Publications
2023
Bratic Hench I, Roma L, Conticelli F, Bubendorf L, Calgua B, Le Magnen C, Piscuoglio S, Rubin MA, Chirindel A, Nicolas GP, Vlajnic T, Zellweger T, Templeton AJ, Stenner F, Ruiz C, Rentsch C, Bubendorf L. Cell-Free DNA Genomic Profiling and Its Clinical Implementation in Advanced Prostate Cancer. Cancers (Basel). 2023 Dec 21;16(1):45. PMID: 38201475.
Akhoundova D, Francica P, Rottenberg S, Rubin MA. DNA Damage Response and Mismatch Repair Gene Defects in Advanced and Metastatic Prostate Cancer. Adv Anat Pathol. 2024 Mar 1;31(2):61-69. Epub 2023 Nov 27. PMID: 38008971; PMCID: PMC10846598.
Papachristodoulou A, Heidegger I, Virk RK, Di Bernardo M, Kim JY, Laplaca C, Picech F, Schäfer G, De Castro GJ, Hibshoosh H, Loda M, Klocker H, Rubin MA, Zheng T, Benson MC, McKiernan JM, Dutta A, Abate-Shen C. Metformin Overcomes the Consequences of NKX3.1 Loss to Suppress Prostate Cancer Progression. Eur Urol. 2023 Aug 31:S0302-2838(23)03016-6. Epub ahead of print. PMID: 37659962; PMCID: PMC10902192.
Nocini R, Tondulli L, D'Ambrosio C, Luchini C, Biankin AV, Casolino R, Scarpa A; ICGC-ARGO; Milella M, Lawlor RT. ICGC ARGO precision medicine: genomic profiling-informed prediction of immunotherapy response in two patients with metastatic head and neck squamous cell carcinoma. Lancet Oncol. 2023 Aug;24(8):851-853. PMID: 37541270.
Van Emmenis L, Ku SY, Gayvert K, Branch JR, Brady NJ, Basu S, Russell M, Cyrta J, Vosoughi A, Sailer V, Alnajar H, Dardenne E, Koumis E, Puca L, Robinson BD, Feldkamp MD, Winkis A, Majewski N, Rupnow B, Gottardis MM, Elemento O, Rubin MA, Beltran H, Rickman DS. The Identification of CELSR3 and Other Potential Cell Surface Targets in Neuroendocrine Prostate Cancer. Cancer Res Commun. 2023 Aug 3;3(8):1447-1459. CRC-22-0491. PMID: 37546702; PMCID: PMC10401480.
Planas-Paz L, Pliego-Mendieta A, Hagedorn C, Aguilera-Garcia D, Haberecker M, Arnold F, Herzog M, Bankel L, Guggenberger R, Steiner S, Chen Y, Kahraman A, Zoche M, Rubin MA, Moch H, Britschgi C, Pauli C. Unravelling homologous recombination repair deficiency and therapeutic opportunities in soft tissue and bone sarcoma. EMBO Mol Med. 2023 Apr 11;15(4):e16863. Epub 2023 Feb 13. PMID: 36779660; PMCID: PMC10086583.
Netto GJ, Amin MB, Compérat EM, Gill AJ, Hartmann A, Moch H, Menon S, Raspollini MR, Rubin MA, Srigley JR, Hoon Tan P, Tickoo SK, Tsuzuki T, Turajlic S, Cree I, Berney DM. Prostate Adenocarcinoma Grade Group 1: Rationale for Retaining a Cancer Label in the 2022 World Health Organization Classification. Eur Urol. 2023 Apr;83(4):301-303. Epub 2022 Oct 4. PMID: 36202687.
Li Z, Huang Y, Patil D, Rubin M, Sanda MG. Covariate-specific evaluation of continuous biomarker. Stat Med. 2023 Mar 30;42(7):953-969. Epub 2023 Jan 4. PMID: 36600184; PMCID: PMC10071998.
Menon S, Moch H, Berney DM, Cree IA, Srigley JR, Tsuzuki T, Compérat E, Hartmann A, Netto G, Rubin MA, Gill AJ, Turajlic S, Tan PH, Raspollini MR, Tickoo SK, Amin MB. WHO 2022 classification of penile and scrotal cancers: updates and evolution. Histopathology. 2023 Mar;82(4):508-520. Epub 2022 Nov 9. PMID: 36221864.
Schnidrig D, Garofoli A, Benjak A, Rätsch G, Rubin MA; SOCIBP consortium; Piscuoglio S, Ng CKY. PipeIT2: A tumor-only somatic variant calling workflow for molecular diagnostic Ion Torrent sequencing data. Genomics. 2023 Mar;115(2):110587. Epub 2023 Feb 14. PMID: 36796655.
