Latest publications of CIBIO affiliates (last updated on August 1st, 2020)

Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Sakharova E, Parks DH, Hugenholtz P, Segata N, Kyrpides NC, Finn RD (2020) A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol., doi:10.1038/s41587-020-0603-3.
http://www.ncbi.nlm.nih.gov/pubmed/32690973

Malchiodi L, Ricciardi G, Salandini A, Caricasulo R, Cucchi A, Ghensi P (2020) Influence of crown-implant ratio on implant success rate of ultra-short dental implants: results of a 8- to 10-year retrospective study. Clin Oral Investig, doi:10.1007/s00784-020-03195-7.
http://www.ncbi.nlm.nih.gov/pubmed/32681422

Covello G, Rossello FJ, Filosi M, Gajardo F, Duchemin AL, Tremonti BF, Eichenlaub M, Polo JM, Powell D, Ngai J, Allende ML, Domenici E, Ramialison M, Poggi L (2020) Transcriptome analysis of the zebrafish  FASEB Bioadv, 2(7):434-448, doi:10.1096/fba.2020-00030.
http://www.ncbi.nlm.nih.gov/pubmed/32676583

Hamadou I, Garritano S, Romanel A, Naimi D, Hammada T, Demichelis F (2020) Inherited variant in NFκB-1 promoter is associated with increased risk of IBD in an Algerian population and modulates SOX9 binding. Cancer Rep (Hoboken), 3(3):e1240, doi:10.1002/cnr2.1240.
http://www.ncbi.nlm.nih.gov/pubmed/32671985

Caffa I, Spagnolo V, Vernieri C, Valdemarin F, Becherini P, Wei M, Brandhorst S, Zucal C, Driehuis E, Ferrando L, Piacente F, Tagliafico A, Cilli M, Mastracci L, Vellone VG, Piazza S, Cremonini AL, Gradaschi R, Mantero C, Passalacqua M, Ballestrero A, Zoppoli G, Cea M, Arrighi A, Odetti P, Monacelli F, Salvadori G, Cortellino S, Clevers H, De Braud F, Sukkar SG, Provenzani A, Longo VD, Nencioni A (2020) Fasting-mimicking diet and hormone therapy induce breast cancer regression. Nature, 583(7817):620-624, doi:10.1038/s41586-020-2502-7.
http://www.ncbi.nlm.nih.gov/pubmed/32669709

Conteduca V, Wetterskog D, Scarpi E, Romanel A, Gurioli G, Jayaram A, Lolli C, Tandefelt DG, Schepisi G, Casadei C, Wingate A, Matteucci F, Paganelli G, Gonzalez-Billalabeitia E, Demichelis F, De Giorgi U, Attard G (2020) Plasma tumour DNA as an early indicator of treatment response in metastatic castration-resistant prostate cancer. Br. J. Cancer, doi:10.1038/s41416-020-0969-5.
http://www.ncbi.nlm.nih.gov/pubmed/32669676

Foladori P, Cutrupi F, Segata N, Manara S, Pinto F, Malpei F, Bruni L, La Rosa G (2020) SARS-CoV-2 from faeces to wastewater treatment: What do we know? A review. Sci. Total Environ., 743:140444, doi:10.1016/j.scitotenv.2020.140444.
http://www.ncbi.nlm.nih.gov/pubmed/32649988

Bacci G, Taccetti G, Dolce D, Armanini F, Segata N, Di Cesare F, Lucidi V, Fiscarelli E, Morelli P, Casciaro R, Negroni A, Mengoni A, Bevivino A (2020) Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease. Microorganisms, 8(7), doi:10.3390/microorganisms8071003.
http://www.ncbi.nlm.nih.gov/pubmed/32635564

De Felice D, Alaimo A (2020) Mechanosensitive Piezo Channels in Cancer: Focus on altered Calcium Signaling in Cancer Cells and in Tumor Progression. Cancers (Basel), 12(7), doi:10.3390/cancers12071780.
http://www.ncbi.nlm.nih.gov/pubmed/32635333

