Synthetic Lethal Phenotype Identification through Cancer Evolution Analysis

Project Information

SPICE

Grant agreement ID: 648670

DOI 10.3030/648670

Project closed

EC signature date 3 July 2015

Start date 1 October 2015

End date 31 March 2021

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 996 428,00

EU contribution € 1 996 428,00

Coordinated by

UNIVERSITA DEGLI STUDI DI TRENTO
Italy

Publications

Peer reviewed articles (17)

Mutation–selection balance and compensatory mechanisms in tumour evolution

Author(s): Erez Persi, Yuri I. Wolf, David Horn, Eytan Ruppin, Francesca Demichelis, Robert A. Gatenby, Robert J. Gillies, Eugene V. Koonin
Published in: Nature Reviews Genetics, Issue 22/4, 2021, Page(s) 251-262, ISSN 1471-0056
Publisher: Nature Publishing Group
DOI: 10.1038/s41576-020-00299-4

Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity

Author(s): Joanna Cyrta, Anke Augspach, Maria Rosaria De Filippo, Davide Prandi, Phillip Thienger, Matteo Benelli, Victoria Cooley, Rohan Bareja, David Wilkes, Sung-Suk Chae, Paola Cavaliere, Noah Dephoure, Anne-Christine Uldry, Sophie Braga Lagache, Luca Roma, Sandra Cohen, Muriel Jaquet, Laura P. Brandt, Mohammed Alshalalfa, Loredana Puca, Andrea Sboner, Felix Feng, Shangqian Wang, Himisha Beltran, Tamara
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19328-1

Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer

Author(s): Himisha Beltran, Alessandro Romanel, Vincenza Conteduca, Nicola Casiraghi, Michael Sigouros, Gian Marco Franceschini, Francesco Orlando, Tarcisio Fedrizzi, Sheng-Yu Ku, Emma Dann, Alicia Alonso, Juan Miguel Mosquera, Andrea Sboner, Jenny Xiang, Olivier Elemento, David M. Nanus, Scott T. Tagawa, Matteo Benelli, Francesca Demichelis
Published in: Journal of Clinical Investigation, Issue 130/4, 2020, Page(s) 1653-1668, ISSN 0021-9738
Publisher: American Society for Clinical Investigation
DOI: 10.1172/jci131041

Genomic correlates of clinical outcome in advanced prostate cancer

Author(s): Wassim Abida, Joanna Cyrta, Glenn Heller, Davide Prandi, Joshua Armenia, Ilsa Coleman, Marcin Cieslik, Matteo Benelli, Dan Robinson, Eliezer M. Van Allen, Andrea Sboner, Tarcisio Fedrizzi, Juan Miguel Mosquera, Brian D. Robinson, Navonil De Sarkar, Lakshmi P. Kunju, Scott Tomlins, Yi Mi Wu, Daniel Nava Rodrigues, Massimo Loda, Anuradha Gopalan, Victor E. Reuter, Colin C. Pritchard, Joaquin Mateo,
Published in: Proceedings of the National Academy of Sciences, Issue 116/23, 2019, Page(s) 11428-11436, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1902651116

N-Myc Induces an EZH2-Mediated Transcriptional Program Driving Neuroendocrine Prostate Cancer

Author(s): Etienne Dardenne, Himisha Beltran, Matteo Benelli, Kaitlyn Gayvert, Adeline Berger, Loredana Puca, Joanna Cyrta, Andrea Sboner, Zohal Noorzad, Theresa MacDonald, Cynthia Cheung, Ka Shing Yuen, Dong Gao, Yu Chen, Martin Eilers, Juan-Miguel Mosquera, Brian D. Robinson, Olivier Elemento, Mark A. Rubin, Francesca Demichelis, David S. Rickman
Published in: Cancer Cell, Issue 30/4, 2016, Page(s) 563-577, ISSN 1535-6108
Publisher: Cell Press
DOI: 10.1016/j.ccell.2016.09.005

Tumor purity quantification by clonal DNA methylation signatures

Author(s): Matteo Benelli, Dario Romagnoli, Francesca Demichelis
Published in: Bioinformatics, 2018, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty011

Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine

Author(s): Chantal Pauli, Benjamin D. Hopkins, Davide Prandi, Reid Shaw, Tarcisio Fedrizzi, Andrea Sboner, Verena Sailer, Michael Augello, Loredana Puca, Rachele Rosati, Terra J. McNary, Yelena Churakova, Cynthia Cheung, Joanna Triscott, David Pisapia, Rema Rao, Juan Miguel Mosquera, Brian Robinson, Bishoy M. Faltas, Brooke E. Emerling, Vijayakrishna K. Gadi, Brady Bernard, Olivier Elemento, Himisha Beltran,
Published in: Cancer Discovery, Issue 7/5, 2017, Page(s) 462-477, ISSN 2159-8274
Publisher: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.CD-16-1154

EthSEQ: ethnicity annotation from whole exome sequencing data

Author(s): Alessandro Romanel, Tuo Zhang, Olivier Elemento, Francesca Demichelis
Published in: Bioinformatics, Issue 33/15, 2017, Page(s) 2402-2404, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btx165

