions such as oncolog ical diseases [3]\, neurodegenerative disorders\, [4]\, as it will be disc ussed in the current presentation. \n\n[1] Iacobucci I. et al. J Proteomic s. J Proteomics. 2021 Jan 6\; 230: 103990. \n[2] Cozzolino F. et al PLoS O ne. 2020 Sep 4\;15(9): e0238037.\n[3] Federico A. et al. Biochim Biophys A cta Gene Regul Mech. 2019 Apr\;1 862(4):509-521.\n[4] Cozzolino F. et al. Hum Mol Genet. 2021 Jun 17\;30(13):1175-1187.\n\nhttps://indico.unina.it/e vent/57/contributions/470/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/470/ END:VEVENT BEGIN:VEVENT SUMMARY:Red blood cell deformability and aggregation: implications for omi cs analysis DTSTART;VALUE=DATE-TIME:20220228T135000Z DTEND;VALUE=DATE-TIME:20220228T140000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-469@cern.ch DESCRIPTION:Speakers: GIOVANNA TOMAIUOLO (Dipartimento di Ingegneria Chimi ca\, dei Materiali e della Produzione Industriale\, Università di Napoli Federico II)\nBlood is a complex fluid with non-Newtonian characteristics. It consists primarily of a concentrated suspension of deformable red bloo d cells (RBCs) [1] which tend to aggregate reversibly in microstructures\, such as rouleaux\; this tendency is a major contributor to the viscoelast ic flow behavior of blood. Human blood mechanical response is strongly aff ected by RBC properties\, such as volume fraction\, deformability and aggr egation [2]. In particular\, the tendency of RBCs to form packed structure s plays an important role in blood flow behavior\, causing the increase of blood viscosity\, especially at low shear rates. Currently\, both researc h and clinical hemorheology is mostly based on steady shear measurements t o obtain the apparent blood viscosity [3]. However\, linear viscoelastic t ests\, such as oscillatory shear\, can provide valuable information about blood microstructure\, but few results are available in the literature. Re cently\, blood viscoelastic moduli have been investigated by passive micro rheology [4]\, but the application of this technique to a heterogeneous ma terial such as blood is questionable.\nHere\, we present a systematic set of oscillatory shear measurements by conventional bulk rheology to evaluat e storage and loss moduli of whole human blood. The rheological behavior o f human blood was characterized both in physiological conditions and in RB C aggregating media. The latter ones were obtained by the addition of a po lymer and by increasing the hematocrit above the normal physiological leve ls [5].\n\n\n[1] G. Tomaiuolo et al.\, Soft Matter 5\, 2009.\n[2] O. K. Ba skurt\, and H. J. Meiselman\, in Seminars in thrombosis and hemostasis (Ne w York: Stratton Intercontinental Medical Book Corporation\, 2003.\n[3] O. K. Baskurt et al.\, Clinical hemorheology and microcirculation 42\, 2009. \n[4] L. Campo-Deaño et al.\, Biomicrofluidics 7\, 2013.\n[5] Tomai uolo G et al. Rheologica Acta 55(6)\, 2016.\n\nhttps://indico.unina.it/eve nt/57/contributions/469/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/469/ END:VEVENT BEGIN:VEVENT SUMMARY:Cell regulation and multicellular control for applications in Synt hetic Biology DTSTART;VALUE=DATE-TIME:20220228T142000Z DTEND;VALUE=DATE-TIME:20220228T143000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-468@cern.ch DESCRIPTION:Speakers: DAVIDE FIORE (Università degli Studi di Napoli "Fed erico II")\nSynthetic Biology aims at engineering biological systems with new functionalities\, with applications ranging from health treatments to bioremediation\, production of biofuels and drugs in bioreactors. This is made possible by embedding artificial genetic circuits into living cells\, such as bacteria\, yeast\, and fungi\, modifying their natural behavior\; that is\, by synthetically modifying when and how much genes are expresse d to produce proteins or other chemicals of interest.\nIn this talk we wil l briefly present the work that we have done at the University of Naples i n the context of the project COSY-BIO funded by the European Union\, which finished last year\, and some of the ongoing research.\nOur work has been focused on the exploitation of the so-called “genetic toggle-switch”\ , which is a fundamental component in Synthetic Biology as it plays a key role in cell differentiation and decision making. Its importance comes fro m its ability to endow host cells with memory of previous stimuli allowing them to completely change their behavior in response. Specifically\, we p resent how\, thanks to its characteristics\, the genetic toggle-switch can be used either to regulate the expression of two proteins of interest to some intermediate level [1-2] or as a reversible memory mechanism allowing cells to differentiate and balance labor in multicellular applications [3 -4]. Moreover\, we present some recent results on the control of the ratio and the growth rate of cell populations for biomedical and industrial app lications [5-7].\n\n\n[1] D. Fiore\, A. Guarino\, M. di Bernardo – “An alysis and control of genetic toggle switches subject to periodic multi-in put stimulation”\, IEEE Control Systems Letters (2018)\n\n[2] A. Guarino \, D. Fiore\, D. Salzano\, M. di Bernardo – "Balancing cell populations endowed with a synthetic toggle switch via adaptive pulsatile feedback con trol"\, ACS Synthetic Biology (2020)\n\n[3] D. Fiore\, D. Salzano\, E. Cri stòbal-Cóppulo\, J.M. Olm\, M. di Bernardo – "Multicellular feedback c ontrol of a genetic toggle-switch in microbial consortia"\, IEEE Control S ystems Letters (2020)\n\n[4] D. Salzano\, D. Fiore\, M. di Bernardo – “Ratiometric control for differentiation of cell populations endowed wit h synthetic toggle switches”\, Proc. of the 58th IEEE Conference on Deci sion and Control (2019)\n\n[5] D. Fiore\, F. Della Rossa\, A. Guarino\, M. di Bernardo – "Feedback ratiometric control of two microbial population s in a single chemostat"\, IEEE Control Systems Letters (2021)\n\n[6] V. F usco\, D. Salzano\, D. Fiore\, M. di Bernardo – "Embedded control of cel l growth using tunable genetic systems"\, International Journal of Robust and Nonlinear Control (2022)\n\n[7] G. Perrino\, S. Napolitano\, F. Galdi\ , A. La Regina\, D. Fiore\, T. Giuliano\, M. di Bernardo\, D. di Bernardo – "Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control"\, Nature Communications (2021)\n\nhttps://in dico.unina.it/event/57/contributions/468/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/468/ END:VEVENT BEGIN:VEVENT SUMMARY:TOWARDS THE DESIGN OF CELL DIVISION CYCLE 25 PHOSPHATASES INHIBITO RS AS ANTICANCER AGENTS DTSTART;VALUE=DATE-TIME:20220228T164500Z DTEND;VALUE=DATE-TIME:20220228T165500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-467@cern.ch