Augspach A, Drake KD, Roma L, Qian E, Lee SR, Clarke D, Kumar S, Jaquet M, Gallon J, Bolis M, Triscott J, Galván JA, Chen Y, Thalmann GN, Kruithof-de Julio M, Theurillat JP, Wuchty S, Gerstein M, Piscuoglio S, Kanadia RN, Rubin MA. Minor intron splicing is critical for survival of lethal prostate cancer. Mol Cell. 2023 Jun 15;83(12):1983-2002.e11. Epub 2023 Jun 8.
Kashani E, Schnidrig D, Gheinani AH, Ninck MS, Zens P, Maragkou T, Baumgartner U, Schucht P, Rätsch G, Rubin MA; SOCIBP consortium; Berezowska S, Ng CKY, Vassella E. Integrated longitudinal analysis of adult grade 4 diffuse gliomas with long-term relapse interval revealed upregulation of TGF-β signaling in recurrent tumors. Neuro Oncol. 2023 Apr 6;25(4):662-673. Erratum in: Neuro Oncol. 2023 Feb 14;25(2):430.
Gillessen S et al. Management of Patients with Advanced Prostate Cancer. Part I: Intermediate-/High-risk and Locally Advanced Disease, Biochemical Relapse, and Side Effects of Hormonal Treatment: Report of the Advanced Prostate Cancer Consensus Conference 2022. Eur Urol. 2023 Mar;83(3):267-293. Epub 2022 Dec 6.
Gallon J, Rodriguez-Calero A, Benjak A, Akhoundova D, Maletti S, Amstutz U, Hewer E, Genitsch V, Fleischmann A, Rushing EJ, Grobholz R, Fischer I, Jochum W, Cathomas G, Osunkoya AO, Bubendorf L, Moch H, Thalmann G, Feng FY, Gillessen S, Ng CKY, Rubin MA, Piscuoglio S. DNA methylation landscapes of prostate cancer brain metastasis are shaped by early driver genetic alterations. Cancer Res. 2023 Feb 7:CAN-22-2236. Epub ahead of print.
Vasciaveo A, Arriaga JM, de Almeida FN, Zou M, Douglass EF, Picech F, Shibata M, Rodriguez-Calero A, de Brot S, Mitrofanova A, Chua CW, Karan C, Realubit R, Pampou S, Kim JY, Afari SN, Mukhammadov T, Zanella L, Corey E, Alvarez MJ, Rubin MA, Shen MM, Califano A, Abate-Shen C. OncoLoop: A Network-Based Precision Cancer Medicine Framework. Cancer Discov. 2023 Feb 6;13(2):386-409.
Triscott, J., Reist, M., Küng. L, Moselle, F.C., Lehner, M., Gallon, J., Ravi, A., Arora, G.K., de Brot, S., Lundquist, M., Gallart-Ayala, H., Ivanisevic, J., Piscuoglio, S., Cantley, L.C., Emerling, B.M., and Rubin, M.A. “PI5P4Kα supports prostate cancer metabolism and exposes a survival vulnerability during androgen receptor (AR) inhibition.” Sci Adv. 2023 Feb 3;9(5):eade8641. Epub 2023 Feb 1.
2022
Cyrta J, Rosiene J, Bareja R, Kudman S, Al Zoughbi W, Motanagh S, Wilkes DC, Eng K, Zhang T, Sticca E, Mathew S, Rubin MA, Sboner A, Elemento O, Rubin BP, Imielinski M, Mosquera JM. Whole-genome characterization of myoepithelial carcinomas of the soft tissue. Cold Spring Harb Mol Case Stud. 2022 Dec 28;8(7):a006227.
Akhoundova D, Feng FY, Pritchard CC, Rubin MA. Molecular Genetics of Prostate Cancer and Role of Genomic Testing. Surg Pathol Clin. 2022 Dec;15(4):617-628. Epub 2022 Oct 13.
Zeng Q, Saghafinia S, Chryplewicz A, Fournier N, Christe L, Xie YQ, Guillot J, Yucel S, Li P, Galván JA, Karamitopoulou E, Zlobec I, Ataca D, Gallean F, Zhang P, Rodriguez-Calero JA, Rubin M, Tichet M, Homicsko K, Hanahan D. Aberrant hyperexpression of the RNA binding protein FMRP in tumors mediates immune evasion. Science. 2022 Nov 18;378(6621):eabl7207. Epub 2022 Nov 18.
