Gemelli Computational Biology and Bioinformatics Lab

Read our new paper in Journal of Crohn’s & Colitis: “Inflammatory Bowel Disease is associated with increased intestinal extrachromosomal circular DNA: an emerging biomarker for IBD type and activity.” Link: https://lnkd.in/dcRa8nNg In this study, we found that intestinal biopsies from IBD patients contain significantly higher levels of extrachromosomal circular DNA (eccDNA) compared to healthy controls, with distinct patterns linked to disease activity in ulcerative colitis and Crohn’s disease. eccDNA fragments carrying specific gene sequences were consistently detected in patients, highlighting genomic hotspots that characterize active IBD. Bioinformatics played a key role in enriching, sequencing and analysing circular DNA using tools like Circle Finder and bedtools, enabling robust stratification of patients and identification of disease-associated eccDNA signatures. This work opens new avenues for non-invasive biomarkers that could improve diagnosis and monitoring in IBD. Made by Valentina Petito Daniela Gerovska Antonia Piazzesi Federica di Vincenzo Alessandra Russo Laura Turchini Letizia Masi Valeria Emoli Elisabetta Tabolacci Maria Cristina Giustiniani Tommaso Mazza Lucrezia Laterza Alfredo Papa Loris Riccardo Lopetuso lorenza putignani Antonio Gasbarrini Marcos J. Arauzo-Bravo Franco Scaldaferri #InflammatoryBowelDisease #Biomarkers #eccDNA #Bioinformatics #ClinicalGenomics #LiquidBiopsy #TranslationalResearch Fondazione Policlinico Universitario Agostino Gemelli IRCCS

Liver diseases impose a massive global toll, causing over 2 million deaths. When cells in our body die, they release in the bloodstream DNA and histones. Here we show, in a cohort of patients, a circulating histone signature marking the progression from metabolic associated steatotic liver disease (MASLD) to metabolic associated steatohepatitis (MASH) to hepatocellular carcinoma (HCC). Thanks to Diana Buzova Tommaso Mazza Salvatore Daniele Bianco Luca Miele Anna Alisi Antonio Gasbarrini Jan Červený Andrea Urbani Antonio Liguori https://lnkd.in/eTXnr4Gx

#merrychristmas

Introducing FPG 360, one of Italy’s first in-house liquid biopsy testing services at the Fondazione Policlinico Universitario Agostino Gemelli IRCCS in Rome. Powered by our Guardant360® CDx technology, this new service expands access to precision oncology diagnostics and supports both routine care and clinical research. “This collaboration of public healthcare and private innovation enables broader access for blood-based cancer profiling and genomic insights,” underscored our Co-CEO Helmy Eltoukhy. “Bringing our liquid biopsy technology to one of Europe’s leading cancer centers is another step in our mission to help clinicians worldwide create more personalized treatment plans and improve outcomes.”

🎓 ISCRIZIONI ANCORA APERTE! Corso di Perfezionamento in Epidemiologia e Biostatistica per la Ricerca Clinica e di Popolazione 📍 Università Cattolica del Sacro Cuore – Roma 💥 Vuoi fare la differenza nella ricerca clinica e nella sanità pubblica? Questo è il momento giusto per investire nelle competenze che stanno guidando l’innovazione nel settore. 📊 Oggi i dati non bastano: serve la capacità di leggerli, interpretarli e trasformarli in decisioni informate. 💡 Chi padroneggia epidemiologia e statistica è un passo avanti nel mondo della ricerca e della gestione sanitaria. 🎯 Cosa imparerai: 📈 Statistica di base 📊 Misure epidemiologiche 🧩 Disegni di studio 🧪 Test statistici parametrici e non parametrici 💉 Trial clinici 📉 Regressione lineare e logistica ⏱ Durata: 108 ore strutturate in moduli didattici 📅 Scadenza iscrizioni: 6 gennaio 2026 🔗 Iscriviti ora: https://lnkd.in/eUmZtucz 📘 Programma completo: https://lnkd.in/eM2F-asA 💼 Il corso prepara professionisti in grado di operare in istituzioni sanitarie, enti di ricerca e organizzazioni pubbliche e private, contribuendo alla progettazione e conduzione di studi epidemiologici di alta qualità. 🚀 Rafforza le tue competenze. Costruisci evidenze. Guida il futuro della sanità pubblica. #Epidemiologia #Biostatistica #RicercaClinica #SanitàPubblica #UniversitàCattolica #Formazione #EvidenceBased #PublicHealth #CorsiDiPerfezionamento #UCSC

Inaugurata al Gemelli la biopsia liquida in house: un significativo passo avanti per la diagnostica e i percorsi terapeutici in oncologia. Grazie alla partnership con Guardant Health, questa tecnologia avanzata permette di eseguire l’innovativo test di biopsia liquida direttamente in ospedale, riducendo i tempi di refertazione e favorendo decisioni terapeutiche più rapide ed efficaci. “L’evoluzione di questi studi pionieristici entra oggi concretamente nel percorso assistenziale del Gemelli, diventando un pilastro della diagnostica molecolare per i pazienti oncologici italiani” spiega il professor Urbani, evidenziando anche come questa innovazione rappresenti un’opportunità formativa unica per gli studenti dell’Università Cattolica di Roma, costantemente esposti all’evoluzione della ricerca biomedica. Leggi la news: https://lnkd.in/epy_sF-q