DESCRIPTION:Speakers: Carmen Cerchia (Department of Pharmacy\, “Drug Dis covery” Laboratory\, University of Naples Federico II\, Via D. Montesano \, 49\, 80131 Naples\, Italy)\nCDC25 phosphatases (CDC25S) are members of the family of dual-specificity phosphatases (DSPs) and play a critical rol e in the regulation of the cell cycle. The overexpression of CDC25s in man y human cancers supports their clinical significance and has encouraged th e pursuit of specific small-molecule inhibitors. Unfortunately\, there are currently no available CDC25 inhibitors with clinical utility. In recent years\, our research group has been actively involved in this field\, by d iscovering new drug-like CDC25s targeting molecules endowed with marked an tiproliferative effect at cancer cells. Starting from the initial identifi cation of new lead compounds by structure-based virtual screening [1]\, we then embarked on a medicinal chemistry optimization program\, involving m ultidisciplinary approaches and in particular computational techniques\, w hich eventually led to the discovery of novel chemotypes able to potently inhibit melanoma cells proliferation by triggering apoptosis [2\,3]. Thus\ , CDC25s targeting might open up a new avenue for drug intervention in ant imelanoma therapy.\n\n\n\nReferences\n\n[1] Lavecchia\, A. et al. J. Med. Chem. 2012\, 55\, 4142-4158.\n\n[2] Capasso\, A. et al. Oncotarget 2015\, 6\, 40202-40222.\n\n[3] Cerchia\, C. et al. J. Med. Chem. 2019\, 62\, 708 9-7110.\n\nhttps://indico.unina.it/event/57/contributions/467/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/467/ END:VEVENT BEGIN:VEVENT SUMMARY:Insights on Gastric Cancer: applied bioinformatics approaches DTSTART;VALUE=DATE-TIME:20220228T121000Z DTEND;VALUE=DATE-TIME:20220228T122000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-465@cern.ch DESCRIPTION:Speakers: Pietro Zoppoli (DMMBM - Federico II)\nGastric cancer (GC) remains one of the major causes of cancer-related mortality worldwid e. Molecular heterogeneity is a major determinant for the clinical outcome s and an exhaustive tumor classification is currently missing. Histologica lly normal tissue adjacent to the tumor (NAT) is commonly used as a contro l in cancer studies\, nevertheless shows unique characteristics in several tumor types\, possibly leading to suboptimal tumor features definition. M oreover\, several limitations to the success of current therapeutic GC tre atments may be due to cancer drug resistance that leads to tumor recurrenc e and metastasis. Apoptosis evasion represents a causative factor for trea tment failure in GC as in other cancers and intracellular calcium homeosta sis regulation has been found to be associated with apoptosis resistance. Finally\, although extensive literature was produced to better define Laur en’s classification subgroups\, characterizing pathways and actionable c andidates in clinical practice are still missing.\nHere I’d like to show :\n\n 1. Our efforts to molecularly define the gastric NATs and their\n confounding impact on GC analyses. \n 2. The prognostic value for TRPV2 calcium channel expression in GC and its role as potential target for over coming cisplatin resistance by promoting apoptosis.\n 3. The molecular dif ferences\, the active subnetworks\, the prognostic and\n actionable can didates between Lauren’s Diffuse and the Intestinal\n subtypes.\n\nBi bliography\n\nRussi S\, Calice G\, Ruggieri V\, Laurino S\, La Rocca F\, A mendola E\, Lapadula C\, Compare D\, Nardone G\, Musto P\, De Felice M\, F alco G\, Zoppoli P. Gastric Normal Adjacent Mucosa Versus Healthy and Canc er Tissues: Distinctive Transcriptomic Profiles and Biological Features. C ancers (Basel). 2019 Aug 26\;11(9):1248. doi: 10.3390/cancers11091248. PMI D: 31454993\; PMCID: PMC6769942.\n\nZoppoli P\, Calice G\, Laurino S\, Rug gieri V\, La Rocca F\, La Torre G\, Ciuffi M\, Amendola E\, De Vita F\, Pe trillo A\, Napolitano G\, Falco G\, Russi S. TRPV2 Calcium Channel Gene Ex pression and Outcomes in Gastric Cancer Patients: A Clinically Relevant As sociation. J Clin Med. 2019 May 11\;8(5):662. doi: 10.3390/jcm8050662. PMI D: 31083561\; PMCID: PMC6572141.\n\nLaurino S\, Mazzone P\, Ruggieri V\, Z oppoli P\, Calice G\, Lapenta A\, Ciuffi M\, Ignomirelli O\, Vita G\, Sgam bato A\, Russi S\, Falco G. Cationic Channel TRPV2 Overexpression Promotes Resistance to Cisplatin-Induced Apoptosis in Gastric Cancer Cells. Front Pharmacol. 2021 Oct 4\;12:746628. doi: 10.3389/fphar.2021.746628. PMID: 34 671260\; PMCID: PMC8521017.\n\nhttps://indico.unina.it/event/57/contributi ons/465/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/465/ END:VEVENT BEGIN:VEVENT SUMMARY:Global transcriptome and chromatin occupancy analysis reveal the c rucial role of p63 and p73 in skin carcinoma development DTSTART;VALUE=DATE-TIME:20220228T163500Z DTEND;VALUE=DATE-TIME:20220228T164500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-464@cern.ch DESCRIPTION:Speakers: DARIO ANTONINI (Università di Napoli "Federico II") \nAberrant expression of transcriptional regulators can affect oncogenic g ene expression programs in cancer. Mutations in the tumor suppressor TP53 (p53) are commonly found in UV-damaged skin and are thought to protect dam aged epidermal cells from senescence and or oncogene-induced apoptosis\, f avoring cancer formation. In contrast\, the other p53 family members TP63 (p63) and TP73 (p73) are rarely mutated in cancer and TP63 is often amplif ied or overexpressed in squamous cell carcinoma (SCC). Here\, we demonstra te that both p63 and p73 are required for cell proliferation in skin SCC a nd are overexpressed in preneoplastic lesions and in skin SCCs. p63/p73 fo rm heterotetramers and co-occupy thousands of regulatory regions\, jointly controlling a transcriptional program that promotes cell proliferation an d tumorigenesis. Combining gene targeting with transcriptomic and epigenet ic analyses revealed that p63 and p73 control a transcriptional feed-forwa rd circuit that sustains cell proliferation. We find that in skin SCC a ke y signaling pathway downstream of p63/p73 is the Epidermal Growth Factor R eceptor (EGFR)/MAP kinase. p63/p73 directly and positively control transcr iption of the EGFR ligands\, among which amphiregulin (AREG) is the most h ighly expressed. p63\, p73 and AREG are required to maintain skin SCC prol iferative potential\, anchorage independent growth\, and to promote tumori genesis. Thus\, p63 and p73 act as oncogenic drivers in skin SCC\, and ARE G is a crucial non-cell-autonomous effector downstream of p63 and p73 in s kin SCC formation.