Ferguson AM, Rubin MA. Lineage plasticity in prostate cancer: Looking beyond intrinsic alterations. Cancer Lett. 2022 Nov 1;548:215901. Epub 2022 Sep 6.
Akhoundova D, Rubin MA. Clinical application of advanced multi-omics tumor profiling: Shaping precision oncology of the future. Cancer Cell. 2022 Sep 12;40(9):920-938. Epub 2022 Sep 1.
Cotter K, Rubin MA. The evolving landscape of prostate cancer somatic mutations. Prostate. 2022 Aug; 82 Suppl 1(Suppl 1):S13-S24.
Co-Editor, WHO Classification of Tumours Editorial Board. WHO Genitourinary Tumor Blue Book/Urinary and Male Genital Tumours WHO Classification of Tumours, 5th Edition, Volume 8. IARC Press: Lyon 2022.
Raman R, Villefranc JA, Ullmann TM, Thiesmeyer J, Anelli V, Yao J, Hurley JR, Pauli C, Bareja R, Wha Eng K, Dorsaint P, Wilkes DC, Beg S, Kudman S, Shaw R, Churchill M, Ahmed A, Keefer L, Misner I, Nichol D, Gumpeni N, Scognamiglio T, Rubin MA, Grandori C, Solomon JP, Song W, Mosquera JM, Dephoure N, Sboner A, Elemento O, Houvras Y. Inhibition of FGF receptor blocks adaptive resistance to RET inhibition in CCDC6-RET-rearranged thyroid cancer. J Exp Med. 2022 Jun 6.
Janowczyk A, Baumhoer D, Dirnhofer S, Grobholz R, Kipar A, de Leval L, Merkler D, Michielin O, Moch H, Perren A, Rottenberg S, Rubbia-Brandt L, Rubin MA, Sempoux C, Tolnay M, Zlobec I, Koelzer VH; Swiss Digital Pathology Consortium (SDiPath). Towards a national strategy for digital pathology in Switzerland. Virchows Arch. 2022 May 27. Epub ahead of print.
Orlando F, Romanel A, Trujillo B, Sigouros M, Wetterskog D, Quaini O, Leone G, Xiang JZ, Wingate A, Tagawa S, Jayaram A, Linch M; PEACE Consortium, Jamal-Hanjani M, Swanton C, Rubin MA, Wyatt AW, Beltran H, Attard G, Demichelis F. Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay. NAR Cancer. 2022 May 27.
Rodriguez-Calero A, Gallon J, Akhoundova D, Maletti S, Ferguson A, Cyrta J, Amstutz U, Garofoli A, Paradiso V, Tomlins S, Hewer E, Genitsch V, Fleischmann A, Vassella E, Rushing E, Grobholz R, Fischer I, Jochum W, Cathomas G, Osunkoya A, Bubendorf L, Moch H, Thalmann G, Ng C, Gillessen S, Piscuoglio S, Rubin MA. Alterations in Homologous Recombination Repair Genes in Prostate Cancer Brain Metastases. Nature Communications. 2022 May 3.
Cyrta J, Prandi D, Arora A, Hovelson DH, Sboner A, Rodriguez A, Fedrizzi T, Beltran H, Robinson DR, Gopalan A, True L, Nelson PS, Robinson BD, Mosquera JM, Tomlins SA, Shen R, Demichelis F, Rubin MA. Comparative genomics of primary prostate cancer and paired metastases: insights from 12 molecular case studies. J. Patho. 2022.
Fontugne J, Cai PY, Alnajar H, Bhinder B, Park K, Ye H, Beg S, Sailer V, Siddiqui J, Blattner-Johnson M, Croyle JA, Noorzad Z, Calagua C, MacDonald TY, Axcrona U, Bogaard M, Axcrona K, Scherr DS, Sanda MG, Johannessen B, Chinnaiyan AM, Elemento O, Skotheim RI, Rubin MA, Barbieri CE, Mosquera JM. Collision tumors revealed by prospectively assessing subtype-defining molecular alterations in 904 individual prostate cancer foci. JCI Insight. 2022 Jan 20.
