The Center for Cancer Systems Pharmacology

Publications

LSP Bibliography

1.
Gui F, Jiang B, Jiang J, He Z, Tsujino T, Takai T, Arai S, Pana C, Köllermann J, Bradshaw GA, Eisert R, Kalocsay M, Fassl A, Balk SP, Kibel AS, Jia L. Acute BRCAness induction and AR pathway blockage through CDK12/7/9 degradation enhances PARP inhibitor sensitivity in prostate cancer. Sci Adv. 2025 Apr 25;11(17):eadu0847. PMCID: PMC12017310
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Gevertz JL, Greene JM, Prosperi S, Comandante-Lou N, Sontag ED. Understanding therapeutic tolerance through a mathematical model of drug-induced resistance. NPJ Syst Biol Appl. 2025 Apr 10;11(1):30. PMCID: PMC11982405
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Ma XC, Clardy J. Spontaneous Generation of an Endogenous RORγt Agonist. J Am Chem Soc. 2025 Apr 9;147(14):11688–11692. PMCID: PMC11987011
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Kelley LP, Hu SH, Boswell SA, Sorger PK, Ringel AE, Haigis MC. Integrated analysis of transcriptional and metabolic responses to mitochondrial stress. Cell Rep Methods. 2025 Apr 8;101027. PMID: 40233762
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de Bruijn I, Nikolov M, Lau C, Clayton A, Gibbs DL, Mitraka E, Pozhidayeva D, Lash A, Sumer SO, Altreuter J, Anton K, DeFelice M, Li X, Lisman A, Longabaugh WJR, Muhlich J, Santagata S, Nandakumar S, Sorger PK, Suver C, Doan X, Guinney J, Schultz N, Taylor AJ, Thorsson V, Cerami E, Eddy JA. Sharing data from the Human Tumor Atlas Network through standards, infrastructure and community engagement. Nat Methods. 2025 Apr;22(4):664–671. PMID: 40164800
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Břinda K, Lima L, Pignotti S, Quinones-Olvera N, Salikhov K, Chikhi R, Kucherov G, Iqbal Z, Baym M. Efficient and robust search of microbial genomes via phylogenetic compression. Nat Methods. 2025 Apr;22(4):692–697. PMID: 40205174
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Mukhija S, Sunog M, Magdamo C, Albers MW. Impact of Severe COVID-19 on Accelerating Dementia Onset: Clinical and Epidemiological Insights. medRxiv; 2025. PMCID: PMC11974976
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Jobin B, Magdamo C, Delphus D, Runde A, Reineke S, Soto AA, Ergun B, Mukhija S, Albers AD, Albers MW. The AROMHA brain health test is a remote olfactory assessment to screen for cognitive impairment. Sci Rep. 2025 Mar 24;15(1):9290. PMCID: PMC11933705
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Mon-Wei Yu S, Choi JY, Kady J, De Cos M, Wong JS, King E, Younis N, Al Rahy N, Al Chaar S, Djebli H, Eskandari S, Samuel S, Merhej T, Sukumar N, Lin JR, Chen JY, Xu Y, Santagata S, Weins A, Yeung M, Cravedi P, Campbell KN, Lemos D, Bonventre JV, Brehm M, Azzi J. Transplantation of human kidney organoids elicited a robust allogeneic response in a humanized mouse model. Kidney Int. 2025 Mar 22;S0085-2538(25)00255–8. PMID: 40127865
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Zhou FY, Marin Z, Yapp C, Zou Q, Nanes BA, Daetwyler S, Jamieson A, Islam MT, Jenkins E, Gihana GM, Lin J, Borges HM, Chang BJ, Weems A, Morrison SJ, Sorger PK, Fiolka RP, Dean KM, Danuser G. Universal consensus 3D segmentation of cells from 2D segmented stacks. bioRxiv; 2025. PMCID: PMC11100681