Bendotti C, Bonetto V, Pupillo E, Logroscino G, Al-Chalabi A, Lunetta C, Riva N, Mora G, Lauria G, Weishaupt JH, Agosta F, Malaspina A, Basso M, Greensmith L, Van Den Bosch L, Ratti A, Corbo M, Hardiman O, Chiò A, Silani V, Beghi E (2020) Focus on the heterogeneity of amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener, doi:10.1080/21678421.2020.1779298.
http://www.ncbi.nlm.nih.gov/pubmed/32583689

Caio G, Lungaro L, Segata N, Guarino M, Zoli G, Volta U, De Giorgio R (2020) Effect of Gluten-Free Diet on Gut Microbiota Composition in Patients with Celiac Disease and Non-Celiac Gluten/Wheat Sensitivity. Nutrients, 12(6), doi:10.3390/nu12061832.
http://www.ncbi.nlm.nih.gov/pubmed/32575561

Vázquez-Manjarrez N, Ulaszewska M, Garcia-Aloy M, Mattivi F, Praticò G, Dragsted LO, Manach C (2020) Biomarkers of intake for tropical fruits. Genes Nutr, 15(1):11, doi:10.1186/s12263-020-00670-4.
http://www.ncbi.nlm.nih.gov/pubmed/32560627

Obergasteiger J, Frapporti G, Lamonaca G, Pizzi S, Picard A, Lavdas AA, Pischedda F, Piccoli G, Hilfiker S, Lobbestael E, Baekelandt V, Hicks AA, Corti C, Pramstaller PP, Volta M (2020) Kinase inhibition of G2019S-LRRK2 enhances autolysosome formation and function to reduce endogenous alpha-synuclein intracellular inclusions. Cell Death Discov, 6:45, doi:10.1038/s41420-020-0279-y.
http://www.ncbi.nlm.nih.gov/pubmed/32550012

Detassis S, Del Vescovo V, Grasso M, Masella S, Cantaloni C, Cima L, Cavazza A, Graziano P, Rossi G, Barbareschi M, Ricci L, Denti MA (2020) miR375-3p Distinguishes Low-Grade Neuroendocrine From Non-neuroendocrine Lung Tumors in FFPE Samples. Front Mol Biosci, 7:86, doi:10.3389/fmolb.2020.00086.
http://www.ncbi.nlm.nih.gov/pubmed/32528971

Berry SE, Valdes AM, Drew DA, Asnicar F, Mazidi M, Wolf J, Capdevila J, Hadjigeorgiou G, Davies R, Al Khatib H, Bonnett C, Ganesh S, Bakker E, Hart D, Mangino M, Merino J, Linenberg I, Wyatt P, Ordovas JM, Gardner CD, Delahanty LM, Chan AT, Segata N, Franks PW, Spector TD (2020) Human postprandial responses to food and potential for precision nutrition. Nat. Med., 26(6):964-973, doi:10.1038/s41591-020-0934-0.
http://www.ncbi.nlm.nih.gov/pubmed/32528151

Destefanis F, Manara V, Bellosta P (2020) Myc as a Regulator of Ribosome Biogenesis and Cell Competition: A Link to Cancer. Int J Mol Sci, 21(11), doi:10.3390/ijms21114037.
http://www.ncbi.nlm.nih.gov/pubmed/32516899

Allouch A, Di Primio C, Paoletti A, Lê-Bury G, Subra F, Quercioli V, Nardacci R, David A, Saïdi H, Cereseto A, Ojcius DM, Montagnac G, Niedergang F, Pancino G, Saez-Cirion A, Piacentini M, Gougeon ML, Kroemer G, Perfettini JL (2020) SUGT1 controls susceptibility to HIV-1 infection by stabilizing microtubule plus-ends. Cell Death Differ., doi:10.1038/s41418-020-0573-5.
http://www.ncbi.nlm.nih.gov/pubmed/32514048

Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, Armanini F, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Valles-Colomer M, Raffaetà R, Rota-Stabelli O, Collado MC, Zeller G, Falush D, Maixner F, Walker AW, Huttenhower C, Segata N (2020) Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome Biol., 21(1):138, doi:10.1186/s13059-020-02042-y.
http://www.ncbi.nlm.nih.gov/pubmed/32513234

Fevola C, Rossi C, Rosso F, Girardi M, Rosà R, Manica M, Delucchi L, Rocchini D, Garzon-Lopez CX, Arnoldi D, Bianchi A, Buzan E, Charbonnel N, Collini M, Ďureje Ľ, Ecke F, Ferrari N, Fischer S, Gillingham EL, Hörnfeldt B, Kazimírová M, Konečný A, Maas M, Magnusson M, Miller A, Niemimaa J, Nordström Å, Obiegala A, Olsson G, Pedrini P, Piálek J, Reusken CB, Rizzolli F, Romeo C, Silaghi C, Sironen T, Stanko M, Tagliapietra V, Ulrich RG, Vapalahti O, Voutilainen L, Wauters L, Rizzoli A, Vaheri A, Jääskeläinen AJ, Henttonen H, Hauffe HC (2020) Geographical Distribution of Ljungan Virus in Small Mammals in Europe. Vector Borne Zoonotic Dis., doi:10.1089/vbz.2019.2542.
http://www.ncbi.nlm.nih.gov/pubmed/32487013

Maule G, Arosio D, Cereseto A (2020) Gene Therapy for Cystic Fibrosis: Progress and Challenges of Genome Editing. Int J Mol Sci, 21(11), doi:10.3390/ijms21113903.
http://www.ncbi.nlm.nih.gov/pubmed/32486152

Albadri S, Armant O, Aljand-Geschwill T, Del Bene F, Carl M, Strähle U, Poggi L (2020) Expression of a Barhl1a reporter in subsets of retinal ganglion cells and commissural neurons of the developing zebrafish brain. Sci Rep, 10(1):8814, doi:10.1038/s41598-020-65435-w.
http://www.ncbi.nlm.nih.gov/pubmed/32483163

Herviou P, Le Bras M, Dumas L, Hieblot C, Gilhodes J, Cioci G, Hugnot JP, Ameadan A, Guillonneau F, Dassi E, Cammas A, Millevoi S (2020) hnRNP H/F drive RNA G-quadruplex-mediated translation linked to genomic instability and therapy resistance in glioblastoma. Nat Commun, 11(1):2661, doi:10.1038/s41467-020-16168-x.
http://www.ncbi.nlm.nih.gov/pubmed/32461552

Pasolli E, De Filippis F, Mauriello IE, Cumbo F, Walsh AM, Leech J, Cotter PD, Segata N, Ercolini D (2020) Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nat Commun, 11(1):2610, doi:10.1038/s41467-020-16438-8.
http://www.ncbi.nlm.nih.gov/pubmed/32451391

Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N (2020) Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun, 11(1):2500, doi:10.1038/s41467-020-16366-7.
http://www.ncbi.nlm.nih.gov/pubmed/32427907

Garcia-Aloy M, Ulaszewska M, Franceschi P, Estruel-Amades S, Weinert CH, Tor-Roca A, Urpi-Sarda M, Mattivi F, Andres-Lacueva C (2020) Discovery of Intake Biomarkers of Lentils, Chickpeas, and White Beans by Untargeted LC-MS Metabolomics in Serum and Urine. Mol Nutr Food Res, 64(13):e1901137, doi:10.1002/mnfr.201901137.
http://www.ncbi.nlm.nih.gov/pubmed/32420683

Ciciani M, Cantore T, Lauria M (2020) rScudo: an R package for classification of molecular profiles using rank-based signatures. Bioinformatics, 36(13):4095-4096, doi:10.1093/bioinformatics/btaa296.
http://www.ncbi.nlm.nih.gov/pubmed/32399554