2021
Bolis M, Bossi D, Vallerga A, Ceserani V, Cavalli M, Rito Ld, Zoni E, Mosole S, Rinaldi A, Mestre RP, D'Antonio E, Ferrari M, Stoffel F, Jermini F, Sommer SG, Bubendorf L, Schraml P, Moch H, Spahn M, Thalmann G, Julio MK, Rubin MA, Theurillat J. Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression. Nat Commun. 2021 Dec 2
Pauli C, De Boni L, Pauwels JE, Chen Y, Planas-Paz L, Shaw R, Emerling BM, Grandori C, Hopkins BD, Rubin MA. A Functional Precision Oncology Approach to Identify Treatment Strategies for Myxofibrosarcoma Patients. Mol Cancer Res. 2021 Nov 2
Mukhopadhyay C, Yang C, Xu L, Liu D, Wang Y, Huang D, Deonarine LD, Cyrta J, Davicioni E, Sboner A, Robinson BD, Chinnaiyan AM, Rubin MA, Barbieri CE, Zhou P. G3BP1 inhibits Cul3SPOP to amplify AR signaling and promote prostate cancer. Nat Commun. 2021 Nov 18
Ryman-Tubb T, Lothion-Roy JH, Metzler VM, Harris AE, Robinson BD, Rizvanov AA, Jeyapalan JN, James VH, England G, Rutland CS, Persson JL, Kenner L, Rubin MA, Mongan NP, de Brot S. Comparative pathology of dog and human prostate cancer. Vet Med Sci. 2021 Oct 10. doi: 10.1002/vms3.642. Epub ahead of print.
Papachristodoulou A, Rodriguez-Calero A, Panja S, Margolskee E, Virk R, Milner T, Martina LP, Kim J, Di Bernardo M, Williams A, Maliza E, Caputo J, Haas Ch, Wang V, De Castro GJ, Wenske S, Hibshoosh H, McKiernan J, Shen M, Rubin MA, Mitrofanova A, Dutta A, Abate-Shen C. NKX3.1 localization to mitochondria suppresses prostate cancer initiation. Cancer Discov. 2021 Sep 11.
El Tekle G, Bernasocchi T, Unni AM, Bertoni F, Rossi D, Rubin MA, Theurillat JP. Co-occurrence and mutual exclusivity: what cross-cancer mutation patterns can tell us. Trends Cancer. 2021 Sep 7.
Servant R, Garioni M, Vlajnic T, Blind M, Pueschel H, Müller DC, Zellweger T, Templeton AJ, Garofoli A, Maletti S, Piscuoglio S, Rubin MA, Seifert H, Rentsch CA, Bubendorf L, Le Magnen C. Prostate cancer patient-derived organoids: detailed outcome from a prospective cohort of 81 clinical specimens. J Pathol. 2021 Aug
Cotter KA, Gallon J, Uebersax N, Rubin PH, Meyer KD, Piscuoglio S, Jaffrey SR, Rubin MA. Mapping of m6A and Its Regulatory Targets in Prostate Cancer Reveals a METTL3-low Induction of Therapy Resistance. Mol Cancer Res. 2021 Aug 19.
Ravi A, Palamiuc L, Loughran R, Triscott J, Arora G, Kumar A, Tieu V, Pauli C, Reist M, Lew R, Houlihan S, Fellmann C, Metallo C, Rubin MA, Emerling B. PI5P4Ks drive metabolic homeostasis through peroxisome-mitochondria interplay. Dev Cell. 2021 Jun 7.
Guzman M, Sugita M, Wilkes D, Bareja R, Eng K, Nataraj S, Jimenez-Flores R, Yan L, De Leon J, Croyle J, Kaner J, Merugu S, Sharma S, MacDonald T, Noorzad Z, Pancirer D, Cheng S, Xiang J, Olson L, Van Besien K, Rickman D, Tam W, Rubin MA, Beltran H, Sboner A, Hassane D, Chiosis G, Elemento O, Roboz G, Mosquera JM, Panchal P, Matthew S. Targeting the Epichaperome As an Effective Precision Medicine Approach in a Novel PML-SYK Fusion Acute Myeloid Leukemia. npj Precision Oncology 2021 February 18.
de Brot S, Lothion-Roy J, Grau-Roma L, White E, Guscetti F, Rubin MA, Mongan NP. Histological and immunohistochemical investigation of canine prostate carcinoma with identification of common intraductal carcinoma component. Vet Comp Oncol. 2021 May 7.
