PUBLICATIONS
ORIGINAL RESEARCH ARTICLES
Click the title of the article to access the PDF
GENOME BIOLOGY
(2024)
Jubran J. *, Slutsky R. *, Rozenblum N., Rokach L., Ben-David U., # and Yeger-Lotem E. #. Machine-learning analysis reveals an important contribution for negative selection in shaping cancer aneuploidy landscapes. https://doi.org/10.1186/s13059-024-03225-7 (* Equally-contributing first authors; # Equally-contributing last authors)
MOLECULAR CANCER
(2023)
Sacconi A, Muti P, Pulito C, Urbani G, Allegretti M, Pellini R, Mehterov N, Ben-David U, Strano S, Bossi P, Blandino G. Immunosignatures associated with TP53 status and co-mutations classify prognostically head and neck cancer patients. doi: 10.1186/s12943-023-01905-9
GENOME BIOLOGY
(2023)
Alonso de la Vega A, Temiz NA, Tasakis R, Somogyi K, Salgueiro L, Zimmer E, Ramos M, Diaz-Jimenez A, Chocarro S, Fernández-Vaquero M, Stefanovska B, Reuveni E, Ben-David U, Stenzinger A, Poth T, Heikenwälder M, Papavasiliou N, Harris RS, Sotillo R. Acute expression of human APOBEC3B in mice results in RNA editing and lethality. doi: 10.1186/s13059-023-03115-4
CANCER DISCOVERY
(2023)
Stossel C, Raitses-Gurevich M, Atias D, Beller T, Glick Gorman Y, Halperin S, Peer E, Denroche RE, Zhang A, Notta F, Wilson JM, O'Kane GM, Haimov Talmoud E, Amison N, Schvimer M, Salpeter SJ, Bar V, Zundelevich A, Tirosh I, Tal R, Dinstag G, Kinar Y, Eliezer Y, Ben-David U, Gavert NS, Straussman R, Gallinger SJ, Berger R, Golan T. Spectrum of Response to Platinum and PARP Inhibitors in Germline BRCA-Associated Pancreatic Cancer in the Clinical and Preclinical Setting. doi: 10.1158/2159-8290.CD-22-0412
NPJ PRECISION ONCOLOGY
(2023)
Chang T., Cao Y.*, Shulman E.D., Ben-David U., Schaffer A.A., and Ruppin E. Optimizing cancer immunotherapy response prediction by tumor aneuploidy score and fraction of copy number alterations. doi: 10.1038/s41698-023-00408-6
NATURE COMMUNICATIONS
(2023)
De Feudis G.*, Garriba L.*, Martis V., Galli M., Dumont M., Eliezer Y., Wardenaar R., Ippolito M., Iyer D.R., Tijhuis A.E., Spierings D.C.J., Schubert M., Rind N., Foijer F., Ben-David U., Fachinetti D., Doksani Y., and Santaguida S. Short-term molecular consequences of chromosome mis-segregation for genome stability. doi: 10.1038/s43018-023-00513-2
NATURE CANCER
(2023)
Altea-Manzano P., Doglioni G., Liu Y., Cuadros A.M., Nolan E., Fernandez-Garcia J., Wu Q., Montagne A., Planque M., Laue K.J., Cidre-Aranaz F., Liu X., Marin-Bejar O., Van Elsen J., Vermeire I., Broekaert D., Demeyer S., Spotbeen X., Alkan H.F., Demicco M., Rabas N., Riera-Domingo C., Richard F., Geukens T., Maxim De Schepper14, Sophia Leduc5, Sigrid Hatse5, Yentl Lambrechts5, Emily Jane Kay15, Sergio Lilla15, Alekseenko A., Geldhof V., Boeckx B.,, de la Calle Arregui C., Floris G., Swinnen J., Marine J.C., Lambrechts D., Pelechano V., Mazzone M., Zanivan S., Cools J., Wildiers H., Baud V., Grünewald T.G.P., Ben-David U., Desmedt C., Malanchi I., Fendt S.-M. A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation resulting in preo-metastatic NF-κB signaling. doi: 10.1038/s43018-023-00513-2
ESMO OPEN
(2022)
Waissengrin B., Zahavi T., Samon-Divon M., Tenne T., Goldberg A., Wolf I., Rubinek T., Winkler T., Farkash O., Grinshpun A., Zubkov A., Khatib M., Shachar S.S., Keren N., Carmy-Levy I., Ben-David U., and Sonnenblick A. The effect of non-oncology drugs on clinical and genomic risk in early luminal breast cancer. doi: 10.1016/j.esmoop.2022.100648
NATURE BIOTECHNOLOGY
(2022)
Nahmad A.D.*, Reuveni E.*, Goldschmidt E.*, Tenne T., Liberman M., Horovitz-Fried M., Khosravi R., Kobo H., Reinstein E., Madi. A.#, Ben-David U.#, and Barzel A.# Frequent aneuploidy in primary human T cells following CRISPR-Cas9 cleavage. doi.org/10.1038/s41587-022-01377-0 (* Equally contributing first authors; # Equally contributing last authors)
CANCER RESEARCH
(2022)
Prasad K., Bloomfield M., Levi H., Keuper K., Bernhard S.V., Baudoin N.C., Leor G., Eliezer Y., Giam M., Wong C.K., Rancati G., Storchova Z., Cimini D., and Ben-David U. Whole-genome duplication shapes the aneuploidy landscape of human cancers. Cancer Res (2022). doi.org/10.1158/0008-5472.CAN-21-2065
DEVELOPMENTAL CELL
(2021)
Ippolito M., Martis V., Hong C., Wardenaar R., Zerbib J., Spierings D.C.J., Ben-David U., Foijer F., and Santaguida S. Gene copy-number changes and chromosomal instability induced by aneuploidy confer resistance to chemotherapy. Dev Cell, 2021, doi: 10.1016/j.devcel.2021.07.006.