Read our “Comprehensive Molecular Screening by Next Generation Sequencing of Gastrointestinal Stromal Tumors (GISTs): In Silico Analysis and Classification of Rare KIT Exon 11 Mutations” published in Cancer Medicine. 🔗 https://lnkd.in/d7c9Bqyk In this study we applied NGS to a cohort of 31 GIST patients and combined molecular profiling with detailed computational modeling of rare KIT exon 11 variants. Importantly, for three patients carrying previously unreported exon 11 deletions, our in-silico structural analyses predicted altered KIT protein conformation and perturbed binding of the drug imatinib, supporting pathogenic classification under ACMG-AMP and ASCO-CAP guidelines. #GIST #CancerGenomics #Bioinformatics #StructuralBiology #PrecisionMedicine #NGS We did it with Maria Grazia Rodriquenz, Barbara Pasculli, Michelina Tendina, Francesco Petrizzelli, Tommaso Mazza, Antonio Petracca, Bartolomeo Augello, Michelina Coco, Teresa Balsamo, Anna Troiano, magda zanelli, Evaristo Maiello, Paolo Graziano, Paola Parente, and Paola Parrella

Interested in "Histone‑based liquid biopsy in cancer research"? Go ahead and read: "Histone‑based liquid biopsy discriminates between myelodysplastic syndrome and solid malignancies" published in Clinical Epigenetics. Read it here: https://rdcu.be/eRwKs In this study, we analysed circulating histones and histone complexes in plasma from healthy individuals and patients with either myelodysplastic syndrome (MDS) or solid cancers (colorectal, lung, breast). We discovered that cancers release distinct histone signatures: for instance, elevated levels of H2A and macroH2A1.2, alongside decreased H2A/H2B/H3/H4 and H3/H4 complexes, enabled discrimination between MDS and solid tumours. We made it with Desislava Tsoneva, Diana Buzova, Salvatore Daniele Bianco, Ilina Micheva, Merlin Efraim, Nikol Daskalova, Igor Resnick, Maria Teneva, Trifon Chervenkov, Nikolay Vladimirov Concev, Rostislav Manev, Dragomir Svetozarov Stoyanov, Jan Červený, Tommaso Mazza, Manlio Vinciguerra #bioinformatics #computationalbiology #biostatistics #liquidbiopsy #cancer #myelodysplasticsyndrome

Hypophosphatasia is a genetic bone disease caused by partial/total inactivation of alkaline phosphatase. Because it is a metabolic syndrome and depends on the residual activity of this enzyme, genotype-phenotype correlations are difficult to make due to the diverse clinical presentations. In our article, recently published in Cells (https://lnkd.in/dcTsf9Ep) we present, for the first time for an italian cohort of HPP patients, a multifaceted correlation of functional data obtained from benchtop in vitro tests, high-throughput in silico analyses, and detailed clinical assessments. This cross-referencing of multiple data points led us to obtain a strong correlation in over 70% of alkaline hypophosphatase cases, confirming that interdisciplinary studies on complex genetic diseases can be a valuable aid for physicians caring for HPP patients. Heartfelt thanks to my eccellent colleagues and dear friends, with whom I shared this result 👍

What are the clinical and molecular features of neurofibromatosis type 1 (NF1)-associated breast cancers? Our new study reveals that breast cancers in Neurofibromatosis type 1 (NF1) patients emerge earlier, tend to be more aggressive, and bear distinct NF1‑gene mutation patterns. This was proved from the computational front as well. Our team applied in‑silico structural workflows including Missense3D to flag structural rearrangements, introduced amino‑acid substitutions in ChimeraX, performed energy minimisation in Amber/SANDER, and calculated ΔΔG values via FoldX 5.0 to identify destabilising variants. Read it at: https://lnkd.in/dZYDgu3N Powered by: Paola Daniele, Francesco Petrizzelli, Chiara Iacovino, Chiara Canciani, Maria Luisa Garau, Claudia Santoro, Valentina Trevisan, Arianna Panfili, Stefania Cavone, Valentina Guida, Maria Cecilia D'Asdia, Laura Bernardini, Silvia Majore, Alessandro Ferraris, Michele Valiante, Francesca Gensini, Francesca Clementina Radio, Giada Tortora, Matteo Cassina, Giuseppina Miele, Manuela Priolo, Fabio sirchia, Ludovica Piccinno, Elisabetta Flex, Giuseppe Zampino, Maurizio Genuardi, Vincenzo Nigro, Leonardo Salviati, Laura Papi, Paola Grammatico, Chiara Leoni, Giulio Piluso, Sandra Giustini, Tommaso Mazza, Meena Upadhyaya, Marco Tartaglia, Eva Trevisson, Alessandro De Luca #BreastCancer #NF1 #Bioinformatics #StructuralBioinformatics #ComputationalGenomics Fondazione Policlinico Universitario Agostino Gemelli IRCCS