Epstein JI, Amin MB, Fine SW, Algaba F, Aron M, Baydar DE, Beltran AL, Brimo F, Cheville JC, Colecchia M, Comperat E, da Cunha IW, Delprado W, DeMarzo AM, Giannico GA, Gordetsky JB, Guo CC, Hansel DE, Hirsch MS, Huang J, Humphrey PA, Jimenez RE, Khani F, Kong Q, Kryvenko ON, Kunju LP, Lal P, Latour M, Lotan T, Maclean F, Magi-Galluzzi C, Mehra R, Menon S, Miyamoto H, Montironi R, Netto GJ, Nguyen JK, Osunkoya AO, Parwani A, Robinson BD, Rubin MA, Shah RB, So JS, Takahashi H, Tavora F, Tretiakova MS, True L, Wobker SE, Yang XJ, Zhou M, Zynger DL, Trpkov K. The 2019 Genitourinary Pathology Society (GUPS) White Paper on Contemporary Grading of Prostate Cancer. Arch Pathol Lab Med. 2021 Apr 1;145(4):461-493. PMID: 32589068
Guo C, Crespo M, Gurel B, Dolling D, Rekowski J, Sharp A, Petremolo A, Sumanasuriya S, Rodrigues DN, Ferreira A, Pereira R, Figueiredo I, Mehra N, Lambros MBK, Neeb A, Gil V, Seed G, Terstappen L, Alimonti A, Drake CG, Yuan W, de Bono JS; International SU2C PCF Prostate Cancer Dream Team. CD38 in Advanced Prostate Cancers. Eur Urol. 2021 Mar 1:S0302-2838(21)00022-1.. PMID: 33678520
Karkampouna S, La Manna F, Benjak A, De Filippo MR, Kiener M, De Menna M, Zoni E, Grosjean J, Klima I, Garofoli A, Vallerga A, Bolis M, Theurillat JP, Genitsch V, Keller D, Booij TH, Stirnimann CU, Eng K, Sboner A, Ng CKY, Piscuoglio S, Gray PC, Spahn M, Rubin MA, Thalmann GN, Kruithof-de Julio M. Patient-derived xenografts and organoids model therapy response in prostate cancer. Nat Commun 2021 Feb 18;12(1):1117. PMID: 33602919
Armstrong AJ, Li X, Tucker M, Li S, Mu XJ, Eng KW, Sboner A, Rubin MA*, Gerstein M. Molecular Medicine Tumor Board: Whole Genome Sequencing to Inform on Personalized Medicine for a Man with Advanced Prostate Cancer. Prostate Cancer and Prostatic Diseases 2021 Feb 10, PMID: 33568750. *Co-corresponding author
Bernasocchi T, El Tekle G, Bolis M, Mutti A, Vallerga A, Brandt LP, Spriano F, Svinkina T, Zoma M, Ceserani V, Rinaldi A, Janouskova H, Bossi D, Cavalli M, Mosole S, Geiger R, Dong Z, Yang C.-G, Albino D, Rinaldi A, Schraml P, Linder S, Carbone GM, Alimonti A, Bertoni F, Moch H, Carr SA, Zwart W, Kruithof-de Julio M, Rubin MA, Udeshi ND, Theurillat J.-P.P. Dual functions of SPOP and ERG dictate androgen therapy responses in prostate cancer. Nat Commun 2021 Feb 2;12(1). PMID 33531470
Hommerding O, Allory Y, Argani P, Bismar TA, Bubendorf L, Canete-Portillo S, Chaux A, Chen YB, Cheng L, Cubilla AL, Egevad L, Gill AJ, Grignon DJ, Hartmann A, Hes O, Idrees MT, Kao CS, Knowles MA, Looijenga LHJ, Lotan TL, Pritchard CC, Rubin MA, Tomlins SA, Van der Kwast TH, Velazquez EF, Warrick JI, Williamson SR, Kristiansen G. Molekularpathologie bei urologischen Tumoren : Empfehlungen der Konsenskonferenz der Internationalen Gesellschaft für Uropathologie (ISUP) 2019 [Molecular pathology of urogenital tumors : Recommendations from the 2019 International Society of Urological Pathology (ISUP) Consensus Conference]. Pathologe. 2021 Jan 4. German.. PMID: 33398501
2020
Vosoughi A, Zhang T, Shohdy KS, Vlachostergios PJ, Wilkes DC, Bhinder B, Tagawa ST, Nanus DM, Molina AM, Beltran H, Sternberg CN, Motanagh S, Robinson BD, Xiang J, Fan X, Chung WK, Rubin MA, Elemento O, Sboner A, Mosquera JM, Faltas BM. Common germline-somatic variant interactions in advanced urothelial cancer. Nat Commun. 2020 Dec 3;11(1):6195. PMID: 33273457
Cyrta J, Augspach A, de Filippo MR, Prandi D, Thienger P, Benelli M, Cooley V, Bareja R, Wilkes D, Chae S-S, Cavaliere P, Dephure N, Uldry A-C, Lagache SB, Roma L, Cohen S, Jaquet M, Brandt LP, Alshalalfa M, Sboner A, Feng F, Wang S, Beltran H, Lotan T, Spahn M, Kruithof-de Julio M, Chen Y, Ballman KV, Demichelis F, Piscuoglio S, Rubin MA*. Role of Specialized Composition of SWI/SNF Complexes in Prostate Cancer Lineage Plasticity. Nat Commun. 2020; 11: 5549. https://doi.org/10.1038/s41467-020-19328-1 *Corresponding Author