CELL DEATH & DISEASE
(2021)
Vaz S., Ferreira F.J., Macedo J.C., Leor G., Ben-David U., Bessa J., and Logarinho E. BMF repression by FoxM1 inhibits anoikis during mitosis and is a biomarker for antimitotic chemotherapy response. Cell Death & Disease (2021). doi: 10.1038/s41419-021-03822-5.
EMBO REPORTS
(2021)
Wang R.W., Vigano S., Ben-David U., Amon A., and Santaguida S. Aneuploid senescent cells activate NF-κB to promote their immune clearance by NK cells. EMBO Rep (2021). doi: 10.15252/embr.202052032.
NPJ PRECISION ONCOLOGY
(2022)
Hoge A.C.H.*, Getz M.*, Zimmerr A., Ko M., Raz L., Beroukhim R., Golub T.R., Ha G.# and Ben-David U.# DNA-based copy number analysis confirms genomic evolution of PDX models. doi.org/10.1038/s41698-022-00268-6 (* Equally contributing first authors; # Equally contributing last authors)
PNAS
(2020)
Repolgle J., Zhou W., Amaro A., McFarland J., Villalobos-Oritz M., Ryan J., Letai, A., Yilmaz O., Sheltzer J., Lippard S., Ben-David U., and Amon A. Aneuploidy increases resistance to chemotherapeutics by antagonizing cell division. Proc Natl Acad Sci U S A (2020). doi.org/10.1073/pnas.2009506117.). doi: 10.15252/embr.202052032.
INTERNATIONAL JOURNAL OF CANCER
(2020)
Winkler T. and Ben-David U. Elevated ACE2 expression levels in tumor-adjacent normal tissues of cancer patients. Int J Cancer (2020). doi: 10.1002/ijc.33145.
NATURE GENETICS
(2020)
Enache O.M.*, Rendo V.*, Abdusamad M., Lam D., Davison D., Pal S., Currimjee N., Hess J., Sanson K., Pantel S., Nag A., Thorner A., Root D., Doench J.G., Vazquez F., Beroukhim R., Golub T.R., and Ben-David U. Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nature Genetics (2020). doi: 10.1038/s41588-020-0623-4. (* Equally contributing first authors)
NATURE CANCER
(2020)
Corsello S.M., Nagari R.T., Spangler R.D., Rossen J., Kocak M., Bryan J.G., Humeidi R., Peck D., Wu X., Tang A.A., Wang V.M., Bender S.A., Lemire E., Narayan R., Montgomery P., Ben-David U., Chen Y., Rees M.G., Lyons N.J., McFarland J.M., Wong B.T., Wang L., Dumont N., O'Hearn P.J., Stefan E., Doench J.G., Greulich H., Meyerson M., Vazquez F., Subramanian A., Roth J.A., Bittker J.A., Boehm J.S., Mader C.C., Tsherniak A., and Golub T.R. Discovering the anticancer potential of non-oncology drugs by systematic viability profiling. Nature Cancer (2020). doi: 10.1038/s43018-019-0018-6.