\n\nhttps://indico.unina.it/event/57/contributions/464/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/464/ END:VEVENT BEGIN:VEVENT SUMMARY:MultiOmics Network Embedding for SubType Analysis DTSTART;VALUE=DATE-TIME:20220228T120000Z DTEND;VALUE=DATE-TIME:20220228T121000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-463@cern.ch DESCRIPTION:Speakers: Giovanni Scala ()\nBiological systems are complex en tities whose behavior emerges from an enormous number of reactions taking place within and among different internal molecular districts. The dissect ion and the modeling of the entities and the interactions constituting the se interactions are essential in biological processes behind normal and pa thological conditions as well as the perturbations induced by the exposure to external molecules like drugs. The recent explosion of omics data fuel ed the creation of diverse systems biology models. The majority of these a re focused on the representation of interactions taking place in single mo lecular districts and have been successfully used to perform sample strati fication\, especially in cancer disease. Despite the usefulness proven by these models\, they still did not reach the level of complexity needed to distinguish different biological conditions. \n\nOne step forward in this direction is the creation of multi-omics models capturing the dynamics ta king place within and between omics layers. This latter approach needs pow erful modeling strategies and is still an open research field. \nWe propos e the application of a powerful AI technique based on graph embedding for the creation of a system that\, starting from multi-omics measurements\, i s able to model and generate knowledge about multi-omics interactions.\n\n Here we present a novel approach implemented as an R package named MultiOm ics Network Embedding forSubType Analysis (MoNETA) for the identification of relevant multi omics relationships between biological samples.\nThis ap proach has been applied in the identification of different cancer subtypes using multi omics data form the The Cancer Genome Atlas (TCGA) and the Cl inical Proteomic Tumor Analysis Consortium (CPTAC) datasets.\nMoNETA will be freely available as an R package at https://github.com/BioinfoUninaScal a/MoNETA.\n\nhttps://indico.unina.it/event/57/contributions/463/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/463/ END:VEVENT BEGIN:VEVENT SUMMARY:EpiStatProfiler: a novel workflow for the qualitative analysis of DNA methylation DTSTART;VALUE=DATE-TIME:20220228T181500Z DTEND;VALUE=DATE-TIME:20220228T182500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-462@cern.ch DESCRIPTION:Speakers: Antonella Sarnataro (Molecular Medicine and Medical Biotechnology\, University Federico II)\nMotivation: DNA methylation is an epigenetic modification\, primarily occurring at CpG sites\, that is invo lved in major biological mechanisms\, such as the regulation of gene expre ssion and the genome stability. Typically\, association studies based on t his modification are focused on the identification of genomic regions whos e average DNA methylation differs among distinct conditions. However\, stu dying the methylation status of cytosines at single-molecule level can pro vide additional insights about the cell-to-cell heterogeneity and the cell clonality within a sample. In this context\, all the different combinatio ns of CpGs methylation states that can be observed in a given locus are de fined as epialleles. Several bioinformatic tools have been developed to ex tract epiallelic information from bisulfite sequencing data. Nevertheless\ , these tools have some limitations on the selection of the regions that c an be profiled (e.g.\, number of CpG sites) and they do not provide suppor t on the availability of dedicated statistical tests on the epiallele comp ositions derived from their output. \n\nMethods: Here we present a novel w orkflow that can be used to retrieve epiallelic profiles from bisulfite se quencing data. In particular our workflow allows: data loading and filteri ng\, regions design\, and epialleles extraction. Dedicated statistical tes ts can then be used to identify regions that differ among groups based on their epiallelic composition. \n\nResults: We developed EpiStatProfiler\, a new R-package providing a library of functions that can be used to extra ct and summarise epialleles from any type of bisulfite sequencing data and to perform downstream statistical comparisons among different groups. The tool is intended to enable a customized selection of target regions\, acc ording to a set of user-defined parameters (minimum coverage\, number of c ytosines\, minimum window size). Furthermore\, it is also possible to anal yse strand specific and non-CG methylation. Epialleles information is stor ed by EpiStatProfiler in two different outputs: a compressed 0-1 matrix co ntaining the epialleles composition for each analysed region and an additi onal output containing basic features and multiple metrics derived from th e profiled regions. EpiStatProfiler provides a set of functions to perform epiallele-based comparisons in longitudinal and cross-sectional studies. We believe that this package could represent a valuable tool to qualitativ ely analyse the methylation heterogeneity in a variety of systems\, such a s tumor evolution\, cell differentiation and disease conditions.\n\nhttps: //indico.unina.it/event/57/contributions/462/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/462/ END:VEVENT BEGIN:VEVENT SUMMARY:8-oxodG accumulation within super-enhancers marks fragile CTCF-med iated chromatin loops. DTSTART;VALUE=DATE-TIME:20220228T114000Z DTEND;VALUE=DATE-TIME:20220228T115000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-461@cern.ch DESCRIPTION:Speakers: Amente Stefano (Department of Molecular Medicine and Medical Biotechnologies\, University of Naples ‘Federico II’\, Naples \, Italy)\n8-oxo-7\,8-dihydro-2′-deoxyguanosine (8-oxodG)\, a major prod uct of the DNA oxidization process\, has been proposed to have an epigenet ic function in gene regulation and has been associated with genome instabi lity. NGS-based methodologies are contributing to the characterization of the 8-oxodG role in many genome-related functions. However\, the number of studies addressing the 8-oxodG epigenetic role at a genomic level is stil l low and the mechanisms controlling genomic 8-oxodG accumulation/maintena nce have not yet been fully characterized.