Arriaga J, Panja S, Alshalalfa M, Zhao J, Zou M, Giacobbe A, Madubata CJ, Kim JY, Rodriguez A, Coleman I, Virk RK, Hibshoosh H, Ertunc O, Ozbek B, Fountain J, Karnes RJ, Luo J, Antonarakis ES, Nelson PS, Feng FY, Rubin MA, De Marzo AM, Rabadan R, Sims PA, Mitrofanova A, Abate-Shen C. A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance. Nat Cancer. 2020; https://doi.org/10.1038/s43018-020-00125-0
Bailey MH, Meyerson WU, Dursi LJ; Wang L, Dong G, Liang W, Weerasinghe A, Li S, Kelso S, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding Li, PCAWG Consortium. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020; 11: 4748. https://doi.org/10.1038/s41467-020-18151-y
Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, PCAWG Tumour Subtypes and Clinical Translation, Boutros PC, PCAWG Consortium. Sex differences in oncogenic mutational processes. Nat Commun. 2020;11: 4330. https://doi.org/10.1038/s41467-020-17359-2
Aurélie Auguste, Félix Blanc-Durand, Marc Deloger, Audrey Le Formal, Rohan Bareja, David C. Wilkes, Catherine Richon, Béatrice Brunn, Olivier Caron, Mojgan Devouassoux-Shisheboran, Sébastien Gouy, Philippe Morice, Enrica Bentivegna, Andrea Sboner, Olivier Elemento, Mark A. Rubin, Patricia Pautier, Catherine Genestie, Joanna Cyrta, Alexandra Leary. Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) beyond SMARCA4 Mutations: A Comprehensive Genomic Analysis. Cells. 2020 Jun 19; 9(6), 1496; https://doi.org/10.3390/cells9061496
Pisapia DJ, Ohara K, Bareja R, Wilkes DC, Hissong E, Croyle JA, Kim JH, Saab J, MacDonald TY, Beg S, O'Reilly C, Kudman S; Rubin MA, Elemento O, Sboner A, Greenfield J, Mosquera JM. Fusions involving BCOR and CREBBP are rare events in infiltrating glioma. Acta Neuropathol Commun 2020 Jun 3;8(1):80. https://doi.org/10.1186/s40478-020-00951-4
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium [1341 authors]. Pan-cancer analysis of whole genomes. Nature. 2020 Feb;578(7793):82-93. https://doi.org/10.1038/s41586-020-1969-6
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell P, López-Bigas N, PCAWG Drivers and Functional Interpretation Working Group [128 authors], PCAWG Structural Variation Working Group [73 authors], Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G , PCAWG Consortium. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 Feb;578(7793):102-111. https://doi.org/10.1038/s41586-020-1965-x
Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A, PCAWG Drivers and Functional Interpretation Working Group [103 authors], Raphael BJ, PCAWG Consortium. Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications. 2020 February 05; 11(1):729. https://doi.org/10.1038/s41467-020-14367-0
Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS, PCAWG Drivers and Functional Interpretation Working Group [130 authors], Johnson R, PCAWG Consortium. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Communications Biology. 2020 February 05; 3(1):56. https://doi.org/10.1038/s42003-019-0741-7
Shuai S, PCAWG Drivers and Functional Interpretation Working Group [128 authors], Gallinger S, Stein L, PCAWG Consortium. Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature Communications. 2020 February 05; 11(1):734. https://doi.org/10.1038/s41467-019-13929-1
Jiao W, Atwal G, Polak P, Karlic R, Cuppen E, PCAWG Tumor Subtypes and Clinical Translation Working Group [48 authors], Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris Q, Stein LD, PCAWG Consortium. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nature Communications. 2020 February 05; 11(1):728. https://doi.org/10.1038/s41467-019-13825-8
Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group [126 authors], Reimand J, PCAWG Consortium. Integrative pathway enrichment analysis of multivariate omics data. Nature Communications. 2020 February 05; 11(1):735. https://doi.org/10.1038/s41467-019-13983-9
Lotan TL, Tomlins SA, Bismar TA, Van der Kwast TH, Grignon D, Egevad L, Kristiansen G, Pritchard CC, Rubin MA, Bubendorf L. Report from the International Society of Urological Pathology (ISUP) Consultation Conference on Molecular Pathology of Urogenital Cancers: I. Molecular Biomarkers in Prostate Cancer. American Journal of Surgical Pathology. 2020 Feb 10. doi: 10.1097. DOI: 10.1097/pas.0000000000001450