Carrot-Zhang J, Chambwe N, Damrauer JS, Knijnenburg TA, Robertson AG, Yau C, Zhou W, Berger AC, Huang KL, Newberg JY, Mashl RJ, Romanel A, Sayaman RW, Demichelis F, Felau I, Frampton GM, Han S, Hoadley KA, Kemal A, Laird PW, Lazar AJ, Le X, Oak N, Shen H, Wong CK, Zenklusen JC, Ziv E, Cancer Genome Atlas Analysis Network, Cherniack AD, Beroukhim R (2020) Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer. Cancer Cell, 37(5):639-654.e6, doi:10.1016/j.ccell.2020.04.012.
http://www.ncbi.nlm.nih.gov/pubmed/32396860

Tigani W, Rossi MP, Artimagnella O, Santo M, Rauti R, Sorbo T, Ulloa Severino FP, Provenzano G, Allegra M, Caleo M, Ballerini L, Bozzi Y, Mallamaci A (2020) Foxg1 Upregulation Enhances Neocortical Activity. Cereb. Cortex, 30(9):5147-5165, doi:10.1093/cercor/bhaa107.
http://www.ncbi.nlm.nih.gov/pubmed/32383447

Derosa L, Routy B, Fidelle M, Iebba V, Alla L, Pasolli E, Segata N, Desnoyer A, Pietrantonio F, Ferrere G, Fahrner JE, Le Chatellier E, Pons N, Galleron N, Roume H, Duong CPM, Mondragón L, Iribarren K, Bonvalet M, Terrisse S, Rauber C, Goubet AG, Daillère R, Lemaitre F, Reni A, Casu B, Alou MT, Alves Costa Silva C, Raoult D, Fizazi K, Escudier B, Kroemer G, Albiges L, Zitvogel L (2020) Gut Bacteria Composition Drives Primary Resistance to Cancer Immunotherapy in Renal Cell Carcinoma Patients. Eur. Urol., 78(2):195-206, doi:10.1016/j.eururo.2020.04.044.
http://www.ncbi.nlm.nih.gov/pubmed/32376136

Cussotto S, Delgado I, Anesi A, Dexpert S, Aubert A, Beau C, Forestier D, Ledaguenel P, Magne E, Mattivi F, Capuron L (2020) Tryptophan Metabolic Pathways Are Altered in Obesity and Are Associated With Systemic Inflammation. Front Immunol, 11:557, doi:10.3389/fimmu.2020.00557.
http://www.ncbi.nlm.nih.gov/pubmed/32351500

Zhou X, Ulaszewska MM, Cuparencu C, De Gobba C, Vázquez-Manjarrez N, Gürdeniz G, Chen J, Mattivi F, Dragsted LO (2020) Urine Metabolome Profiling Reveals Imprints of Food Heating Processes after Dietary Intervention with Differently Cooked Potatoes. J. Agric. Food Chem., 68(22):6122-6131, doi:10.1021/acs.jafc.0c01136.
http://www.ncbi.nlm.nih.gov/pubmed/32338001

Liu D, Shoag JE, Poliak D, Goueli RS, Ravikumar V, Redmond D, Vosoughi A, Fontugne J, Pan H, Lee D, Thomas D, Salari K, Wang Z, Romanel A, Te A, Lee R, Chughtai B, Olumi AF, Mosquera JM, Demichelis F, Elemento O, Rubin MA, Sboner A, Barbieri CE (2020) Integrative multiplatform molecular profiling of benign prostatic hyperplasia identifies distinct subtypes. Nat Commun, 11(1):1987, doi:10.1038/s41467-020-15913-6.
http://www.ncbi.nlm.nih.gov/pubmed/32332823

Idilli AI, Pagani F, Kerschbamer E, Berardinelli F, Bernabé M, Cayuela ML, Piazza S, Poliani PL, Cusanelli E, Mione MC (2020) Changes in the Expression of Pre-Replicative Complex Genes in hTERT and ALT Pediatric Brain Tumors. Cancers (Basel), 12(4), doi:10.3390/cancers12041028.
http://www.ncbi.nlm.nih.gov/pubmed/32331249

