Overview | Research projects | Group members | Collaborations | Selected Publications
Overview
Our research focuses on understanding how genetic diversity and genomic aberrations contribute to tumor evolution and progression.
The laboratory integrates large-scale computational and experimental work to dissect tumors heterogeneity with main focus on prostate and bladder cancer.
The ultimate goal of our work is to contribute to the field of Precision Oncology by identifying biomarkers to predict progression, to select pharmacological treatment and to monitor cancer patients’ treatment response.
Laboratory website demichelislab.eu
Research Projects
- To nomination potential synthetic lethal combinations via pan-cancer computational analysis of thousands of sequenced tumors and in vitro validate and characterize relevant hits (funded by ERC-Consolidator, MIUR, FTRT);
- To identify the molecular features involved in the trans-differentiation of prostate cancer adenocarcinoma to AR indifferent phenotype (funded by NIH, PCF);
- To study the effect of inherited variants within transcriptionally active regions and chromatin regulators on molecularly defined prostate cancer sub-classes (funded by AIRC);
- To design, optimize and use liquid biopsies tools for translational and clinical research (funded by NIH, PCF, CRUK-AIRC-Accelerator Award, Fondazione Caritro).
Group members
- Nicola Casiraghi, post-doc
- Yari Ciani, post-doc
- Francesca Demichelis, PI
- Tarcisio Fedrizzi, research fellow
- Giulia Fracassi, PhD student
- Gian Marco Franceschini, PhD student
- Paola Gasperini, post-doc
- Francesca Lorenzin, post-doc
- Francesco Orlando, PhD student
- Davide Prandi, post-doc
- Blerta Stringa, PhD student
- Orsetta Quaini, research fellow
- Alessio Locallo, Master student
- Davide Dalfovo, Master student (with A. Romanel)
Open positions are available, please contact: f.demichelis [at] unitn.it
Collaborations
- Bishoy Faltas, Weill Cornell Medicine, New York
- Dolores Di Vizio, Cedars-Sinai, Los Angeles
- Gert Attard, UCL, London
- Helmut Klocker, University Hospital Innsbruck, Innsbruck
- Himisha Beltran, DFCI, Boston
- Mark A Rubin, University of Bern, Bern
- Olivier Elemento, Weill Cornell Medicine, New York
Selected publications (2011-2017)
Nava Rodrigues D*, Casiraghi N*, Romanel A, Crespo M, Miranda S, Rescigno P, Figueiredo I, Riisnaes R, Carreira S, Sumanasuriya S, Gasperini P, Sharp A, Mateo J, Makay A, McNair C, Schiewer M, Knudsen K, Boysen G, Demichelis F., de Bono JS&#. RB1 Heterogeneity in Advanced Metastatic Castration Resistant Prostate Cancer. Clin Cancer Res. 2018.
Benelli M, Romagnoli D, Demichelis F. Tumor purity quantification by clonal DNA methylation signatures. Bioinformatics. 2018 Jan 8. doi: 10.1093/bioinformatics/bty011.
Mu P, Zhang Z, Benelli M, Karthaus WR, Hoover E, Chen C-C, Wongvipat J, Ku S-Y, Gao D, Cao Z, Shah N, Adams EJ, Abida W, Watson PA, Prandi D, Huang C-H, de Stanchina E, Lowe SW, Ellis L, Beltran H, Rubin MA, Goodrich DW, Demichelis F, Sawyers CL. SOX2 promotes lineage plasticity and antiandrogen resistance in TP53 and RB1 deficient prostate cancer. Science. 2017 Jan 6;355(6320):84-88.
Romanel A, Zhang T, Elemento O, Demichelis F. EthSEQ: ethnicity annotation from whole exome sequencing data. Bioinformatics. 2017 Mar 27. doi: 10.1093/bioinformatics/btx165.