2019
Beltran H, Oromendia C, Danila DC, Montgomery B, Hoimes C, Szmulewitz RZ, Vaishampayan U, Armstrong AJ, Stein M, Pinski J, et al. A Phase II Trial of the Aurora Kinase A Inhibitor Alisertib for Patients with Castration-resistant and Neuroendocrine Prostate Cancer: Efficacy and Biomarkers. Clinical Cancer Reseach. 2019; 25(1):43-51. doi: 10.1158/1078-0432.CCR-18-1912
Skvortsova K, Masle-Farquhar E, Luu P-L, Song JZ, Qu W, Zotenko E, Gould CM, Du Q, Peters TJ, Colino-Sanguino Y, Pidsley R, Nair SS, Khoury A, Smith GC, Miosge LA, Reed JH, Kench JG, Rubin MA, Horvath L, Bogdanovic O, Lim SM, Polo JM, Goodnow CC, Stirzaker C, Clark SJ. DNA Hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation Patterns. Cancer Cell. 2019 Feb 11; 35(2):297-314.e298. https://doi.org/10.1016/j.ccell.2019.01.004
Karkampouna S, Grosjean J, Klima I, Genitsch V, Sboner A, K. Y. Ng C, De Filippo MR, Piscuoglio S, Spahn M, Rubin MA, Thalmann GN, Kruithof-De Julio M. Establishment of an androgen-sensitive patient derived xenograft model of prostate cancer. European Urology Supplements. 2019 March 1; 18(1):e1154. https://doi.org/10.1016/S1569-9056(19)30831-0
Lee RS, Zhang L, Berger A, Lawrence MG, Song J, Niranjan B, Davies RG, Lister NL, Sandhu SK, Rubin MA, Risbridger GP, Taylor RA, Rickman DS, Horvath LG, Daly RJ. Characterization of the ERG-regulated kinome in prostate cancer identifies TNIK as a potential therapeutic target. Neoplasia. 2019 April 01; 21(4):389-400. https://doi.org/10.1016/j.neo.2019.02.005
Abida W, Cyrta J, Heller G, Prandi D, Armenia J, Coleman I, Cieslik M, Benelli M, Robinson D, Van Allen EM, et al. Genomic correlates of clinical outcome in advanced prostate cancer. PNAS. 2019. doi: 10.1073/pnas.1902651116
Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EW, Chen Y, et al. CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Cancer Cell. 2019; 35(4):603-617. doi: 10.1016/j.ccell.2019.03.001
Persi E, Prandi D, Wolf YI, Pozniak Y, Barnabas GD, Levanon K, Barshack I, Barbieri C, Gasperini P, Beltran H, Faltas BM, Rubin MA, Geiger T, Koonin EV, Demichelis F, Horn D. Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues. PNAS. 2019 August 20, 116 (34) 16987-16996. https://doi.org/10.1073/pnas.1908790116
Lou S, Cotter KA, Li T, Liang J, Mohsen H, Liu J, Zhang J, Cohen S, Xu J, Yu H, Rubin MA, Gerstein M. GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner. PLOS Genetics. 2019 Aug 30; 15(8):e1007860. https://doi.org/10.1371/journal.pgen.1007860
2018
Aytes A, Giacobbe A, Mitrofanova A, Ruggero K, Cyrta J, Arriaga J, Palomero L, Farran-Matas S, Rubin MA, Shen MM, Califano A, Abate-Shen C. NSD2 is a conserved driver of metastatic prostate cancer progression. Nature Communications. 2018;9(1):5201. doi: 10.1038/s41467-018-07511-4
Boysen G, Rodrigues DN, Rescigno P, Seed G, Dolling D, Riisnaes R, Crespo M, Zafeiriou Z, Sumanasuriya S, Bianchini D, et al. SPOP-Mutated/CHD1-Deleted Lethal Prostate Cancer and Abiraterone Sensitivity. Clinical Cancer Research. 2018; 24(22):5585-5593. doi: 10.1158/1078-0432.CCR-18-0937
Nava Rodrigues D, Rescigno P, Liu D, Yuan W, Carreira S, Lambros MB, Seed G, Mateo J, Riisnaes R, Mullane S, et al. Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer. The Journal of Clinical Investigation. 2018; 128(10):4441-4453. doi: 10.1172/JCI121924
Cotter K, Rubin MA; Sequence of events in prostate cancer Nature 2018 Aug 24, doi: 10.1038/d41586-018-06029-5
Hopkins BD, Pauli C, Du X, Wang DG, Li X, Wu D, Amadiume SC, Goncalves MD, Hodakoski C, Lundquist MR, Bareja R, Ma Y, Harris EM, Sboner A, Beltran H, Rubin MA, Mukherjee S, Cantley LC. Suppression of insulin feedback enhances the efficacy of PI3K inhibitors. Nature. 2018; 560(7719):499-503. doi: 10.1038/s41586-018-0343-4
Puca L, Bareja R, Prandi D, Shaw R, Benelli M, Karthaus WR, Hess J, Sigouros M, Donoghue A, Kossai M, et al. Patient derived organoids to model rare prostate cancer phenotypes. Nature Communications. 2018; 9(1):2404. doi: 10.1038/s41467-018-04495-z.