NATURE
(2018)
Ben-David U., Siranosian B., Ha G., Tang H., Oren Y., Hinohara K., Strathdeec.A., Dempster J., Lyons N.J., Burns R., Nag A., Kugener G., Cimini B., Tsvetkov P., Maruvka Y.E., O’Rourke R., Garrity A., Tubelli A.A., Bandopadhayay P., Tsherniak A., Vazquez F., Wong B., Birger C., Ghandi M, Thorner A.R., Bittker J.A., Meyerson M., Getz G., Beroukhim R. and Golub T.R. Genetic and transcriptional evolution alters cancer cell line drug response. Nature, 2018. 560(7718):325-330. doi: 10.1038/s41586-018-0409-3.
CELL DEATH & DISEASE
(2018)
Abdeen S.A., Ben-David U., Maly B. and Aqueilan R. Somatic loss of WWOX drives triple-negative breast cancer through perturbation of TP53. Cell Death Dis, 2018, 9(8):832. doi: 10.1038/s41419-018-0896-z.
NATURE GENETICS
(2017)
Ben-David U., Ha G., Tseng Y.Y., Greenwald N.F., Oh C., Shih J., McFarland J.M., Wong B., Boehm J.S., Beroukhim R. and Golub T.R. Patient-derived xenografts undergo mouse-specific tumor evolution. Nature Genetics, 2017, 49(11):1567-1575. doi:10.1038/ng.3967.
CLINICAL CANCER RESEARCH
(2016)
Bi W.L., Horowtiz P., Greenwald N., Abedalthagafi M., Agarwalla P.K., Gibson W.J., Mei Y, Schumacher S.E., Ben-David U., Chevalier A., Carter S.L., Tiao G., Brastianos P.K., Ligon A.H., Ducar M., MacConaill L.E., Laws E.R., Santagata S., Beroukhim R., Dunn IF. Landscape of genomic alterations in pituitary adenomas. Clinical Cancer Research, 2016, 23(7):1841-1851. doi: 10.1158/1078-0432.CCR-16-0790.
CANCER DISCOVERY
(2016)
Aguirre A., Meyers R., Weir B., Vazquez F., Zhang C.Z., Ben-David U., Cook A., Ha G., Harrington W., Doshi M., Gill S., Xu H., Ali L., Jiang G., Pantel S., Lee Y., Goodale A., Cherniack A., Oh C., Kryukov G., Cowley G., Garraway L., Stegmaier K., Roberts C., Golub T.R., Meyerson M., Root D., Tsherniak A., and Hahn W. Genomic copy number dictates a gene-independent cell response to CRISPR-Cas9 targeting. Cancer Discovery, 2016, 6(8):914-29. doi: 10.1158/2159-8290.CD-16-0154.
NATURE COMMUNICATIONS
(2016)
Ben-David U., Ha G., Khadka P., Jin X., Wong B., Franke L. and Golub T.R. The landscape of chromosomal aberrations in breast cancer mouse models reveals driver-specific routes to tumorigenesis. Nature Communications, 2016, 7:12160. doi:10.1038/ncomms12160.
CELL STEM CELL
(2016)
Lamm N., Ben-David U., Kerem B. and Benvenisty N. Genomic instability in human pluripotent stem cells arises from replicative stress and chromosome condensation defects. Cell Stem Cell, 2016, 18(2): 253-61.
STEM CELLS
(2015)
Ben-David U., Cowell Ian G., Austin Caroline C. and Benvenisty N. Controlling the survival of human pluripotent stem cells by small molecule-based targeting of topoisomerase II alpha. Stem Cells, 2015, 33(3): 1013-9. doi: 10.1002/stem.1888.
CELL STEM CELL
(2014)
Weissbein U., Ben-David U. and Benvenisty N. Virtual karyotyping revelas greater chromosomal stability in neural cells derived by transdifferentiation than those from stem cells. Cell Stem Cell, 2014, 15(6):687-91. doi: 10.1016/j.stem.2014.10.018.
NATURE COMMUNICATIONS
(2014)
Ben-David U., Arad G., Weissbein U., Mandefro B., Maimon A., Narwani K., Clark A.T., Andrews P.W., Benvenisty N., and Biancotti J.C. Aneuploidy induces profound changes in gene expression, proliferation and tumorigenicity of human pluripotent stem cells. Nature Communications, 2014, 5:4825, doi: 10.1038/ncomms5825.
JOURNAL OF MOLECULAR CELL BIOLOGY
(2014)
Ben-David U.*, Biran A. *, Scaffidi P., Boehringer M., Meshorer E. and Benvenisty N. Elimination of undifferentiated cancer cells by pluripotent stem cell inhibitors. Journal of Molecular Cell Biology, 2014, 6(3):267-9. doi: 10.1093/jmcb/mju012. (* Equally contributing first authors)
NATURE PROTOCOLS
(2014)
Ben-David U. and Benvenisty N. Chemical ablation of tumor-initiating human pluripotent stem cells. Nature Protocols, 2014, 9(3):729-40. doi: 10.1038/nprot.2014.050.
