Latest publications of CIBIO affiliates (last updated on May 1st, 2024)
Spathopoulou A, Sauerwein GA, Marteau V, Podlesnic M, Lindlbauer T, Kipura T, Hotze M, Gabassi E, Kruszewski K, Koskuvi M, Réthelyi JM, Apáti Á, Conti L, Ku M, Koal T, Müller U, Talmazan RA, Ojansuu I, Vaurio O, Lähteenvuo M, Lehtonen Š, Mertens J, Kwiatkowski M, Günther K, Tiihonen J, Koistinaho J, Trajanoski Z, Edenhofer F (2024) Integrative metabolomics-genomics analysis identifies key networks in a stem cell-based model of schizophrenia. Mol Psychiatry, doi:10.1038/s41380-024-02568-8.
http://www.ncbi.nlm.nih.gov/pubmed/38684795
Koralewska N, Corradi E, Milewski MC, Masante L, Szczepanska A, Kierzek R, Figlerowicz M, Baudet ML, Kurzynska-Kokorniak A (2024) Short 2'-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo. Nucleic Acids Res, doi:10.1093/nar/gkae284.
http://www.ncbi.nlm.nih.gov/pubmed/38676942
Mangiapane G, Notarangelo M, Canarutto G, Fabbiano F, Dalla E, Degrassi M, Antoniali G, Gualandi N, De Sanctis V, Piazza S, D'Agostino VG, Tell G (2024) The DNA-repair protein APE1 participates with hnRNPA2B1 to motif-enriched and prognostic miRNA secretion. Oncogene, doi:10.1038/s41388-024-03039-8.
http://www.ncbi.nlm.nih.gov/pubmed/38664500
Pedrazzoli E, Demozzi M, Visentin E, Ciciani M, Bonuzzi I, Pezzè L, Lucchetta L, Maule G, Amistadi S, Esposito F, Lupo M, Miccio A, Auricchio A, Casini A, Segata N, Cereseto A (2024) CoCas9 is a compact nuclease from the human microbiome for efficient and precise genome editing. Nat Commun, 15(1):3478, doi:10.1038/s41467-024-47800-9.
http://www.ncbi.nlm.nih.gov/pubmed/38658578
Pedace L, Pizzi S, Abballe L, Vinci M, Antonacci C, Patrizi S, Nardini C, Del Bufalo F, Rossi S, Pericoli G, Gianno F, Besharat ZM, Tiberi L, Mastronuzzi A, Ferretti E, Tartaglia M, Locatelli F, Ciolfi A, Miele E (2024) Evaluating cell culture reliability in pediatric brain tumor primary cells through DNA methylation profiling. NPJ Precis Oncol, 8(1):92, doi:10.1038/s41698-024-00578-x.
http://www.ncbi.nlm.nih.gov/pubmed/38637626
Barros O, D'Agostino VG, Lara Santos L, Vitorino R, Ferreira R (2024) Shaping the future of oral cancer diagnosis: advances in salivary proteomics. Expert Rev Proteomics, doi:10.1080/14789450.2024.2343585.
http://www.ncbi.nlm.nih.gov/pubmed/38626289
Casagrande S, Sopetto GB, Bertalot G, Bortolotti R, Racanelli V, Caffo O, Giometto B, Berti A, Veccia A (2024) Immune-Related Adverse Events Due to Cancer Immunotherapy: Immune Mechanisms and Clinical Manifestations. Cancers (Basel), 16(7), doi:10.3390/cancers16071440.
http://www.ncbi.nlm.nih.gov/pubmed/38611115
Sarhan MS, Filosi M, Maixner F, Fuchsberger C (2024) Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy. bioRxiv, doi:10.1101/2024.03.22.586347.
http://www.ncbi.nlm.nih.gov/pubmed/38585727
Rossetto D, Sebastianelli L, Oberegger S, Todorovic S, Haas H, Mansy SS (2024) Peptide Mimics of the Cysteine-Rich Regions of HapX and SreA Bind a [2Fe-2S] Cluster In Vitro. Adv Biol (Weinh), doi:10.1002/adbi.202300545.
http://www.ncbi.nlm.nih.gov/pubmed/38574244
Ruiz-Serra V, Valentini S, Madroñero S, Valencia A, Porta-Pardo E (2024) 3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures. Bioinformatics, 40(4), doi:10.1093/bioinformatics/btae171.