Triscott J, Rubin MA; Prostate Power Play: Does Pik3ca Accelerate Pten-Deficient Cancer Progression? Cancer Discovery June 2018. 8.6: 682-685. doi: 10.1158/2159-8290.CD-18-0369
Lundquist MR, Goncalves MD, Loughran RM, Possik E, Vijayaraghavan T, Yang A, Pauli C, Ravi A, Verma A, Yang Z, et al. Phosphatidylinositol-5-Phosphate 4-Kinases Regulate Cellular Lipid Metabolism By Facilitating Autophagy. Molecular Cell. 2018; 70(3):531-544.e9. doi: 10.1016/j.molcel.2018.03.037.
Mateo J, Cheng HH, Beltran H, Dolling D, Xu W, Pritchard CC, Mossop H, Rescigno P, Perez-Lopez R, Sailer V, Kolinsky M, Balasopoulou A, Bertan C, Nanus DM, Tagawa ST, Thorne H, Montgomery B, Carreira S, Sandhu S, Rubin MA, Nelson PS, de Bono JS. Clinical Outcome of Prostate Cancer Patients with Germline DNA Repair Mutations: Retrospective Analysis from an International Study. European Urology. 2018; 73(5):687-693. doi: 10.1016/j.eururo.2018.01.010
Demichelis F, Rubin MA; The Genomics of Prostate Cancer: A Historic Perspective Cold Spring Harb Perspect Med. 2018 Apr 30. pii: a034942. doi: 10.1101/cshperspect.a034942.
Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, et al. The Immune Landscape of Cancer. Immunity. 2018; 48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023
Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, et al. The long tail of oncogenic drivers in prostate cancer, Nat Genet. 2018 Apr 2. doi: 10.1038/s41588-018-0078-z.
Sailer V, Schiffman MH, Kossai M, Cyrta J, Beg S, Sullivan B, Pua BB, Lee KS, Talenfeld AD, Nanus DM, Tagawa ST, Robinson BD, Rao RA, Pauli C, Bareja R, Beltran LS, Sigaras A, Eng KW, Elemento O, Sboner A, Rubin MA, Beltran H, Mosquera JM. Bone biopsy protocol for advanced prostate cancer in the era of precision medicine. Cancer. 2018; 124(5):1008-1015. doi: 10.1002/cncr.31173
McNair C, Xu K, Mandigo AC, Benelli M, Leiby B, Rodrigues D, Lindberg J, Gronberg H, Crespo M, De Laere B, Dirix L, Visakorpi T, Li F, Feng FY, de Bono J, Demichelis F, Rubin MA, Brown M, Knudsen KE. Differential impact of RB status on E2F1 reprogramming in human cancer. The Journal of Clinical Investigation. 2018; 128(1):341-358. doi: 10.1172/JCI93566
Gillessen S, Attard G, Beer TM, Beltran H, Bossi A, Bristow R, Carver B, Castellano D, Chung BH, Clarke N, et al. Management of Patients with Advanced Prostate Cancer: The Report of the Advanced Prostate Cancer Consensus Conference APCCC 2017. European Urology. 2018; 73(2):178-211. doi: 10.1016/j.eururo.2017.06.002.
Shoag J, Liu D, Blattner M, Sboner A, Park K, Deonarine L, Robinson BD, Mosquera JM, Chen Y, Rubin MA, Barbieri CE. SPOP mutation drives prostate neoplasia without stabilizing oncogenic transcription factor ERG. The Journal of Clinical Investigation. 2018; 128(1):381-386. doi: 10.1172/JCI96551
D'Alfonso TM, Subramaniyam S, Ginter PS, Mosquera JM, Croyle J, Liu YF, Rubin MA, Shin SJ. Characterization of CD34-deficient myofibroblastomas of the breast. The Breast Journal. 2018; 24(1):55-61. doi: 10.1111/tbj.12835