\nIn this study\, we report the identification and the characterization of a set of enhancer regions accum ulating 8-oxodG in human epithelial cells. We found that these oxidized en hancers are mainly super-enhancers and are associated with bidirectional-t ranscribed enhancer RNAs and DNA Damage Response activation. Moreover\, us ing ChIA-PET and HiC data\, we identified specific CTCF-mediated chromatin loops in which the oxidized enhancer and promoter regions physically asso ciate. Oxidized enhancers and their associated chromatin loops accumulate endogenous double-strand breaks which are in turn repaired by NHEJ pathway through a transcription-dependent mechanism. Our work provides novel mech anistic insights on the intrinsic fragility of chromatin loops containing oxidized enhancers-promoters pairs and suggests that 8-oxodG accumulation in these latter occurs in a transcription-dependent manner.\n\nhttps://ind ico.unina.it/event/57/contributions/461/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/461/ END:VEVENT BEGIN:VEVENT SUMMARY:Multi-Omics Visible Drug Activity prediction\, interpreting the bi ological processes underlying drug sensitivity DTSTART;VALUE=DATE-TIME:20220228T180500Z DTEND;VALUE=DATE-TIME:20220228T181500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-460@cern.ch DESCRIPTION:Speakers: Luigi Ferraro (University of Naples\, Federico II\, DIETI)\nCancer is a genetic disease resulting from the accumulation of gen omics alterations in living cells. Large scale genomics studies have been instrumental to understand the recurrent somatic genetic\nalteration s within a cell\, including chromosome translocations\, single base substi tutions\, and copy-number alterations and for the characterization of thei r functional effects in transformed cells. One of the main challenging qu estions in this field is how to exploit all these molecular information to identify therapeutic targets and to develop personalized therapies. The u nderstanding of the molecular features influencing sensitivity to drugs is the key element for the development of personalized therapies and to pred ict which patients should be treated and with which drugs and finally to e valuate eligibility criteria for oncology trials. \nMachine learning model s are able to exploit multi-modal screening datasets such as Projects such as Genomics of Drug Sensitivity in Cancer (GDSC)\, Cancer Cell Line Encyc lopedia (CCLE)\, Cancer Therapeutics Response Portal\, NCI-60 and others t o develop predictive algorithms useful to associate omics features with re sponse. The basic approach is to use the data from these screenings to tra in a machine learning model that predicts the 50% inhibitory concentration (IC50) of a drug from the multi-omics profile of a cell line or a tissue sample. There have been several attempts at applying this approach using v arious machine learning frameworks such as Variational Autoencoders\, Dee p Networks\, Convolutional Neural Networks\, ensemble Neural Network mod els and combination of these approaches with different encodings of the features . \nMost of these studies use the machine learning models as “black boxes" optimized for prediction accuracy without the possibility to interpret the biological mechanisms underlying predicted outcomes. \n\ nRecently\, some models were proposed to address this issue\, but many of them just rely on somatic single nucleotide variations of the screened models\; activity of the pathways\, measured by gene expression profiling \, is not taken into account\, neither other important genomics alterat ions\, such as copy number variations (CNV) that are of particular in terest in cancer progression. Second\, they do not take into account the u nbalanced nature of the data since\, in all large scale screening reposito ries\, the values of IC50 are clustered around the value representing lack of sensitivity (for measures of sensitivity based on AUC\, this value is 1) with a small minority of values representing sensitivity of a cell line to a specific drug.\nIn order to address these limitations we propose a M ulti-Omics Visible Drug Activity prediction (MOViDA) neural network model that extends the visible network approach incorporating functional informa tion in terms of pathway activity from gene expression and copy number dat a into a neural network. Moreover\, MOViDA is trained considering the unba lance of the dataset\, we used a random sampler based on a multinomial dis tribution that accounts for the skewness of the dataset. We compare MOViDA with DrugCell showing that it is more accurate in predicting sensitivity to drugs\, especially in the classes corresponding to lower AUC that repre sent those of more interest. In order to exploit the biological interpreta tion of network nodes we also develop an ad hoc network explanation method that scores the pathways that affect the prediction of sensitivity of a g iven cell line to a drug. \nTo make this data useful for other purposes\, we have identified which GOs and genes are good predictors for high sensit ivity of a cell line to a drug. This explanation is the basis to hypothesi ze drug combinations and cell editing aimed at the identification of cell vulnerabilities.\n\nhttps://indico.unina.it/event/57/contributions/460/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/460/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational approach to epiallele profiling DTSTART;VALUE=DATE-TIME:20220228T172500Z DTEND;VALUE=DATE-TIME:20220228T173500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-458@cern.ch DESCRIPTION:Speakers: Giulia De Riso (Department of Molecular Medicine and Medical Biotechnology\, University of Naples Federico II)\nDNA methylatio n is one of the most studied epigenetic modifications\, with an establishe d role in regulating gene expression and genome stability. It consists of enzyme mediated addition of a methyl-group to DNA bases. By acting in conc ert with other epigenetic marks\, DNA methylation shapes the fate and engr aves the identity of a cell. Its dysregulation has been linked to patholog ical conditions\, both as an epiphenomenon and as a driver event.\n\nThe m ethylation status of a cytosine residue is usually represented as the prop ortion of molecules in which the residue is methylated (average methylatio n)\, and differential analysis are concerned at finding residues whose met hylation status shifts among conditions. As an alternative approach\, the methylation status of a locus can be explored in terms of epialleles\, i.e .\, the possible arrangements of methylated and unmethylated cytosines in individual DNA molecules. Epiallele profiling (the assessment of the frequ ency of the possible epialleles) enables to dissect methylation heterogene ity of a locus.