http://www.ncbi.nlm.nih.gov/pubmed/38565273
Busarello E, Biancon G, Lauria F, Ibnat Z, Ramirez C, Tomè G, Aass KR, VanOudenhove J, Standal T, Viero G, Halene S, Tebaldi T (2024) Interpreting single-cell messages in normal and aberrant hematopoiesis with the Cell Marker Accordion. bioRxiv, doi:10.1101/2024.03.08.584053.
http://www.ncbi.nlm.nih.gov/pubmed/38559181
Cai T, Tamanini I, Odorizzi K, Gallelli L, Lanzafame M, Mazzoli S, Lanzafame P, Massidda O, Palmieri A, Wagenlehner FME, Bjerklund Johansen TE, De Nunzio C (2024) The diagnostic yield of the Meares & Stamey test can be significantly improved by symptom-based patient selection and the experience of the test performer. Prostate Cancer Prostatic Dis, doi:10.1038/s41391-024-00824-0.
http://www.ncbi.nlm.nih.gov/pubmed/38555411
Blanco-Míguez A, Carloni S, Cardenas C, Dioguardi CC, Lambroia L, Capretti G, Nappo G, Fugazza A, Capogreco A, Armanini F, Asnicar F, Dubois L, Golzato D, Manghi P, Pinto F, Scuderi C, Casari E, Montorsi M, Anderloni A, Rescigno M, Repici A, Zerbi A, Peano C, Tamburini S, Rusconi R, Segata N (2024) Microbial composition associated with biliary stents in patients undergoing pancreatic resection for cancer. NPJ Biofilms Microbiomes, 10(1):35, doi:10.1038/s41522-024-00506-8.
http://www.ncbi.nlm.nih.gov/pubmed/38555334
Habicher J, Sanvido I, Bühler A, Sartori S, Piccoli G, Carl M (2024) The Risk Genes for Neuropsychiatric Disorders Genes (Basel), 15(3), doi:10.3390/genes15030363.
http://www.ncbi.nlm.nih.gov/pubmed/38540422
Barros O, D'Agostino VG, Santos L, Ferreira R, Vitorino R (2024) Revisiting Multi-Omics Data to Unravel Galectins as Prognostic Factors in Head and Neck Squamous Cell Carcinoma. Biomedicines, 12(3), doi:10.3390/biomedicines12030529.
http://www.ncbi.nlm.nih.gov/pubmed/38540141
Mattioni L, Barbieri A, Grigoli A, Balasco L, Bozzi Y, Provenzano G (2024) Alterations of Perineuronal Net Expression and Abnormal Social Behavior and Whisker-dependent Texture Discrimination in Mice Lacking the Autism Candidate Gene Engrailed 2. Neuroscience, 546:63-74, doi:10.1016/j.neuroscience.2024.03.023.
http://www.ncbi.nlm.nih.gov/pubmed/38537894
Ruta GV, Ciciani M, Kheir E, Gentile MD, Amistadi S, Casini A, Cereseto A (2024) Eukaryotic-driven directed evolution of Cas9 nucleases. Genome Biol, 25(1):79, doi:10.1186/s13059-024-03215-9.
http://www.ncbi.nlm.nih.gov/pubmed/38528620
Michelatti D, Beyes S, Bernardis C, Negri ML, Morelli L, Bediaga NG, Poli V, Fagnocchi L, Lago S, D'Annunzio S, Cona N, Gaspardo I, Bianchi A, Jovetic J, Gianesello M, Turdo A, D'Accardo C, Gaggianesi M, Dori M, Forcato M, Crispatzu G, Rada-Iglesias A, Sosa MS, Timmers HTM, Bicciato S, Todaro M, Tiberi L, Zippo A (2024) Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting transcriptional memory. Nat Commun, 15(1):2198, doi:10.1038/s41467-024-46524-0.
http://www.ncbi.nlm.nih.gov/pubmed/38503727
D'Ambrosio A, Bressan D, Ferracci E, Carbone F, Mulè P, Rossi F, Barbieri C, Sorrenti E, Fiaccadori G, Detone T, Vezzoli E, Bianchi S, Sartori C, Corso S, Fukuda A, Bertalot G, Falqui A, Barbareschi M, Romanel A, Pasini D, Chiacchiera F (2024) Increased genomic instability and reshaping of tissue microenvironment underlie oncogenic properties of Sci Adv, 10(11):eadh4435, doi:10.1126/sciadv.adh4435.