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Vidović D, Shamsaei B, Schürer SC, Kogan P, Chojnacki S, Kouril M, Medvedovic M, Niu W, Azeloglu EU, Birtwistle MR, Chen Y, Chen T, Hansen J, Hu B, Iyengar R, Jayaraman G, Li H, Liu T, Sobie EA, Xiong Y, Berberich MJ, Bradshaw G, Chung M, Everley RA, Gaudio B, Hafner M, Kalocsay M, Mills CE, Nariya MK, Sorger PK, Subramanian K, Victor C, Banuelos M, Dardov V, Holewinski R, Manalo DM, Mandefro B, Matlock AD, Ornelas L, Sareen D, Svendsen CN, Vaibhav V, Van Eyk JE, Venkatraman V, Finkbiener S, Fraenkel E, Rothstein J, Thompson L, Asiedu J, Carr SA, Christianson KE, Davison D, Dele-Oni DO, DeRuff KC, Egri SB, Jacome ASV, Jaffe JD, Lam D, Litichevskiy L, Lu X, Mullahoo J, Officer A, Papanastasiou M, Peckner R, Toder C, Blanchard J, Bula M, Ko T, Tsai LH, Young JZ, Sharma V, Pillai A, Meller J, MacCoss MJ. Comprehensive proteomics metadata and integrative web portals facilitate sharing and integration of LINCS multiomics data. Mol Cell Proteomics. 2025 Mar 13;100947. PMID: 40089066
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Deng X, Bradshaw G, Kalocsay M, Mitchison T. Tubulin Regulates the Stability and Localization of STMN2 by Binding Preferentially to Its Soluble Form. bioRxiv; 2025. PMCID: PMC11888388
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Fang R, Vallius T, Zhang A, Van Cura D, Alicandri F, Fischer G, Draper E, Xu S, Pelletier R, Wang J, Mandinova A, Katsyv I, Sorger PK, Murphy GF, Lian CG. PRAME expression in melanoma is negatively regulated by TET2-mediated DNA hydroxymethylation. Lab Invest. 2025 Feb 28;104123. PMID: 40024557
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He X, Wang Q, Cheng X, Wang W, Li Y, Nan Y, Wu J, Xiu B, Jiang T, Bergholz JS, Gu H, Chen F, Fan G, Sun L, Xie S, Zou J, Lin S, Wei Y, Lee J, Asara JM, Zhang K, Cantley LC, Zhao JJ. Lysine vitcylation is a vitamin C-derived protein modification that enhances STAT1-mediated immune response. Cell. 2025 Feb 27;S0092-8674(25)00145-X. PMID: 40023152
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Cortés-Ríos J, Rodriguez-Fernandez M, Sorger PK, Fröhlich F. Dynamic Modeling of Cell Cycle Arrest Through Integrated Single-Cell and Mathematical Modelling Approaches [Internet]. bioRxiv; 2025. Available from: https://doi.org/10.1101/2025.02.20.639240 PMCID: PMC11888159
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Mears KS, Rossine FW, Quinones-Olvera N, Souque C, Baym M. RNA-guided nucleases enable a gene drive of insertion sequences in plasmids [Internet]. 2025 [cited 2025 Apr 7]. Available from: http://biorxiv.org/lookup/doi/10.1101/2025.02.20.638934 PMCID: PMC11870625
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Rossine F, Sanchez C, Eaton D, Paulsson J, Baym M. Intracellular competition shapes plasmid population dynamics [Internet]. bioRxiv; 2025 [cited 2025 Apr 7]. Available from: http://biorxiv.org/lookup/doi/10.1101/2025.02.19.639193 PMCID: PMC11870584
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Rendo V, Lee EQ, Bossi C, Khuu N, Rudek MA, Pal S, Azazmeh N, Rashid R, Lin JR, Cusick M, Reynolds ARN, Fassinou ACR, Ayoub G, Malinowski S, Lapinskas E, Pisano W, Jeang J, Stopka SA, Regan MS, Spetz J, Desai A, Lieberman F, Palanichamy K, Fisher JD, Pelton K, Huang RY, Sarosiek KA, Nabors LB, Holdhoff M, Danda N, Strowd R, Desideri S, Walbert T, Ye X, Chakravarti A, Sorger PK, Santagata S, Agar NYR, Grossman SA, Alexander BM, Wen PY, Ligon KL, Beroukhim R. A window-of-opportunity trial reveals mechanisms of response and resistance to navtemadlin in patients with recurrent glioblastoma. Sci Transl Med. 2025 Feb 19;17(786):eadn6274. PMCID: PMC11994224
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Prabhakaran S, Yapp C, Baker GJ, Beyer J, Chang YH, Creason AL, Krueger R, Muhlich J, Patterson NH, Sidak K, Sudar D, Taylor AJ, Ternes L, Troidl J, Yubin X, Sokolov A, Tyson DR. Addressing persistent challenges in digital image analysis of cancer tissue: resources developed from a hackathon. Mol Oncol. 2025 Feb 10; PMID: 39927650