\n\nIn recent years\, our group developed bioinformatic too ls and computational methods to analyze epiallele profiles in ultra-deep ( UD) amplicon bisulfite sequencing data\, a targeted sequencing assay in wh ich one or few loci are sequenced at high depth\, thus enabling a robust e stimate of epialleles [1\,2\,3\,4]. In this way\, we were able to gain ins ights on DNA methylation dynamics\, showing that 1) DNA methylation is hig hly heterogeneous among cells\; 2) DNA methylation is mostly a non-stochas tic phenomenon\, with epiallele profiles being stable across different ind ividuals\; 3) According to mathematical models\, the observed heterogeneit y is compatible with a dynamic equilibrium between DNA methylation and dem ethylation\; 4) Epiallele profiles can be a cell-specific signature. Study ing epiallele profiles can aid to track the spatiotemporal evolution of ce ll-to-cell methylation differences in a cell population. \n\nIn the last t wo years\, our group was concerned at applying the analysis of epiallele p rofiles to genome-wide data. To this aim\, in collaboration with the group of Dr. Giovanni Scala\, we developed a bioinformatic tool\, EpistatProfil er. Currently\, we are applying this approach to track the dynamic of epia llele profiles upon neuronal differentiation. We are also investigating ho w this dynamic can be disrupted in epigenetically dysregulated contexts\, as enzymatic machinery knock-out and cancer. \n\nReferences\n\n1. Scala\, G.\, Affinito\, O.\, Palumbo\, D. et al. ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite seque nced amplicons. BMC Bioinformatics 17\, 484 (2016). https://doi.org/10.118 6/s12859-016-1380-3\n2. Affinito\, O.\, Scala\, G.\, Palumbo\, D. et al. M odeling DNA methylation by analyzing the individual configurations of sing le molecules\, Epigenetics\, 11:12\, 881-888 (2016). https://doi.org/10.10 80/15592294.2016.1246108\n3. Affinito\, O. et al. Nucleotide distance infl uences co-methylation between nearby CpG sites.\nGenomics\, 112\, 144-150 (220) https://doi.org/10.1016/j.ygeno.2019.05.007.\n3. De Riso\, G.\; Fior illo\, D.F.G. et al. Modeling DNA Methylation Profiles through a Dynamic E quilibrium between Methylation and Demethylation. Biomolecules\, 10\, 1271 (2020). https://doi.org/10.3390/biom10091271\n\nhttps://indico.unina.it/e vent/57/contributions/458/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/458/ END:VEVENT BEGIN:VEVENT SUMMARY:Hybrid Particle-Field Coarse-grained models for biological simulat ions DTSTART;VALUE=DATE-TIME:20220228T175500Z DTEND;VALUE=DATE-TIME:20220228T180500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-457@cern.ch DESCRIPTION:Speakers: Antonio De Nicola (Scuola Superiore Meridionale\, Un iversita' di Napoli Federico II)\nMolecular Dynamics (MD) is a powerful co mputational technique used to understand the physical basis of the structu re and function of biological systems.[1] In this context\, coarse-grained (CG) models have been successfully applied to a broad range of bio-molecu lar systems\, including the self-assembly of lipids in aqueous solutions. However\, many biologically relevant processes occur on timescales that fa r exceed the timescales of typical MD simulations using CG models. Thanks to an innovative simulation technique\, name hybrid particle-field (hPF)\, [2\,3] is possible to study large scale systems beyond what is feasible wi th traditional MD and CG models.[4] A special class of CG models\, develop ed for the hPF technique\, have been successfully used to investigate seve ral problems in biophysics.5–8 The first application of CG hPF models\, with parameters for phospholipids only\, was published by the Milano group in 2011.[5] Thanks to the speed up of dynamics\, due to the hPF approach\ , the self-diffusion acceleration lead to a fast self-assembly process. Th e net effect is that the developed CG models can reproduce\, via self-ass embly\, the lamellar and non-lamellar structure phases of many lipids and surfactants.[5–8] Our aim is to highlight recent applications and provid e a comprehensive overview of hPF CG models for biological applications.\ n\n(1) Karplus\, M.\; McCammon\, J. A. Molecular Dynamics Simulations of Biomolecules. Nat. Struct. Biol. 2002\, 9 (9)\, 646–652. https://doi.org /10.1038/nsb0902-646.\n(2) Milano\, G.\; Kawakatsu\, T. Hybrid Particle-F ield Molecular Dynamics Simulations for Dense Polymer Systems. J. Chem. Ph ys. 2009\, 130 (21)\, 214106. https://doi.org/10.1063/1.3142103.\n(3) Mil ano\, G.\; Kawakatsu\, T. Pressure Calculation in Hybrid Particle-Field Si mulations. J. Chem. Phys. 2010\, 133 (21)\, 214102. https://doi.org/10.106 3/1.3506776.\n(4) Milano\, G.\; Kawakatsu\, T.\; De Nicola\, A. A Hybrid Particle–Field Molecular Dynamics Approach: A Route toward Efficient Coa rse-Grained Models for Biomembranes. Phys. Biol. 2013\, 10 (4)\, 045007. h ttps://doi.org/10.1088/1478-3975/10/4/045007.\n(5) De Nicola\, A.\; Zhao\ , Y.\; Kawakatsu\, T.\; Roccatano\, D.\; Milano\, G. Hybrid Particle Field Coarse Grained Models for Biological Phospholipids. J. Chem. Theory Compu t. 2011\, 7 (9)\, 2947–2962. https://doi.org/10.1021/ct200132n.\n(6) De Nicola\, Antonio\; Kawakatsu\, T.\; Rosano\, C.\; Celino\, M.\; Rocco\, M .\; Milano\, G. Self-Assembly of Triton X‑100 in Water Solutions: A Mult iscale Simulation Study Linking Mesoscale to Atomistic Models. J Chem Theo ry Comput 2015\, 13. https://doi.org/10.1021/acs.jctc.5b00485.\n(7) De Ni cola\, A.\; Kawakatsu\, T.\; Milano\, G. A Hybrid ParticleField CoarseGrai ned Molecular Model for Pluronics Water Mixtures. Macromol Chem Phys 2013\ , 11.\n(8) De Nicola\, A.\; Soares\, T. A.\; Santos\, D. E. S.\; Bore\, S . L.\; Sevink\, G. J. A.\; Cascella\, M.\; Milano\, G. Aggregation of Lipi d A Variants: A Hybrid Particle-Field Model. Biochim. Biophys. Acta BBA - Gen. Subj. 2020\, 129570. https://doi.org/10.1016/j.bbagen.2020.129570.\n\ nhttps://indico.unina.it/event/57/contributions/457/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/457/ END:VEVENT BEGIN:VEVENT SUMMARY:Human X chromosome reactivation: structural and molecular dynamics during pluripotent reprogramming DTSTART;VALUE=DATE-TIME:20220228T133000Z DTEND;VALUE=DATE-TIME:20220228T134000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-456@cern.ch DESCRIPTION:Speakers: Irene Cantone (Department of Molecular Medicine and Medical Biotechnology\, University of Naples Federico II)\nReactivation of the inactive X-chromosome (Xi) has been used to model epigenetic reprogra mming in the mouse. Human studies have\, however\, been hampered by Xi epi genetic instability in pluripotent stem cells and difficulties in tracking emerging iPSCs. Recently\, we have shown that reprogramming female human fibroblast via mouse ESC fusion recapitulates features of in vivo human na ïve pluripotency. We used this unique reprogramming system to examine the earliest chromatin and transcriptional events in Xi reactivation. Our stu dy revealed a rapid (1-2 days) and