Manni G, Lewis V, Senesi M, Spagnolli G, Fallarino F, Collins SJ, Mouillet-Richard S, Biasini E (2020) The cellular prion protein beyond prion diseases. Swiss Med Wkly, 150:w20222, doi:10.4414/smw.2020.20222.
http://www.ncbi.nlm.nih.gov/pubmed/32330284

Mullish BH, Michael DR, McDonald JA, Masetti G, Plummer SF, Marchesi JR (2020) Identifying the factors influencing outcome in probiotic studies in overweight and obese patients: host or microbiome? Gut, doi:10.1136/gutjnl-2020-321110.
http://www.ncbi.nlm.nih.gov/pubmed/32317331

Palomo-Irigoyen M, Pérez-Andrés E, Iruarrizaga-Lejarreta M, Barreira-Manrique A, Tamayo-Caro M, Vila-Vecilla L, Moreno-Cugnon L, Beitia N, Medrano D, Fernández-Ramos D, Lozano JJ, Okawa S, Lavín JL, Martín-Martín N, Sutherland JD, de Juan VG, Gonzalez-Lopez M, Macías-Cámara N, Mosén-Ansorena D, Laraba L, Hanemann CO, Ercolano E, Parkinson DB, Schultz CW, Araúzo-Bravo MJ, Ascensión AM, Gerovska D, Iribar H, Izeta A, Pytel P, Krastel P, Provenzani A, Seneci P, Carrasco RD, Del Sol A, Martinez-Chantar ML, Barrio R, Serra E, Lazaro C, Flanagan AM, Gorospe M, Ratner N, Aransay AM, Carracedo A, Varela-Rey M, Woodhoo A (2020) HuR/ELAVL1 drives malignant peripheral nerve sheath tumor growth and metastasis. J. Clin. Invest., 130(7):3848-3864, doi:10.1172/JCI130379.
http://www.ncbi.nlm.nih.gov/pubmed/32315290

Corbellari R, Nadal L, Villa A, Neri D, De Luca R (2020) The immunocytokine L19-TNF eradicates sarcomas in combination with chemotherapy agents or with immune check-point inhibitors. Anticancer Drugs, doi:10.1097/CAD.0000000000000938.
http://www.ncbi.nlm.nih.gov/pubmed/32304410

Filosi M, Kam-Thong T, Essioux L, Muglia P, Trabetti E, Spooren W, Müller-Myshok B, Italian Autism Network, Domenici E (2020) Transcriptome signatures from discordant sibling pairs reveal changes in peripheral blood immune cell composition in Autism Spectrum Disorder. Transl Psychiatry, 10(1):106, doi:10.1038/s41398-020-0778-x.
http://www.ncbi.nlm.nih.gov/pubmed/32291385

Dalle Vedove A, Zonta F, Zanforlin E, Demitri N, Ribaudo G, Cazzanelli G, Ongaro A, Sarno S, Zagotto G, Battistutta R, Ruzzene M, Lolli G (2020) A novel class of selective CK2 inhibitors targeting its open hinge conformation. Eur J Med Chem, 195:112267, doi:10.1016/j.ejmech.2020.112267.
http://www.ncbi.nlm.nih.gov/pubmed/32283296

Hanczyc MM (2020) Engineering Life: A Review of Synthetic Biology. Artif. Life, 26(2):260-273, doi:10.1162/artl_a_00318.
http://www.ncbi.nlm.nih.gov/pubmed/32271630

Arapitsas P, Ugliano M, Marangon M, Piombino P, Rolle L, Gerbi V, Versari A, Mattivi F (2020) Use of Untargeted Liquid Chromatography-Mass Spectrometry Metabolome To Discriminate Italian Monovarietal Red Wines, Produced in Their Different Terroirs. J. Agric. Food Chem., doi:10.1021/acs.jafc.0c00879.
http://www.ncbi.nlm.nih.gov/pubmed/32271564

