Publications

Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2
H Schmidt, M Zhang, H Mourelatos, FJ Sanchez-Rivera, SW Lowe, Andrea Ventura, Christina S Leslie, Yuri Pritykin
bioRxiv. 2022

Rlf–Mycl Gene Fusion Drives Tumorigenesis and Metastasis in a Mouse Model of Small Cell Lung CancerRlf–Mycl Drives Tumorigenesis and Metastasis of SCLC
Metamia Ciampricotti, Triantafyllia Karakousi, Allison L Richards, Àlvaro Quintanal-Villalonga, Angeliki Karatza, Rebecca Caeser, Emily A Costa, Viola Allaj, Parvathy Manoj, Kyle B Spainhower, Faruk E Kombak, Francisco J Sanchez-Rivera, Janneke E Jaspers, Anastasia-Maria Zavitsanou, Danilo Maddalo, Andrea Ventura, William M Rideout, Elliot H Akama-Garren, Tyler Jacks, Mark TA Donoghue, Triparna Sen, Trudy G Oliver, John T Poirier, Thales Papagiannakopoulos, Charles M Rudin
Cancer discovery 11 (12), 3214-3229. 2022

B Shui, G La Rocca, A Ventura, KM Haigis
Interplay between K-RAS and miRNAs
Trends in Cancer 8 (5), 384-396. 2022

Gaspare La Rocca, Bryan King,  Bing Shui, Xiaoyi Li, Minsi Zhang, Kemal Akat, Paul Ogrodowski, Chiara Mastroleo, Kevin Chen, Vincenzo Cavalieri, Yilun Ma, Viviana Anelli,Doron Betel, Joana A. Vidigal, Thomas Tuschl, Gunter Meister, Craig B. Thompson, Tullia Lindsten, Kevin M. Haigis,  Andrea Ventura
Inducible and reversible inhibition of miRNA-mediated gene repression in vivo
Elife. 2021 Aug 31;10. doi: 10.7554/eLife.70948. [Epub ahead of print] PubMed PMID: 34463618.

Polaski, Jacob T; Udy, Dylan B; Escobar-Hoyos, Luisa F; Askan, Gokce; Leach, Steven D; Ventura, Andrea; Kannan, Ram; Bradley, Robert K
The origins and consequences of UPF1 variants in pancreatic adenosquamous carcinoma.
Elife 10, e62209, 2021

Emiliano Cocco, Ji Eun Lee, Srinivasaraghavan Kannan, Alison M. Schram, Helen H Won, Sophie Shifman, Amanda Kulick, Laura Baldino, Eneda Toska, Amaia Arruabarrena-Aristorena, Srushti Kittane, Fan Wu, Yanyan Cai, Sabrina Arena, Benedetta Mussolin, Ram Kannan, Neil Vasan, Alexander N Gorelick, Michael F. Berger,  Ofra Novoplansky,  Sankar Jagadeeshan, Yi Liao, Uwe Rix, Sandra Misale, Barry S Taylor, Alberto Bardelli, Jaclyn F Hechtman, David M Hyman, Moshe Elkabets, Elisa de Stanchina, Chandra S Verma, Andrea Ventura, Alexander Drilon and Maurizio Scaltriti
TRK xDFG mutations trigger a sensitivity switch from type I to II kinase inhibitors
Cancer Discovery, October 1, 2020. doi: 10.1158/2159-8290.CD-20-0571

Li X., Pritykin Y., Concepcion C.P., Lu Y., La Rocca G., Zhang M., King B., Cook P.J., Au Y. W., Popow O., Paulo J.A., Otis G.A., Mastroleo C., Ogrodowski P., Schreiner R., Haigis K.M., Betel D., Leslie C.S., Ventura A.
High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down
Molecular Cell, June 3, 2020 https://doi.org/10.1016/j.molcel.2020.05.009

Luisa F. Escobar-Hoyos, Alex Penson, Ram Kannan, Hana Cho, Chun-Hao Pan, Rohit K. Singh, Lisa H. Apken, G. Aaron Hobbs, Renhe Luo, Nicolas Lecomte, Sruthi Babu, Fong Cheng Pan, Direna Alonso-Curbelo, John P. Morris IV, Gokce Askan, Olivera Grbovic-Huezo, Paul Ogrodowski, Jonathan Bermeo, Joseph Saglimbeni, Cristian D. Cruz, Yu-Jui Ho, Sharon A. Lawrence, Jerry P. Melchor, Grant A. Goda, Karen Bai, Alessandro Pastore. Simon J. Hogg. Srivatsan Raghavan, Peter Bailey, David K. Chang, Andrew Biankin, Kenneth R. Shroyer, Brian M. Wolpin. Andrew J. Aguirre, Andrea Ventura, Barry Taylor, Channing J. Der, Daniel Dominguez, Daniel Kümmel, Andrea Oeckinghaus, Scott W. Lowe, Robert K. Bradley , Omar Abdel-Wahab, Steven D. Leach
Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer
Cancer Cell, June 18, 2020 DOI:https://doi.org/10.1016/j.ccell.2020.05.010