Romanel A*, Garritano S*, Stringa B, Blattner M, Dalfovo D, Chakravarty D, Cotter KA, Petris G, Dhingra P, Gasperini P, Cereseto A, Elemento O, Sboner A, Khurana E, Inga A, Rubin MA, Demichelis F. Inherited determinants of early recurrent somatic mutations in prostate cancer. Nat Commun. 2017 Jun 29;8(1):48.
Rubin MA, Girelli G, Demichelis F. Genomic Correlates to the newly proposed Grading Prognostic Groups for Prostate Cancer. Eur Urol. 2016 Apr;69(4):557-60.
Beltran H*&, Prandi D*, Mosquera JM, Benelli M, Puca L, Cyrta J, Marotz C, Giannopoulou E, Chakravarthi BV, Varambally S, Tomlins SA, Nanus DM, Tagawa ST, Van Allen EM, Elemento O, Sboner A, Garraway L., Rubin MA., Demichelis F. Divergent clonal evolution of androgen receptor indifferent castration resistant prostate cancer. Nat Med. 2016 Mar;22(3):298-305.
Faltas BM*, Prandi D*, Tagawa ST, Molina AM, Nanus DM, Sternberg C, Rosenberg J, Mosquera J-M, Robinson B, Elemento O, Sboner A, Beltran H., Demichelis F., Rubin MA.. Clonal Evolution of Chemotherapy-resistant Urothelial Carcinoma. Nat Genet. 2016 Dec;48(12):1490-1499.
Garritano S, Romanel A, Ciribilli Y, Bisio A, Gavoci A, Inga A, Demichelis F. In-silico identification and functional validation of allele-dependent AR enhancers. Oncotarget. 2015 Mar 10;6(7):4816-28.
Boysen G*, Barbieri CE*, Prandi D, Blattner M, Chae SS, Dahija A, Nataraj S, Huang D, Marotz C, Xu L, Huang J, Lecca P, Chhangawala S, Liu D, Zhou P, Sboner A, de Bono JS, Demichelis F., Houvras Y., Rubin MA. SPOP mutation leads to genomic instability in prostate cancer. Elife. 2015 Sep 16;4. doi: 10.7554/eLife.09207.
Romanel A*, Gasi Tandefelt D*, Conteduca V, Jayaram A, Casiraghi N, Wetterskog D, Salvi S, Amadori D, Zafeiriou Z, Rescigno P, Bianchini D, Gurioli G, Casadio V, Carreira S, Goodall J, Wingate A, Ferraldeschi R, Tunariu N, Flohr P, De Giorgi U, de Bono JS, Demichelis F., Attard G. Plasma AR and Abiraterone Resistant Prostate Cancer. Sci Transl Med. 2015 Nov 4;7(312):312re10.
Fontugne J, Lee D, Cantaloni C, Barbieri CE, Caffo O, Hanspeter E, Mazzoleni G, Dalla Palma P, Rubin MA, Fellin G, Mosquera JM, Barbareschi M, Demichelis F. Recurrent Prostate Cancer Genomic Alterations Predict Response to Brachytherapy Treatment. Cancer Epidemiol Biomarkers Prev. 2014. 23(4); 1-7.
Carreira S*, Romanel A*, Goodall J*, Grist E, Ferraldeschi R, Miranda S, Prandi D, Lorente D, Frenel J-S, Pezaro C, Omlin A, Nava Rodrigues D, Flohr P, Tunariu N, de Bono JS, Demichelis F., Attard G&#. Tumor clone dynamics in lethal prostate cancer. Sci. Transl. Med. 6, 254ra125 (2014).
Prandi D., Baca S.C., Romanel A., Barbieri C.E., Mosquera J-M., Fontugne J., Beltran H., Sboner A., Garraway L.A., Rubin M.A., Demichelis F. Unraveling the clonal hierarchy of somatic genomic aberrations. Genome Biol. 2014 Aug 26;15(8):439.
Baca SC, Prandi D, Lawrence MS, Mosquera J-M, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat J-P, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F., Rubin MA, Garraway LA. Punctuated Evolution of Prostate Cancer Genomes. Cell. 2013 Apr 25;153(3):666-77.