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Selected Publications (2010-2015)

2016

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 LA*, Rubin MA*, Demichelis F*. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med. 2016 Feb 8. doi: 10.1038/nm.4045.

2015

The Cancer Genome Atlas Research Network (including Davide Prandi and Francesca Demichelis). The Molecular Taxonomy of Primary Prostate Cancer. Cell 4(163), 1011-1025, 2015.

Romanel A*, Gasi Tandefelt D*, Conteduca C, 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. Science Translational Medicine 7, 312re10, 2015.

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.

Beltran H, Demichelis F. Prostate cancer: Intrapatient heterogeneity in prostate cancer. Nat Rev Urol. 2015 Aug;12(8):430-1. Nature Reviews Urology | News and Views

Robinson D, Van Allen EM, et al. Integrative clinical genomics of advanced prostate cancer. Cell. 2015 May 21;161(5):1215-28. doi: 10.1016/j.cell.2015.05.001. SU2C-PCF

Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Pauli C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary T, Herrscher E, Wilkes D, MacDonald T, Xue H, Vacic V, Emde AK, Oschwald D , Tan A, Chen Z, Collins C, Gleave M, Wang Y, Chakravarty D, Schiffman M, Kim R, Campagne F, Robinson B, Nanus D, Tagawa S, Xiang J, Smogorzewska A, Demichelis F, Rickman D, Sboner A, Elemento O, Rubin MA. Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response. Jama Oncology, 2015.

Romanel A, Lago S, Prandi D, Sboner A, Demichelis F. ASEQ: fast allele-specific studies from next-generation sequencing data. BMC Medical Genomics 8(1):9, 2015.

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 6(7):4816-4828, 2015.

2014

Carreira S*, Romanel A*, Goodall J*, Grist E, Ferraldeschi R, Miranda S, Prandi D, Lorente D, Frenel J-S, Pezaro C, Omlin A, Rodrigues DN, Flohr P, Tunariu N, de Bono JS, Demichelis F*, Attard G*. Tumor clone dynamics in lethal prostate cancer. Science Translational Medicine 2014, 6:254ra125.

Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F. Unraveling the clonal hierarchy of somatic genomic aberrations. Genome Biology 2014, 15:439.

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 Apr;23(4):594-600.

Demichelis F, Stanford JL. Genetic predisposition to prostate cancer: Update and future perspectives. Urol Oncol. 2014 Jul 1. pii: S1078-1439(14)00163-X. doi: 10.1016/j.urolonc.2014.04.021. [Epub ahead of print] Review.

2013

Park K, Chiu YL, Rubin MA, Demichelis F(*), Mosquera JM(*). V-ets erythroblastosis virus E26 oncogene homolog (avian)/Trefoil factor 3/high-molecular-weight cytokeratin triple immunostain: a novel tissue-based biomarker in prostate cancer with potential clinical application. Hum Pathol. 2013 Jul 12. doi:pii: S0046-8177(13)00199-8. 10.1016/j.humpath.2013.05.010. [Epub ahead of print]

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.

Schaefer G*, Mosquera J-M*, Ramoner R, Park K, Romanel A, Steiner E, Horninger W, Bektic J, Ladurner-Rennau M, Rubin MA, Demichelis F*, Klocker H*. Distinct ERG rearrangement prevalence in prostate cancer - higher frequency in young age and in low PSA prostate cancer. Prostate Cancer Prostatic Dis. 2013 Jun;16(2):132-8.

Poptsova M, Banerjee S, Gokcumen O, Rubin MA, Demichelis F. Impact of Constitutional Copy Number Variants on Biological Pathway Evolution. BMC Evol Biol. 2013 Jan 23;13(1):19.

Lin PC, Chiu YL, Banerjee S, Park K, Mosquera JM, Giannopoulou E, Alves P, Tewari AK, Gerstein MB, Beltran H, Melnick AM, Elemento O, Demichelis F, Rubin MA. Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression. Cancer Res. 2013 Feb 1;73(3):1232-1244.