NATURE COMMUNICATIONS
(2013)
Ben-David U., Nudel N. and Benvenisty N. Immunologic and chemical targeting of the tight-junction protein Claudin-6 eliminates tumorigenic human pluripotent stem cells. Nature Communications, 2013, 4:1992. doi:10.1038/ncomms2992.
CELL STEM CELL
(2013)
Ben-David U., Gan Q.F., Golan-Lev T., Arora P., Yanuka O., Oren Y.S., Leikin-Frenkel A., Graf M., Garippa R., Boehringer M., Gromo G. and Benvenisty N. Selective elimination of human pluripotent stem cells by an oleate synthesis inhibitor discovered in a high-throughput screen. Cell Stem Cell, 2013, 12(2):167-79. doi: 10.1016/j.stem.2012.11.015.
NATURE COMMUNICATIONS
(2013)
Lee P., Martin N.T., Nakamura K., Azghadi S., Amiri M., Ben-David U., Perlman S., Gatti R.A., Hu H. and Lowry W.E. SMRT compounds abrogate cellular phenotypes of Ataxia Telangiectasia in neural derivatives of patient specific hiPSCs. Nature Communications, 2013, 4:1824. doi:10.1038/ncomms2824.
NATURE PROTOCOLS
(2013)
Ben-David U., Mayshar Y. and Benvenisty N. Virtual karyotyping of pluripotent stem cellson the basis of their global gene expression profiles. Nature Protocols, 2013, 8(5): 989-97. doi: 10.1038/nprot.2013.051.
STEM CELLS
(2012)
Ben-David U. and Benvenisty N. High prevalence of evolutionarily conserved and species-specific genomic aberrations in mouse pluripotent stem cells. Stem Cells, 2012, 30(4):612-22.doi: 10.1002/stem.1057.
CELL STEM CELL
(2011)
Ben-David U., Mayshar Y. and Benvenisty N. Large-scale analysis reveals acquisition of lineage-specific chromosomal aberrations in human adult stem cells. Cell Stem Cell, 2011, 9(2):97-102.doi: 10.1016/j.stem.2011.06.013.
CELL STEM CELL
(2010)
Mayshar Y.*, Ben-David U.*, Lavon N., Biancotti J.C., Yakir B., Clark A.T., Plath K., Lowry W.E. and Benvenisty N. Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell, 2010, 7(4):521-31. doi: 10.1016/j.stem.2010.07.017. (* Equally contributing first authors)
REVIEWS, PERSPECTIVES & COMMENTARIES
Click the title of the article to access the PDF
NATURE
(2022)
Eliezer Y. and Ben-David U. Double genome causes double trouble. Nature, 2022, 10.1038/d41586-022-00849-2
MOLECULAR & CELLULAR ONCOLOGY
(2021)
Cohen-Sharir Y. and Ben-David U. Relevance of aneuploidy for cancer therapies targeting the spindle assembly checkpoint and KIF18A. Mol Cell Oncol, 2021, doi: 10.1080/23723556.2020.1789419.
MOLECULAR & CELLULAR ONCOLOGY
(2020)
Rendo V., Enache O. and Ben-David U. Adding to the CASeload: Unwarranted p53 signaling induced by Cas9. Mol Cell Oncol, 2020, doi: 10.1080/23723556.2020.1789419.
NATURE REVIEWS GENETICS
(2020)
Ben-David U. and Amon A. Context is everything: Aneuploidy in cancer. Nature Reviews Cancer, 2020. doi: 10.1038/s41576-019-0171-x.
NATURE REVIEWS CANCER
(2019)
Ben-David U., Beroukhim R. and Golub T.R. Genomic evolution of cancer models: perils and opportunities. Nature Reviews Cancer, 2019. 19(2):97-109.doi: 10.1038/s41568-018-0095-3.
TRANSPLANTATION
(2018)
Odorico. J., Adams A., Melton D., Greenstein G., Hwa A., Nostro C., Rezania A., Oberholzer J., Pipeleers D., Yang L., Cowan C., Huangfu D., Egli D., Ben-David U., Vallier L., Grey S., Tang Q., Roep B., Ricordi C., Naji A., Orlando G., Anderson D., Poznansky M., Ludwig B., Tomei A., Greiner D., Graham M., Carpenter M., Migliaccio G., D’Amour K., Hering B., Piemonti L., Berney T., Rickels M., Kay T. and Markmann J. Report of the Key Opinion Leaders Meeting on Stem Cell-Derived Beta Cells. Transplantation, 2018, 102(8):1223-1229. doi: 10.1097/TP.0000000000002217.