wide-spread (30-50% of cells) delocaliz ation of XIST RNA and loss of H3K27me3 from the human Xi that precede\, an d are tightly associated with\, the re-expression of selected Xi genes. A fter cell division\, Xi gene reactivation was observed in a similar percen tage of hybrids and remained stable over 6 days. The human pluripotency-sp ecific XACT RNA was instead re-expressed and coated the Xi in rare hybrids (1%)\, suggesting that XACT is not required for early Xi chromatin change s and gene reactivation in the reprogramming context. Collectively\, thes e data distinguish pre- and post- mitotic changes and reveal a hierarchy o f epigenetic events that are required for Xi reactivation. \nInterestingly \, single-cell RNA-FISH and allele-specific RNA sequencing analyses showed that reprogramming-mediated human Xi reactivation was partial and selecti ve for a specific subset of genes. Selective Xi reactivation was not limit ed to gene loci residing within specific chromatin domains neither influen ced by proximity to XIST locus. Reactivation was instead associated with s tochastic Xi expression ahead of reprogramming\, as shown by isogenic fibr oblast clones and single cell analyses. Importantly\, reprogramming-mediat ed reactivation remained partial even in cells examined up to six days aft er fusion\, but it was extended to a second group of Xi loci by DNA demeth ylation. These findings underscore the differential sensitivity of distinc t human Xi genes to reprogramming-mediated reactivation and suggest that m ultiple non-overlapping epigenetic mechanisms maintain silencing along the human Xi.\n\nhttps://indico.unina.it/event/57/contributions/456/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/456/ END:VEVENT BEGIN:VEVENT SUMMARY:Efficient Hybrid Particle-Field Model Schemes for Large Scale Para llel MD Simulations DTSTART;VALUE=DATE-TIME:20220228T113000Z DTEND;VALUE=DATE-TIME:20220228T114000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-455@cern.ch DESCRIPTION:Speakers: GIUSEPPE MILANO (Università di Napoli Federico II)\ nIn recent years\, the success of and insight gained by classical molecula r modeling\, in understanding the fundamentals of complex molecular phenom ena\, have triggered a strong desire to go beyond the limitations of the i nformation that can be extracted from classical Molecular Dynamics MD\, es pecially the limitations that cannot be resolved by advances in computatio nal efficiency. To this aim effective molecular representations have been developed and used for diverse molecular systems in a variety of coarse-gr ained (CG) and multi-scale (MS) techniques. (For a recent review and persp ective see [1]) In the last decade\, hybrid particle-continuum approaches such as Single-Chain in Mean-Field (SCMF) [2] and Hybrid Particle Field MD (hPF-MD)\,[3\,4] which link discrete (particle-based) and continuum (fiel d-based) descriptions in a single simulation volume\, have been increasing ly applied and validated for different systems. In hPF-MD\, the nonbonded forces acting on a particle are expressed as function of the derivatives o f local density gradients. This reformulation enables much more efficient simulations\, especially for large parallel runs\, than standard MD as the evaluation of nonbonded pair forces is replaced by building particle-to-m esh density fields and computing the density field potentials. Both steps are of first order in the number of particles. The hPF-MD model has been d emonstrated to be effective to investigate homopolymers and block copolyme rs at both CG[5] and atomistic resolutions [6] also in the presence of sol id nanoparticles [7-9] and for liquid-vapor interfaces [10]. The hPF-MD mo del was also validated in describing the conformational and dynamical prop erties of biological systems such as lipid bilayers[11-13]\, biosurfactant s [14] and proteins [15]. More recently\, after the integration of electro statics into the hybrid particle-field scheme [16]\, the hPF-MD method was further successfully applied to charged phospholipids [17]. During the ta lk\, after an introduction to the basics of hPF-MD methodology\, I will gi ve an overview of the main results with a special focus on electrostatic i nteractions their implementation and its applications from simple idealize d to complex molecular models [18].\n\nReferences\n\n[1] Unfolding the pro spects of computational (bio)materials modelling G.J.A. Sevink\, A. Liwo\, P. Asinari\, D. MacKernan\, G. Milano\, and I. Pagonabarraga (Featured Ar ticle for the special issue: Classical Molecular Dynamics (MD) Simulation s: Codes\, Algorithms\, Force Fields\, and Applications) J. Chem. Phys. 20 20\, 153\, 100901\n\n[2] Single chain in mean field simulations: Quasi-ins tantaneous field approximation and quantitative comparison with Monte Carl o simulations K. Daoulas\, M. Muller J. Chem. Phys. 125\, 184904 (2006)\n\ n[3] Hybrid Particle-Field Molecular Dynamics Simulations for Dense Polyme r Systems G. Milano\, T. Kawakatsu J. Chem. Phys. 130\, 214106\, (2009)\n\ n[4] Hybrid Particle-Field Molecular Dynamics Simulations: Parallelization and Benckmarks Y. Zhao\, A. De Nicola\, T. Kawakatsu\, G. Milano Journal of Computational Chemistry 33\, 868\, (2012)\n\n[5] Micellar Drug Nanocarr iers and Biomembranes: How do they Interact? A. De Nicola\, S. Hezaveh\, Y . Zhao\, Toshihiro Kawakatsu\, Danilo Roccatano\, Giuseppe Milano Phys. Ch em. Chem. Phys 16\, 5093\, (2014)\n\n[6] Generation of Well Relaxed All At om Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Conti nuum Approach Based on Particle-Field Molecular Dynamics Simulations A. De Nicola\, T. Kawakatsu\, G. Milano J. Chem. Theory Comput.\, 2014\, 10 (12 )\, pp 5651–566\n\n[7] Rational Design of Nanoparticle/Monomer Interface s: A Combined Computational and Experimental Study of In Situ Polymerizati on of Silica Based Nanocomposites A. De Nicola\, R. Avolio\, F. Della Moni ca\, G. Gentile\, M. Cocca\, C. Capacchione\, M. E. Errico and G. Milano R SC Advances 2015\, 5\, 71336-71340\n\n[8] Self-Assembly of Carbon Nanotube s in Polymer Melts: Simulation of Structural and Electrical Behavior by Hy brid Particle-Field Molecular Dynamics Y. Zhao\, M. Byshkin\, Y. Cong\, T. Kawakatsu\, L. Guadagno\, A. De Nicola\, N. Yu\, G. Milano and B. Dong\, Nanoscale 2016\, 8\, 15538-15552\n\n[9] Efficient Hybrid Particle-Field Co arse-Grained Model of Polymer Filler Interactions: Multiscale Hierarchical Structure of Carbon Black Particles in Contact with Polyethylene S. Caput o\, V. Hristov\, A. De Nicola\, H. Herbst\, A. Pizzirusso\, G. Donati\, G. Munaò\, A. R. Albunia and G. Milano J. Chem. Theory Comput. 2021\, 17\, 3\, 1755-1770.