Next-Generation Rapid Autopsies Enable Tumor Evolution Tracking and Generation of Preclinical Models

Author(s): David J. Pisapia, Steven Salvatore, Chantal Pauli, Erika Hissong, Ken Eng, Davide Prandi, Verena-Wilbeth Sailer, Brian D. Robinson, Kyung Park, Joanna Cyrta, Scott T. Tagawa, Myriam Kossai, Jacqueline Fontugne, Robert Kim, Alexandros Sigaras, Rema Rao, Danielle Pancirer, Bishoy Faltas, Rohan Bareja, Ana M. Molina, David M. Nanus, Prajwal Rajappa, Mark M. Souweidane, Jeffrey Greenfield, Anne-Katrin
Published in: JCO Precision Oncology, Issue 1, 2017, Page(s) 1-13, ISSN 2473-4284
Publisher: American Society of Clinical Oncology
DOI: 10.1200/PO.16.00038

The long tail of oncogenic drivers in prostate cancer

Author(s): Joshua Armenia, Stephanie A. M. Wankowicz, David Liu, Jianjiong Gao, Ritika Kundra, Ed Reznik, Walid K. Chatila, Debyani Chakravarty, G. Celine Han, Ilsa Coleman, Bruce Montgomery, Colin Pritchard, Colm Morrissey, Christopher E. Barbieri, Himisha Beltran, Andrea Sboner, Zafeiris Zafeiriou, Susana Miranda, Craig M. Bielski, Alexander V. Penson, Charlotte Tolonen, Franklin W. Huang, Dan Robinson, Yi
Published in: Nature Genetics, Issue 50/5, 2018, Page(s) 645-651, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-018-0078-z

A highly specific SpCas9 variant is identified by in vivo screening in yeast

Author(s): Antonio Casini, Michele Olivieri, Gianluca Petris, Claudia Montagna, Giordano Reginato, Giulia Maule, Francesca Lorenzin, Davide Prandi, Alessandro Romanel, Francesca Demichelis, Alberto Inga, Anna Cereseto
Published in: Nature Biotechnology, Issue 36/3, 2018, Page(s) 265-271, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/nbt.4066

SOX2 promotes lineage plasticity and antiandrogen resistance in TP53 - and RB1 -deficient prostate cancer

Author(s): Ping Mu, Zeda Zhang, Matteo Benelli, Wouter R. Karthaus, Elizabeth Hoover, Chi-Chao Chen, John Wongvipat, Sheng-Yu Ku, Dong Gao, Zhen Cao, Neel Shah, Elizabeth J. Adams, Wassim Abida, Philip A. Watson, Davide Prandi, Chun-Hao Huang, Elisa de Stanchina, Scott W. Lowe, Leigh Ellis, Himisha Beltran, Mark A. Rubin, David W. Goodrich, Francesca Demichelis, Charles L. Sawyers
Published in: Science, Issue 355/6320, 2017, Page(s) 84-88, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aah4307

Hit and go CAS9 delivered through a lentiviral based self-limiting circuit

Author(s): Gianluca Petris, Antonio Casini, Claudia Montagna, Francesca Lorenzin, Davide Prandi, Alessandro Romanel, Jacopo Zasso, Luciano Conti, Francesca Demichelis, Anna Cereseto
Published in: Nature Communications, Issue 8, 2017, Page(s) 15334, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms15334

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer

Author(s): Himisha Beltran, Davide Prandi, Juan Miguel Mosquera, Matteo Benelli, Loredana Puca, Joanna Cyrta, Clarisse Marotz, Eugenia Giannopoulou, Balabhadrapatruni V S K Chakravarthi, Sooryanarayana Varambally, Scott A Tomlins, David M Nanus, Scott T Tagawa, Eliezer M Van Allen, Olivier Elemento, Andrea Sboner, Levi A Garraway, Mark A Rubin, Francesca Demichelis
Published in: Nature Medicine, Issue 22/3, 2016, Page(s) 298-305, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/nm.4045

Clonal evolution of chemotherapy-resistant urothelial carcinoma

Author(s): Bishoy M Faltas, Davide Prandi, Scott T Tagawa, Ana M Molina, David M Nanus, Cora Sternberg, Jonathan Rosenberg, Juan Miguel Mosquera, Brian Robinson, Olivier Elemento, Andrea Sboner, Himisha Beltran, Francesca Demichelis, Mark A Rubin
Published in: Nature Genetics, Issue 48/12, 2016, Page(s) 1490-1499, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/ng.3692

TPES: tumor purity estimation from SNVs

Author(s): Alessio Locallo, Davide Prandi, Tarcisio Fedrizzi, Francesca Demichelis
Published in: Bioinformatics, Issue 35/21, 2019, Page(s) 4433-4435, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz406

Ploidy‐ and Purity‐Adjusted Allele‐Specific DNA Analysis Using CLONETv2

Author(s): Davide Prandi, Francesca Demichelis
Published in: Current Protocols in Bioinformatics, Issue 67/1, 2019, ISSN 1934-3396
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/cpbi.81