STEM CELL REPORTS
(2017)
Andrews P.W., Ben-David U., Benvenisty N., Coffey P., Eggan K., Knowles B.B., Nagy A., Pera M., Reubinoff B., Rugg-Gunn P.J., Stacey G.N. Assessing the safety of human pluripotent stem cells (PSCs) and their derivatives for clinical applications. Stem Cell Reports, 2017, 9(1):1-4. doi: 10.1016/j.stemcr.2017.05.029.
STEM CELLS TRANSLATIONAL MEDICINE
(2015)
Heslop A.J., Hammond T.G., Santeramo I., Piella A.T., Hopp I., Zhou J., Baty R., Graziano, E.I., Bernabe P., Shaw D.A., Bunn I., Caron A., Skold P., Andrews P.W., Baxter M., Hay D., Hamdam J., Sethu S., Sharpe M.E., Patel S., Jones D.R., Reinhardt J., Danen E.H.J., Ben-David U., Stacey G., Bjorquist P., Rowe, C., Pellegrini G., Antoine D., Cross M.J., Murray P., Williams D., Kitteringham N.R., Park B.K. and Goldring C.E.P. Understanding the risks of stem cell-based therapeutics. Stem Cells Translational Medicine, 2015, 4(4):389-400. doi: 10.5966/sctm.2014-0110.
BIOCHIMICA ET BIOPHYSICA ACTA
(2015)
Ben-David U. Genomic instability, driver genes and cell selection: Projections from cancer to stem cells. Biochim Biophys Acta, 2014,1849(4):427-35. doi: 10.1016/j.bbagrm.2014.08.005.
JOURNAL OF CELL BIOLOGY
(2014)
Rendo V., Enache O. and Ben-David U. Adding to the CASeload: Unwarranted p53 signaling induced by Cas9. Mol Cell Oncol, 2020, doi: 10.1080/23723556.2020.1789419.
MOLECULAR AND CELLULAR THERAPIES
(2013)
Ben-David U. Flowing through the CRISPR-CAScade: Will genome editing boost cell therapies? Molecular and Cellular Therapies, 2013, 1:3, doi:10.1186/2052-8426-1-3.
CELL
(2013)
Ben-David U., Nissenbaum J. and Benvenisty N. New balance in pluripotency: reprogrammingwith lineage specifiers. Cell, 2013, 153(5): 939-40. doi: 10.1016/j.cell.2013.04.051.
CELL STEM CELL
(2012)
Ben-David U., Kopper O. and Benvenisty N. Expanding the boundaries of embryonic stem cells. Cell Stem Cell, 2012, 10(6):666-77.doi: 10.1016/j.stem.2012.05.003.
CELL STEM CELL
(2012)
Ben-David U., Mayshar Y. and Benvenisty N. Significant acquisition of chromosomal aberrations in human adult mesenchymal stem cells: Response to Sensenbé et al. Cell Stem Cell, 2012, 10(1):10-11. doi: 10.1016/j.stem.2011.12.007.
STEMBOOK
(2012)
Ben-David U. and Benvenisty N. Analyzing the genomic integrity of stem cells. StemBook, 2012. doi: 10.3824/stembook.1.50.1, http://www.stembook.org.
CELL STEM CELL
(2011)
Goldring C.E.P., Duffy P.A., Benvenisty N., Andrews P.W., Ben-David U., Eakins R., French N., Hanley N.A., Kelly L., Kitteringham N.R., Kurth J., Ladenheim D., Laverty H., McBlane J., Narayanan G., Patel S., Reinhardt J, Rossi A., Sharpe M. and Park K. Assessing the safety of stem cell therapeutics. Cell Stem Cell, 2011, 8(6):618-28. doi: 10.1016/j.stem.2011.05.012.
NATURE REVIEWS CANCER
(2011)
Ben-David U. and Benvenisty N. The tumorigenicity of human embryonic and induced pluripotent stem cells. Nature Reviews Cancer, 2011, 11(4): 268-77.doi: 10.1038/nrc3034.
CELL CYCLE
(2010)
Ben-David U., Benvenisty N. and Mayshar Y. Genetic instability in human induced pluripotent stem cells: Classification of causes and possible safeguards. 10.4161/cc.9.23.14094. Cell Cycle, 2010, 9(23): 4603-4.
PREPRINTS (NOT YET PUBLISHED)
Click the title of the article to access the bioRxiv link