\n\n[10] Efficient and Realistic Simulation of Phase Coexist ence G. J. A. Sevink\, E. M. Blokhuis\, and X. Li\, G. Milano J. Chem. Phy s. 2020\, 153\, 244121.\n\n[11] A hybrid particle-field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes G. Milano\, T. Kawakatsu\, A. De Nicola Physical Biology 10\, 045007\, (2 013)\n\n[12] Toward Chemically Resolved Computer Simulations of Dynamics a nd Remodeling of Biological Membranes T. A. Soares\, S. Vanni\, G. Milano\ , M. Cascella Journal of Physical Chemistry Letters (Perspective) J. Phys. Chem. Lett.\, 2017\, 8 (15)\, pp 3586–3594\n\n[13] Self-Assembly at the Multi-Scale Level: Challenges and New Avenues for Inspired Synthetic Biol ogy Modelling G. Milano\, I. Marzuoli\, C. D. Lorenz and F. Fraternali Syn thetic Biology: Volume 2 Royal Society of Chemistry Book Series 2017\n\n[1 4] Self Assembly of Triton X-100 in water solutions: A Multiscale Simulati on Study Linking Mesoscale to Atomistic Models A- De Nicola\, T. Kawakatsu \, C. Rosano\, M. Celino\, M. Rocco\, G. Milano Journal of Chemical Theory and Computation 2015 11 (10)\, 4959-4971\n\n[15] Hybrid Particle-Field Mo del for Conformational Dynamics of Peptide Chains S. Løland Bore\, G. Mil ano\, M. Cascella Journal of Chemical Theory and Computation 2018\, 14 (2) \, pp 1120–1130\n\n[16] Hybrid particle-field molecular dynamics simulat ion for polyelectrolyte systems YL Zhu\, ZY Lu\, G. Milano\, AC Shi and ZY Sun Phys. Chem. Chem. Phys 2016\, 18\, 9799\n\n[17] Hybrid particle-field molecular dynamics simulations of charged amphiphiles in aqueous environm ent H. B. Kolli\, A. De Nicola\, S. Løland Bore\, K. Schäfer\, T. Kawaka tsu\, ZY Lu\,YL Zhu\, G. Milano\, M. Cascella 2018\, 14 (9)\, pp 4928–49 37ù\n\n[18] Aggregation of Lipid A Variants: A Hybrid Particle-Field Mode l A. De Nicola\, T. A. Soares\, D. E. S. Santos\, S. Løland Bore\, G. J. A. Sevink\, M. Cascella\, G. Milano Biochimica et Biophysica Acta - Genera l Subjects 1865\, 4\, 2021\, 129570\n\nhttps://indico.unina.it/event/57/co ntributions/455/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/455/ END:VEVENT BEGIN:VEVENT SUMMARY:Tumorigenic cis-regulatory mutations in neuroblastoma DTSTART;VALUE=DATE-TIME:20220228T150000Z DTEND;VALUE=DATE-TIME:20220228T151000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-454@cern.ch DESCRIPTION:Speakers: Vito Alessandro Lasorsa (CEINGE - Biotecnologie Avan zate Scarl)\n**Background** | Neuroblastoma is a paediatric tumour of the peripheral sympathetic nervous system originating from the neural-crest ce lls. It is the second most common childhood solid cancer and its cure rema ins a challenge. In recent years\, next generation sequencing of neuroblas toma has documented low somatic mutation rates and few recurrently mutated genes. As a result\, the search for therapy targets is limited. Furthermo re\, as most studies on neuroblastoma relied mainly on whole exome sequenc ing\, the role of somatic mutations in non-coding regulatory regions remai ns underestimated. Moreover\, the growing interest in noncoding cis-regula tory variants as cancer drivers is currently hampered by numerous challeng es and limitations of variant prioritization and interpretation methods an d tools.\n\n**Aims** | We hypothesized that mutated active regulatory elem ents could de-regulate genes involved in the tumorigenesis of neuroblastom a.\n\n**Methods** | To overcome the limitations of noncoding driver analys is\, we focused on active cis-regulatory elements (aCREs) to design a cust omized panel for deep sequencing of 56 neuroblastoma tumor and normal DNA sample pairs. We defined CREs by a reanalysis of H3K27ac ChiP-seq peaks of 25 neuroblastoma cell lines. Common H3K27ac peaks represented our target in which to search for driver mutations. We tested these regulatory genomi c regions for an excess of somatic mutations and assessed the statistical significance with a global approach accounting for chromatin accessibility and replication timing. Additional validation was provided by analyzing w hole-genome sequences of 151 neuroblastomas. HiC data analysis was used to determine the presence of candidate target genes interacting with mutated regions. We also used the k-means clustering algorithm to divide transcri ptomic data of 498 neuroblastoma samples into two groups based on expressi on levels of genes that (according to the HiC results) significantly inter acted with mutated aCREs. Moreover\, we conducted a motif analysis to asse ss whether the somatic variants within the selected aCREs disrupted or cre ated transcription factors binding motifs.\n\n**Results** | We identified a significant excess of somatic mutations in aCREs of diverse genes includ ing IPO7\, HAND2\, and ARID3A\, and used the luciferase reporter gene assa ys and the CRISPR-Cas9 editing to assess the functional consequences of th e mutated IPO7 aCRE on candidate target genes (IPO7\, TMEM41B\, DENND5A) ( P<1.0x10-03). Taken together\, patients with noncoding mutations in aCREs showed inferior overall\, and event-free survival (P<2.0x10-03). By multiv ariable analysis\, we confirmed that the noncoding mutational burden was i ndependent of age at diagnosis\, tumor stage\, risk group\, and MYCN statu s (P<2.0x10-02). We also found that the expression profiles of many of the aCREs target genes (tested singularly and in a combined manner) associate d with markers of unfavorable prognosis and low survival rates (P<5.0x10-0 2). Furthermore\, we conducted a motif analysis to identify transcription factors with altered binding motifs. Overall\, the biological functions of aCRE target genes and those of transcription factors with mutated binding motifs converged towards processes related to embryonic development and i mmune system response (P<5.0x10-02). This suggests that the combined effec t of noncoding cancer driver mutations is the alteration of gene sets invo lved in specific molecular mechanisms underlying neuroblastoma tumorigenes is.\n\n**Conclusion** | We integrated multiple data levels taking epigenom ics\, genomics and transcriptomics information of neuroblastoma to set up an alternative approach for detecting and studying regulatory cancer drive r mutations. Our strategy enabled us to identify mutated regulatory region s that may play an important role in regulating biological processes assoc iated with tumor development and immune escape.