PJ Cook, A Ventura
Cancer diagnosis and immunotherapy in the age of CRISPR
Genes, Chromosomes and Cancer, 2019 58 (4), 233-243

Chen, M., Xu, E. S., Leisenring, N. H., Cardona, D. M., Luo, L., Ma, Y., Ventura, A., Kirsch, D. G.
The fusion oncogene FUS-CHOP drives sarcomagenesis of high-grade spindle cell sarcomas in mice
Sarcoma (2019) 2019: 1340261  PMC6683777

Li, X., Ventura, A.
ALK7 erects a suppressive barrier to tumor progression and metastasis
Developmental Cell (2019) 49(3): 304-305 

Bonetti P, Climent M, Panebianco F, Tordonato C, Santoro A, Marzi MJ, Pelicci PG, Ventura A, Nicassio F.
Dual role for miR-34a in the control of early progenitor proliferation and commitment in the mammary gland and in breast cancer.
Oncogene. 2018 Aug 9. doi: 10.1038/s41388-018-0445-3. [Epub ahead of print] PubMed PMID: 30093634.

Zheng J, Sadot E, Vigidal JA, Klimstra DS, Balachandran VP, Kingham TP, Allen PJ, D’Angelica MI, DeMatteo RP, Jarnagin WR, and Ventura A.
Characterization of hepatocellular adenoma and carcinoma using microRNA profiling and targeted gene sequencing.
PLoS One. 2018 Jul 27;13(7):e0200776. doi: 10.1371/journal.pone.0200776. eCollection 2018. PubMed PMID: 30052636; PubMed Central PMCID: PMC6063411.

Schaub FX, Dhankani V, Berger AC, Trivedi M, Richardson AB, Shaw R, Zhao W, Zhang X, Ventura A, Liu Y, Ayer DE, Hurlin PJ, Cherniack AD, Eisenman RN, Bernard B, Grandori C; Cancer Genome Atlas Network. (2018)
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. 
Cell Syst. 2018 Mar 28;6(3):282-300.e2. doi: 10.1016/j.cels.2018.03.003. PubMed PMID: 29596783.

Ventura, A., and Dow, L. (2018)
Modeling Cancer in the CRISPR Era.
Annual Review of Cancer Biology Vol 2. Issue 1

Cook, PJ., Rozario, T. Kannan, R., de Leon, ES., Drilon, A., Rosenblum, M.K.,  Scaltriti, M., Benezra, R., and Ventura, A. (2017).
Somatic chromosomal engineering identifies BCAN-NTRK1 as a potent glioma driver and therapeutic target.
Nat Commun. 2017;8:15987. PubMed PMID: 28695888 PMCID:PMC5508201.

Perez, A., Pritykin, Y., Vidigal, J., Chhangawala, S., Zamparo, L., Leslie, C., and Ventura, A. (2017).
GuideScan software for improved single and paired CRISPR guide RNA design.
Nature Biotechnology, 2017 Apr;35(4):347-349. PMID: 28263296. PMCID: PMC5607865

Ventura, A. (2016).
NORAD: Defender of the Genome.
Trends in Genetics 32, 390-392.

Maddalo, D., and Ventura, A. (2016).
Somatic Engineering of Oncogenic Chromosomal Rearrangements: A Perspective.
Cancer Research 76, 4918-4923.

Li, X., Wu, R., and Ventura, A. (2016).
The present and future of genome editing in cancer research.
Human Genetics 135, 1083-1092.

Andolina, D., Di Segni, M., Bisicchia, E., D’Alessandro, F., Cestari, V., Ventura, A., Concepcion, C., Puglisi-Allegra, S., and Ventura, R. (2016).
Effects of lack of microRNA-34 on the neural circuitry underlying the stress response and anxiety.
Neuropharmacology 107, 305-316.

Vidigal, J.A., and Ventura, A. (2015a).
Rapid and efficient one-step generation of paired gRNA CRISPR-Cas9 libraries.
Nature communications 2015Aug 17;6:8083. doi: 10.1038/ncomms9083. PubMed PMID: 26278926.

Vidigal, J.A., and Ventura, A. (2015b).
The biological functions of miRNAs: lessons from in vivo studies.
Trends in cell biology 25, 137-147.

Tricarico, R., Cortellino, S., Riccio, A., Jagmohan-Changur, S., Van der Klift, H., Wijnen, J., Turner, D., Ventura, A., Rovella, V., and Percesepe, A. (2015).
Involvement of MBD4 inactivation in mismatch repair-deficient tumorigenesis.
Oncotarget 6, 42892.

La Rocca, G., Olejniczak, S.H., González, A.J., Briskin, D., Vidigal, J.A., Spraggon, L., DeMatteo, R.G., Radler, M.R., Lindsten, T., and Ventura, A. (2015).
In vivo, Argonaute-bound microRNAs exist predominantly in a reservoir of low molecular weight complexes not associated with mRNA.
Proceedings of the National Academy of Sciences 112, 767-772.

Kannan, R., and Ventura, A. (2015).
The CRISPR revolution and its impact on cancer research.
Swiss Med Weekly 145, 14230w.