http://www.ncbi.nlm.nih.gov/pubmed/38489371
Zolfo M, Silverj A, Blanco-Míguez A, Manghi P, Rota-Stabelli O, Heidrich V, Jensen J, Maharjan S, Franzosa E, Menni C, Visconti A, Pinto F, Ciciani M, Huttenhower C, Cereseto A, Asnicar F, Kitano H, Yamada T, Segata N (2024) Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples. bioRxiv, doi:10.1101/2024.02.19.580813.
http://www.ncbi.nlm.nih.gov/pubmed/38464031
Rotta G, Gilardoni E, Ravazza D, Mock J, Seehusen F, Elsayed A, Puca E, De Luca R, Pellegrino C, Look T, Weiss T, Manz MG, Halin C, Neri D, Dakhel Plaza S (2024) A novel strategy to generate immunocytokines with activity-on-demand using small molecule inhibitors. EMBO Mol Med, 16(4):904-926, doi:10.1038/s44321-024-00034-0.
http://www.ncbi.nlm.nih.gov/pubmed/38448543
Tomasi F, Pozzi M, Lauria M (2024) Investigating the mechanisms underlying resistance to chemoterapy and to CRISPR-Cas9 in cancer cell lines. Sci Rep, 14(1):5402, doi:10.1038/s41598-024-55138-x.
http://www.ncbi.nlm.nih.gov/pubmed/38443409
Dalfovo D, Scandino R, Paoli M, Valentini S, Romanel A (2024) Germline determinants of aberrant signaling pathways in cancer. NPJ Precis Oncol, 8(1):57, doi:10.1038/s41698-024-00546-5.
http://www.ncbi.nlm.nih.gov/pubmed/38429380
Monaco S, Bussola N, Buttò S, Sona D, Giobergia F, Jurman G, Xinaris C, Apiletti D (2024) Author Correction: AI models for automated segmentation of engineered polycystic kidney tubules. Sci Rep, 14(1):4781, doi:10.1038/s41598-024-55389-8.
http://www.ncbi.nlm.nih.gov/pubmed/38413717
Mattavelli E, Piperni E, Asnicar F, Redaelli L, Grigore L, Pellegatta F, Nabinejad A, Tamburini S, Segata N, Catapano AL, Baragetti A (2024) High dietary inflammatory index associates with inflammatory proteins in plasma. Diabetol Metab Syndr, 16(1):50, doi:10.1186/s13098-024-01287-y.
http://www.ncbi.nlm.nih.gov/pubmed/38409061
Alves Costa Silva C, Piccinno G, Suissa D, Bourgin M, Schreibelt G, Durand S, Birebent R, Fidelle M, Sow C, Aprahamian F, Manghi P, Punčochář M, Asnicar F, Pinto F, Armanini F, Terrisse S, Routy B, Drubay D, Eggermont AMM, Kroemer G, Segata N, Zitvogel L, Derosa L, Bol KF, de Vries IJM (2024) Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial. Nat Commun, 15(1):1633, doi:10.1038/s41467-024-45357-1.
http://www.ncbi.nlm.nih.gov/pubmed/38395948
Giuriato G, Romanelli MG, Bartolini D, Vernillo G, Pedrinolla A, Moro T, Franchi M, Locatelli E, Andani ME, Laginestra FG, Barbi C, Aloisi GF, Cavedon V, Milanese C, Orlandi E, De Simone T, Fochi S, Patuzzo C, Malerba G, Fabene P, Donadelli M, Stabile AM, Pistilli A, Rende M, Galli F, Schena F, Venturelli M (2024) Sex differences in neuromuscular and biological determinants of isometric maximal force. Acta Physiol (Oxf), 240(4):e14118, doi:10.1111/apha.14118.
http://www.ncbi.nlm.nih.gov/pubmed/38385696
Bazzani D, Heidrich V, Manghi P, Blanco-Miguez A, Asnicar F, Armanini F, Cavaliere S, Bertelle A, Dell'Acqua F, Dellasega E, Waldner R, Vicentini D, Bolzan M, Tomasi C, Segata N, Pasolli E, Ghensi P (2024) Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases. NPJ Biofilms Microbiomes, 10(1):12, doi:10.1038/s41522-024-00482-z.
http://www.ncbi.nlm.nih.gov/pubmed/38374114
Inno A, Veccia A, Madonia G, Berti A, Bortolotti R, Incorvaia L, Russo A, Caffo O, Gori S (2024) Risk of cardiovascular toxicity with combination of immune-checkpoint inhibitors and angiogenesis inhibitors: a meta-analysis. Front Cardiovasc Med, 11:1309100, doi:10.3389/fcvm.2024.1309100.