Swann JR, Rajilic-Stojanovic M, Salonen A, Sakwinska O, Gill C, Meynier A, Fança-Berthon P, Schelkle B, Segata N, Shortt C, Tuohy K, Hasselwander O (2020) Considerations for the design and conduct of human gut microbiota intervention studies relating to foods. Eur J Nutr, doi:10.1007/s00394-020-02232-1.
http://www.ncbi.nlm.nih.gov/pubmed/32246263

Tripathy D, Migazzi A, Costa F, Roncador A, Gatto P, Fusco F, Boeri L, Albani D, Juárez-Hernández JL, Musio C, Colombo L, Salmona M, Wilhelmus MMM, Drukarch B, Pennuto M, Basso M (2020) Increased transcription of transglutaminase 1 mediates neuronal death in in vitro models of neuronal stress and Aβ1-42-mediated toxicity. Neurobiol. Dis., 140:104849, doi:10.1016/j.nbd.2020.104849.
http://www.ncbi.nlm.nih.gov/pubmed/32222473

Berti A, Cornec D, Casal Moura M, Smyth RJ, Dagna L, Specks U, Keogh KA (2020) Eosinophilic Granulomatosis With Polyangiitis: Clinical Predictors of Long-term Asthma Severity. Chest, 157(5):1086-1099, doi:10.1016/j.chest.2019.11.045.
http://www.ncbi.nlm.nih.gov/pubmed/31958440

Casiraghi N, Orlando F, Ciani Y, Xiang J, Sboner A, Elemento O, Attard G, Beltran H, Demichelis F, Romanel A (2020) ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA. Bioinformatics, 36(9):2665-2674, doi:10.1093/bioinformatics/btaa016.
http://www.ncbi.nlm.nih.gov/pubmed/31922552

Mercatelli D, Scalambra L, Triboli L, Ray F, Giorgi FM (2020) Gene regulatory network inference resources: A practical overview. Biochim Biophys Acta Gene Regul Mech, 1863(6):194430, doi:10.1016/j.bbagrm.2019.194430.
http://www.ncbi.nlm.nih.gov/pubmed/31678629

Cozza G, Zonta F, Dalle Vedove A, Venerando A, Dall'Acqua S, Battistutta R, Ruzzene M, Lolli G (2020) Biochemical and cellular mechanism of protein kinase CK2 inhibition by deceptive curcumin. FEBS J., 287(9):1850-1864, doi:10.1111/febs.15111.
http://www.ncbi.nlm.nih.gov/pubmed/31661600

Toparlak ÖD, Karki M, Egas Ortuno V, Krishnamurthy R, Mansy SS (2020) Cyclophospholipids Increase Protocellular Stability to Metal Ions. Small, 16(27):e1903381, doi:10.1002/smll.201903381.
http://www.ncbi.nlm.nih.gov/pubmed/31523894

Agnusdei V, Minuzzo S, Pinazza M, Gasparini A, Pezzè L, Amaro AA, Pasqualini L, Bianco PD, Tognon M, Frasson C, Palumbo P, Ciribilli Y, Pfeffer U, Carella M, Amadori A, Indraccolo S (2020) Dissecting molecular mechanisms of resistance to NOTCH1-targeted therapy in T-cell acute lymphoblastic leukemia xenografts. Haematologica, 105(5):1317-1328, doi:10.3324/haematol.2019.217687.
http://www.ncbi.nlm.nih.gov/pubmed/31467126

Diuba AV, Samigullin DV, Kaszas A, Zonfrillo F, Malkov A, Petukhova E, Casini A, Arosio D, Esclapez M, Gross CT, Bregestovski P (2020) CLARITY analysis of the Cl/pH sensor expression in the brain of transgenic mice. Neuroscience, 439:181-194, doi:10.1016/j.neuroscience.2019.07.010.
http://www.ncbi.nlm.nih.gov/pubmed/31302264