Han, Y.-C., Vidigal, J.A., Mu, P., Yao, E., Singh, I., González, A.J., Concepcion, C.P., Bonetti, C., Ogrodowski, P., and Carver, B. (2015).
An allelic series of miR-17 [sim] 92-mutant mice uncovers functional specialization and cooperation among members of a microRNA polycistron.
Nature genetics 47, 766-775.

Fiori, E., Babicola, L., Andolina, D., Coassin, A., Pascucci, T., Patella, L., Han, Y.-C., Ventura, A., and Ventura, R. (2015).
Neurobehavioral alterations in a genetic murine model of Feingold Syndrome 2.
Behavior genetics 45, 547-559.

Zindy, F., Kawauchi, D., Lee, Y., Ayrault, O., Merzoug, L.B., McKinnon, P.J., Ventura, A., and Roussel, M.F. (2014).
Role of the miR-17∼ 92 cluster family in cerebellar and medulloblastoma development.
Biology open 3, 597-605.

Maddalo, D., Manchado, E., Concepcion, C.P., Bonetti, C., Vidigal, J.A., Han, Y.-C., Ogrodowski, P., Crippa, A., Rekhtman, N., and de Stanchina, E. (2014).
In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system.
Nature 516, 423-427.

Han, Y.-C., and Ventura, A. (2013).
Control of TFH differentiation by a microRNA cluster.
Nature immunology 14, 770-771.

Vidigal, J.A., and Ventura, A. (2012).
Embryonic stem cell miRNAs and their roles in development and disease.
Seminars in cancer biology (Academic Press).

Concepcion, C.P., Han, Y.-C., Mu, P., Bonetti, C., Yao, E., D’andrea, A., Vidigal, J.A., Maughan, W.P., Ogrodowski, P., and Ventura, A. (2012a).
Intact p53-dependent responses in miR-34–deficient mice.
PLoS Genet 8, e1002797.

Concepcion, C.P., Bonetti, C., and Ventura, A. (2012b).
The miR-17-92 family of microRNA clusters in development and disease.
Cancer journal (Sudbury, Mass) 18, 262.

Yao, E., and Ventura, A. (2011).
A new role for miR-182 in DNA repair.
Molecular Cell 41, 135-137.

Yang, J.-S., Phillips, M.D., Betel, D., Mu, P., Ventura, A., Siepel, A.C., Chen, K.C., and Lai, E.C. (2011).
Widespread regulatory activity of vertebrate microRNA* species.
Rna 17, 312-326.

Sage, J., and Ventura, A. (2011).
miR than meets the eye.
Genes & development 25, 1663-1667.

Lal, A., Thomas, M.P., Altschuler, G., Navarro, F., O’Day, E., Li, X.L., Concepcion, C., Han, Y.-C., Thiery, J., and Rajani, D.K. (2011).
Capture of microRNA–bound mRNAs identifies the tumor suppressor miR-34a as a regulator of growth factor signaling.
PLoS genetics 7, e1002363.

de Pontual, L., Yao, E., Callier, P., Faivre, L., Drouin, V., Cariou, S., Van Haeringen, A., Geneviève, D., Goldenberg, A., and Oufadem, M. (2011).
Germline deletion of the miR-17 [sim] 92 cluster causes skeletal and growth defects in humans.
Nature genetics 43, 1026-1030.

Agostini, M., Tucci, P., Steinert, J.R., Shalom-Feuerstein, R., Rouleau, M., Aberdam, D., Forsythe, I.D., Young, K.W., Ventura, A., and Concepcion, C.P. (2011).
microRNA-34a regulates neurite outgrowth, spinal morphology, and function.
Proceedings of the National Academy of Sciences 108, 21099-21104.

Ventura, A., and Jacks, T. (2009).
MicroRNAs and cancer: short RNAs go a long way.
Cell 136, 586-591.

Mu, P., Han, Y.-C., Betel, D., Yao, E., Squatrito, M., Ogrodowski, P., de Stanchina, E., D’Andrea, A., Sander, C., and Ventura, A. (2009).
Genetic dissection of the miR-17∼ 92 cluster of microRNAs in Myc-induced B-cell lymphomas.
Genes & development 23, 2806-2811.

Ventura, A., Young, A.G., Winslow, M.M., Lintault, L., Meissner, A., Erkeland, S.J., Newman, J., Bronson, R.T., Crowley, D., and Stone, J.R. (2008).
Targeted deletion reveals essential and overlapping functions of the miR-17∼ 92 family of miRNA clusters.
Cell 132, 875-886.

Ventura, A., Kirsch, D.G., McLaughlin, M.E., Tuveson, D.A., Grimm, J., Lintault, L., Newman, J., Reczek, E.E., Weissleder, R., and Jacks, T. (2007).
Restoration of p53 function leads to tumour regression in vivo.
Nature 445, 661-665.

Ventura, A., Meissner, A., Dillon, C.P., McManus, M., Sharp, P.A., Van Parijs, L., Jaenisch, R., and Jacks, T. (2004).
Cre-lox-regulated conditional RNA interference from transgenes.
Proceedings of the National Academy of Sciences of the United States of America 101, 10380-10385.