http://www.ncbi.nlm.nih.gov/pubmed/38370161
Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T, Kehrmann J (2024) Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices. Cell Rep Med, 5(3):101426, doi:10.1016/j.xcrm.2024.101426.
http://www.ncbi.nlm.nih.gov/pubmed/38366600
Capasso M, Brignole C, Lasorsa VA, Bensa V, Cantalupo S, Sebastiani E, Quattrone A, Ciampi E, Avitabile M, Sementa AR, Mazzocco K, Cafferata B, Gaggero G, Vellone VG, Cilli M, Calarco E, Giusto E, Perri P, Aveic S, Fruci D, Tondo A, Luksch R, Mura R, Rabusin M, De Leonardis F, Cellini M, Coccia P, Iolascon A, Corrias MV, Conte M, Garaventa A, Amoroso L, Ponzoni M, Pastorino F (2024) From the identification of actionable molecular targets to the generation of faithful neuroblastoma patient-derived preclinical models. J Transl Med, 22(1):151, doi:10.1186/s12967-024-04954-w.
http://www.ncbi.nlm.nih.gov/pubmed/38351008
Lim WC, Marques Da Costa ME, Godefroy K, Jacquet E, Gragert L, Rondof W, Marchais A, Nhiri N, Dalfovo D, Viard M, Labaied N, Khan AM, Dessen P, Romanel A, Pasqualini C, Schleiermacher G, Carrington M, Zitvogel L, Scoazec JY, Geoerger B, Salmon J (2023) Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common Front Immunol, 14:1265469, doi:10.3389/fimmu.2023.1265469.
http://www.ncbi.nlm.nih.gov/pubmed/38318504
Alaimo A, Genovesi S, Annesi N, De Felice D, Subedi S, Macchia A, La Manna F, Ciani Y, Vannuccini F, Mugoni V, Notarangelo M, Libergoli M, Broso F, Taulli R, Ala U, Savino A, Cortese M, Mirzaaghaei S, Poli V, Bonapace IM, Papotti MG, Molinaro L, Doglioni C, Caffo O, Anesi A, Nagler M, Bertalot G, Carbone FG, Barbareschi M, Basso U, Dassi E, Pizzato M, Romanel A, Demichelis F, Kruithof-de Julio M, Lunardi A (2024) Sterile inflammation via TRPM8 RNA-dependent TLR3-NF-kB/IRF3 activation promotes antitumor immunity in prostate cancer. EMBO J, 43(5):780-805, doi:10.1038/s44318-024-00040-5.
http://www.ncbi.nlm.nih.gov/pubmed/38316991
Monaco S, Bussola N, Buttò S, Sona D, Giobergia F, Jurman G, Xinaris C, Apiletti D (2024) AI models for automated segmentation of engineered polycystic kidney tubules. Sci Rep, 14(1):2847, doi:10.1038/s41598-024-52677-1.
http://www.ncbi.nlm.nih.gov/pubmed/38310171
Reali F, Fochesato A, Kaddi C, Visintainer R, Watson S, Levi M, Dartois V, Azer K, Marchetti L (2023) A minimal PBPK model to accelerate preclinical development of drugs against tuberculosis. Front Pharmacol, 14:1272091, doi:10.3389/fphar.2023.1272091.
http://www.ncbi.nlm.nih.gov/pubmed/38239195
Franceschini GM, Quaini O, Mizuno K, Orlando F, Ciani Y, Ku SY, Sigouros M, Rothmann E, Alonso A, Benelli M, Nardella C, Auh J, Freeman D, Hanratty B, Adil M, Elemento O, Tagawa ST, Feng FY, Caffo O, Buttigliero C, Basso U, Nelson PS, Corey E, Haffner MC, Attard G, Aparicio A, Demichelis F, Beltran H (2024) Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation. Cancer Discov, 14(3):424-445, doi:10.1158/2159-8290.CD-23-0754.
http://www.ncbi.nlm.nih.gov/pubmed/38197680
Cappelletto A, Alfì E, Volf N, Vu TVA, Bortolotti F, Ciucci G, Vodret S, Fantuz M, Perin M, Colliva A, Rozzi G, Rossi M, Ruozi G, Zentilin L, Vuerich R, Borin D, Lapasin R, Piazza S, Chiesa M, Lorizio D, Triboli L, Kumar S, Morello G, Tripodo C, Pinamonti M, Piperno GM, Benvenuti F, Rustighi A, Jo H, Piccolo S, Del Sal G, Carrer A, Giacca M, Zacchigna S (2024) EMID2 is a novel biotherapeutic for aggressive cancers identified by in vivo screening. J Exp Clin Cancer Res, 43(1):15, doi:10.1186/s13046-023-02942-4.