Preview/Commentary: Demichelis F and Attard G. A step toward functionally characterized prostate cancer molecular subtypes. News & Views. Nat Med. 2013 Aug 6;19(8):966-7.

Preview/Commentary: Demichelis F, Garraway LA, Rubin MA. Molecular archeology: unearthing androgen-induced structural rearrangements in prostate cancer genomes. Cancer Cell, 2013 Feb 11;23(2):133-5. Preview

2012

Demichelis F, Setlur SR, Banerjee S, Chakravarty D, Chen JYH, Chen CX, Huang J, Beltran H, Oldridge DA, Kitabayashi N, Stenzel B, Schaefer G, Horninger W, Bektic J, Chinnaiyan AM, Goldenberg S, Siddiqui J, Regan M, Kearney M, Soong TD, Rickman DS, Elemento O, Wei JT, Scherr DS, Sanda MA, Bartsch G, Lee C, Klocker H, Rubin MA. Identification of functionally active, low frequency copy number variants at 15q21.3 and 12q21.31 associated with prostate cancer risk. Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6686-91.

Rickman DS, Soong TD, Moss B, Mosquera JM, Dlabal J, Terry S, MacDonald SY, Tripodi J, Bunting K, Najfeld V, Demichelis F, Melnick AM, Elemento O, Rubin MA. Oncogene-Mediated Alterations in Chromatin Conformation. Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):9083-8.

Barbieri CE, Baca SC, Lawrence MS, Demichelis F, et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet. 2012 May 20;44(6):685-9.

2011

Beltran H, Rickman DS, Park K, Chae SS, Sboner A, MacDonald TY, Wang Y, Sheikh KL, Terry S, Tagawa ST, Dhir R, Nelson JB, de la Taille A, Allory Y, Gerstein MB, Perner S, Pienta KJ, Chinnaiyan AM, Wang Y, Collins CC, Gleave ME, Demichelis F, Nanus DM, Rubin MA. Molecular Characterization of Neuroendocrine Prostate Cancer and Identification of New Drug Targets. Cancer Discovery. 2011 Nov;1(6): 487-495.

Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin P-C, Svensson MA, Kitabayashi N, Moss BJ, MacDonald TY, Cao X, Barrette T, Tewari AK, Chee MS, Chinnaiyan AM, Rickman DS, Demichelis F, Gerstein MB, Rubin MA. Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res. 2011 Jan;21(1):56-67.

Berger MF(*), Lawrence MS(*), Demichelis F(*), Drier Y(*), Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA. The genomic complexity of primary human prostate cancer. Nature. 2011 Feb 10;470(7333):214-20.

Banerjee S, Oldridge D, Poptsova M, Hussain WM, Chakravarty D, Demichelis F. A computational framework discovers new copy number variants with functional importance. PLoS One. 2011 Mar 29;6(3):e17539.

2010

Setlur SR, Chen CX, Hossain RR, Ha JS, Van Doren VE, Stenzel B, Steiner E, Oldridge D, Katabayashi N, Banerjee S, Chen JY, Schäfer G, Horninger W, Lee C, Rubin MA, Klocker H, and Demichelis F. Genetic Variation of Genes involved in Dihydrotestosterone Metabolism and the risk of prostate cancer. Cancer Epidemiol Biomarkers Prev. 2010 Jan;19(1):229-39.

Oldridge DA, Banerjee S, Setlur SR, Sboner A, Demichelis F. Optimizing Copy Number Variation Analysis using Genome-Wide Short Sequence Oligonucleotide Arrays. Nucleic Acids Res 2010 Jun;38(10):3275-86.

David S. Rickman, Ying-bei Chen, Samprit Banerjee, Yihang Pan, Jindan Yu, Sven Perner, Christopher Lafargue, Kirsten D. Mertz, Sunita R. Setlur, Kanishka Sircar, Arul M. Chinnaiyan, Tarek A. Bismar, Mark A. Rubin and F. Demichelis. ERG Cooperates with Androgen Receptor in Regulating Trefoil Factor 3 in Prostate Cancer Disease Progression. Neoplasia 2010 Dec:12(12).