\n\nhttps://indico.unina.it /event/57/contributions/454/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/454/ END:VEVENT BEGIN:VEVENT SUMMARY:DNA mutations via Chern-Simons Current DTSTART;VALUE=DATE-TIME:20220228T174500Z DTEND;VALUE=DATE-TIME:20220228T175500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-452@cern.ch DESCRIPTION:Speakers: FRANCESCO BAJARDI (University of Naples "Federico II ")\nThe schematization of DNA structure can be tested by the Chern–Simon s theory\, that is a topological field theory mostly considered in the con text of effective gravity theories. By means of the expectation value of t he Wilson Loop\, derived from this analogue gravity approach\, it is possi ble to find the point-like curvature of genomic strings in KRAS human gene and COVID-19 sequences\, correlating this curvature with the genetic muta tions. The point-like curvature profile\, obtained by means of the Chern –Simons currents\, can be used to infer the position of the given mutati ons within the genetic string. Generally\, mutations take place in the hig hest Chern–Simons current gradient locations and subsequent mutated sequ ences appear to have a smoother curvature than the initial ones\, in agree ment with a free energy minimization argument.\n\nhttps://indico.unina.it/ event/57/contributions/452/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/452/ END:VEVENT BEGIN:VEVENT SUMMARY:SINGLE CELL RNA SEQUENCING UNCOVERS CHEMORESISTANCE GENES AND PATH WAYS OF NEUROBLASTOMA INTRA-TUMOR HETEROGENEITY DTSTART;VALUE=DATE-TIME:20220228T122000Z DTEND;VALUE=DATE-TIME:20220228T123000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-450@cern.ch DESCRIPTION:Speakers: Ferdinando Bonfiglio (University of Naples Federico II)\n**Background and rationale.** Human tumors are complex systems charac terized by molecular\, cellular and spatial diversities. The totality of f eatures demonstrating differences within a tumor is termed intra-tumor het erogeneity (ITH). ITH may be one of the mechanisms at the basis of the dru g resistance and relapse triggered\, for example\, via the selection of ma lignant clones. Single cell sequencing approaches coupled with advanced co mputational analyses have made a huge contribution to understand the molec ular basis of tumor ITH. However\, due to the lack of data at the single-c ell level\, little is known about these dynamics in tumors such as neurobl astoma (NB)\, one of the most common solid tumors of the childhood. NB aff ects the development of sympathetic nervous system and its treatment is st ill unsuccessful in half of the patients diagnosed with the high-risk subt ype. Here we investigated the ITH of Etoposide and Cisplatin resistant NB cell lines and their parental cells through single cell RNA sequencing (sc RNA-seq).\n\n**Methods.** scRNA-seq was performed on 10X Genomics platform and barcode filtering\, alignment of reads and UMI counting were carried out using Cell Ranger 3.0.1. Counts were imported into R for quality contr ol (QC) and downstream analysis. Cells were excluded if fewer than 2000 di stinct genes\, 20\,000 counts or more than 30% of reads mapping to mitocho ndrial genes were detected. Data were normalized\, scaled\, log-transforme d and\, in order to remove confounding sources of variation\, percent of m itochondrial genes\, read counts and cell cycle scores were regressed out using a regularized negative binomial model implemented in Seurat package. The most variable genes were used for dimensionality reduction and cluste ring analysis was carried out with the nearest neighbor algorithm. Gene se t enrichment analysis of marker genes for each cluster was performed with Webgestalt R package. CIBERSORTx was used to deconvolute bulk RNA-seq data sets with scRNA-seq-derived cell clusters and resulting scores were correl ated with clinical and survival data.\n\n**Results.** We obtained transcri ptional profiles of 1514 Etoposide-resistant vs. 2646 parent cells\, and 1 160 Cisplatin-resistant vs. 1674 parental cells after QC. TSNE and UMAP pl ots showed a clear separation of resistant and parental cells for both con ditions and allowed to identify 8 distinct tumor clusters in Etoposide-res istant/parental and 7 in Cisplatin-resistant/parental cells. We found a si gnificant enrichment (FDR ≤ 0.01) of pathways related to the DNA damage response in both drug resistant cells\, suggesting that the upregulation o f the DNA repair machinery may be a potential drug resistance mechanism in these cells. Besides\, both parental cell lines showed cell clusters char acterized by genes involved in embryonal differentiation trajectories and enrichment of neural crest development pathways\, reflecting the dynamics of NB cell development. Deconvolution analysis of bulk RNA-seq data with c luster signatures\, allowed the identification of specific clusters associ ated (logrank P ≤ 0.01) with worse/better survival. \n\n**Conclusions.** In this study\, we applied scRNA-seq and advanced bioinformatic pipeline to analyze the chemo resistant NB cell lines. We identified distinct cell populations characterizing Etoposide and Cisplatin resistant NB cell lines \, provided insights into plausible mechanisms of chemoresistance and high lighted genes and cluster signatures associated with clinical outcomes tha t are potentially actionable as therapeutic targets.\n\n\n**Speaker recent publications**\n\n - **Bonfiglio F**\, Liu X\, Smillie C\, Pandit A\, Kur ilshikov A\, Bacigalupe R\, Zheng T\, Nim H\, Garcia-Etxebarria K\, Bujand a L\, et al. GWAS of stool frequency provides insights into gastrointestin al motility and irritable bowel syndrome. ***Cell Genomics***. 2021. \n - Eijsbouts C\, Zheng T\, Kennedy NA\, **Bonfiglio F**\, Anderson CA\, Mouts ianas L\, Holliday J\, Shi J\, Shringarpure S\; 23andMe Research Team\, et al. Genome-wide analysis of 53\,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders. ***Nat ure Genetics***. 2021. \n - **Bonfiglio F**\, Bruscaggin A\, Guidetti F\, Terzi di Bergamo L\, Faderl M\, Spina V\, Condoluci A\, Bonomini L\, Fores tieri G\, Koch R\, et al. Genetic and Phenotypic Attributes of Splenic Mar ginal Zone Lymphoma. ***Blood***. 2021.\n\nhttps://indico.unina.it/event/5 7/contributions/450/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/450/ END:VEVENT BEGIN:VEVENT SUMMARY:Conclusioni DTSTART;VALUE=DATE-TIME:20220228T183000Z DTEND;VALUE=DATE-TIME:20220228T183500Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-448@cern.ch DESCRIPTION:https://indico.unina.it/event/57/contributions/448/ LOCATION:Centro Congressi Partenope Aula Magna URL:https://indico.unina.it/event/57/contributions/448/ END:VEVENT BEGIN:VEVENT SUMMARY:La TFdA di Biologia Computazionale e Quantitativa (Prof. Mario Nic odemi\, Coordinatore) DTSTART;VALUE=DATE-TIME:20220228T085000Z DTEND;VALUE=DATE-TIME:20220228T090000Z DTSTAMP;VALUE=DATE-TIME:20260608T032442Z UID:indico-contribution-57-443@cern.ch DESCRIPTION:https://indico.unina.it/event/57/contributions/443/ LOCATION: URL:https://indico.unina.it/event/57/contributions/443/ END:VEVENT END:VCALENDAR