http://www.ncbi.nlm.nih.gov/pubmed/38195652
Bianconi I, Spath M, Aschbacher R, Pedron R, Wieser S, Pagani E (2024) Characterization of Verona Integron-Encoded Metallo-β-Lactamase-Type Carbapenemase-Producing Microb Drug Resist, 30(2):91-100, doi:10.1089/mdr.2023.0197.
http://www.ncbi.nlm.nih.gov/pubmed/38150043
Rivosecchi J, Jurikova K, Cusanelli E (2024) Telomere-specific regulation of TERRA and its impact on telomere stability. Semin Cell Dev Biol, 157:3-23, doi:10.1016/j.semcdb.2023.11.001.
http://www.ncbi.nlm.nih.gov/pubmed/38088000
Fornasiero A, Fornoni S, Callovini A, Todesco B, Savoldelli A, Schena F, Holmberg HC, Pellegrini B, Bortolan L (2024) Analysis of Sprint Ski Mountaineering Performance. Int J Sports Physiol Perform, 19(2):155-163, doi:10.1123/ijspp.2023-0075.
http://www.ncbi.nlm.nih.gov/pubmed/38086366
Belkina AC, Roe CE, Tang VA, Back JB, Bispo C, Conway A, Chakraborty U, Daniels KT, de la Cruz G, Ferrer-Font L, Filby A, Gravano DM, Gregory MD, Hall C, Kukat C, Mozes A, Ordoñez-Rueda D, Orlowski-Oliver E, Pesce I, Porat Z, Poulton NJ, Reifel KM, Rieger AM, Sheridan RTC, Van Isterdael G, Walker RV (2024) Guidelines for establishing a cytometry laboratory. Cytometry A, 105(2):88-111, doi:10.1002/cyto.a.24807.
http://www.ncbi.nlm.nih.gov/pubmed/37941128
Munari E, Scarpa A, Cima L, Pozzi M, Pagni F, Vasuri F, Marletta S, Dei Tos AP, Eccher A (2024) Cutting-edge technology and automation in the pathology laboratory. Virchows Arch, 484(4):555-566, doi:10.1007/s00428-023-03637-z.
http://www.ncbi.nlm.nih.gov/pubmed/37930477
Wang Z, Burigotto M, Ghetti S, Vaillant F, Tan T, Capaldo BD, Palmieri M, Hirokawa Y, Tai L, Simpson DS, Chang C, Huang AS, Lieschke E, Diepstraten ST, Kaloni D, Riffkin C, Huang DCS, Li Wai Suen CSN, Garnham AL, Gibbs P, Visvader JE, Sieber OM, Herold MJ, Fava LL, Kelly GL, Strasser A (2024) Loss-of-Function but Not Gain-of-Function Properties of Mutant TP53 Are Critical for the Proliferation, Survival, and Metastasis of a Broad Range of Cancer Cells. Cancer Discov, 14(2):362-379, doi:10.1158/2159-8290.CD-23-0402.
http://www.ncbi.nlm.nih.gov/pubmed/37877779
Bermingham KM, May A, Asnicar F, Capdevila J, Leeming ER, Franks PW, Valdes AM, Wolf J, Hadjigeorgiou G, Delahanty LM, Segata N, Spector TD, Berry SE (2024) Snack quality and snack timing are associated with cardiometabolic blood markers: the ZOE PREDICT study. Eur J Nutr, 63(1):121-133, doi:10.1007/s00394-023-03241-6.
http://www.ncbi.nlm.nih.gov/pubmed/37709944
Hellmich B, Sanchez-Alamo B, Schirmer JH, Berti A, Blockmans D, Cid MC, Holle JU, Hollinger N, Karadag O, Kronbichler A, Little MA, Luqmani RA, Mahr A, Merkel PA, Mohammad AJ, Monti S, Mukhtyar CB, Musial J, Price-Kuehne F, Segelmark M, Teng YKO, Terrier B, Tomasson G, Vaglio A, Vassilopoulos D, Verhoeven P, Jayne D (2024) EULAR recommendations for the management of ANCA-associated vasculitis: 2022 update. Ann Rheum Dis, 83(1):30-47, doi:10.1136/ard-2022-223764.
http://www.ncbi.nlm.nih.gov/pubmed/36927642