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Sun Y, Maggs L, Panda A, Wright SJ, Cicerchia AM, Jenney A, Perricone MD, Mills CE, Cattaneo G, Ventin M, Chen F, Rasmussen MQ, Miranda A, Revach OY, Fang J, Fu A, Bowling PJ, Sharova T, Lawless A, Sorger PK, Bardeesy N, Wang X, Flaherty KT, Boland GM, Mehta A, Sade-Feldman M, Ferrone CR, Jenkins RW. TBK1 Targeting Is Identified as a Therapeutic Strategy to Enhance CAR T-Cell Efficacy Using Patient-Derived Organotypic Tumor Spheroids. Cancer Immunol Res. 2025 Feb 3;13(2):210–228. PMCID: PMC11790382
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Spellberg B, Gilbert DN, Baym M, Bearman G, Boyles T, Casadevall A, Forrest GN, Freling S, Ghanem B, Hamilton F, Luna B, Moore J, Musher DM, Nielsen TB, Nori P, Phillips MC, Pirofski LA, Shorr AF, Tong SYC, Lee TC, McDonald EG. Sustainable solutions to the continuous threat of antimicrobial resistance. Health Aff Sch. 2025 Feb;3(2):qxaf012. PMCID: PMC11798182
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Lee EQ, Alexander BM, Romo CG, Supko JG, Agar NYR, Talebi Z, Ahluwalia MS, Desai AS, Dietrich J, Kaley TJ, Peereboom DM, Gantchev J, Baquer G, Santagata S, Takebe N, Desideri S, Fisher JD, Sims M, Ye X, Ligon KL, Nabors LB, Grossman SA, Wen PY. Phase I study of adavosertib with radiation therapy and temozolomide in newly diagnosed glioblastoma and intratumoral drug levels in recurrent glioblastoma. Clin Cancer Res. 2025 Jan 17; PMID: 39820282
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Kaul A, Souque C, Holland M, Baym M. Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics [Internet]. bioRxiv; 2025 [cited 2025 Apr 7]. Available from: http://biorxiv.org/lookup/doi/10.1101/2025.01.16.633422 PMCID: PMC11761691
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Stojanovic L, Abbotts R, Tripathi K, Coon CM, Rajendran S, Abbasi Farid E, Hostetter G, Guarnieri JW, Wallace DC, Liu S, Wan J, Calendo G, Marker R, Gohari Z, Inayatullah MMA, Tiwari VK, Kader T, Santagata S, Drapkin R, Kommoss S, Pfisterer J, Konecny GE, Coopergard R, Issa JPJ, Winterhoff BJN, Topper MJ, Sandusky GE, Miller KD, Baylin SB, Nephew KP, Rassool FV. ZNFX1 functions as a master regulator of epigenetically induced pathogen mimicry and inflammasome signaling in cancer. Cancer Res. 2025 Jan 13; PMID: 39804147
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MacDonald JA, Bradshaw GA, Jochems F, Bernards R, Letai A. Apoptotic priming in senescence predicts specific senolysis by quantitative analysis of mitochondrial dependencies. Cell Death Differ. 2025 Jan 6; PMID: 39762561
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Morth E, Sidak K, Maliga Z, Moller T, Gehlenborg N, Sorger P, Pfister H, Beyer J, Kruger R. Cell2Cell: Explorative Cell Interaction Analysis in Multi-Volumetric Tissue Data. IEEE Trans Vis Comput Graph. 2025 Jan;31(1):569–579. PMCID: PMC11875984
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Oka T, Hasegawa T, Lee T, Oliver-Garcia VS, Mortaja M, Azin M, Horiba S, Smith SS, Khattab S, Trerice KE, Chen ST, Semenov YR, Demehri S. Langerhans Cells Directly Interact with Resident T Cells in the Human Epidermis. JID Innov. 2025 Jan;5(1):100324. PMCID: PMC11720605
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Mollaoglu G, Tepper A, Falcomatà C, Potak HT, Pia L, Amabile A, Mateus-Tique J, Rabinovich N, Park MD, LaMarche NM, Brody R, Browning L, Lin JR, Zamarin D, Sorger PK, Santagata S, Merad M, Baccarini A, Brown BD. Ovarian cancer-derived IL-4 promotes immunotherapy resistance. Cell. 2024 Dec 26;187(26):7492-7510.e22. PMCID: PMC11682930
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Kader T, Lin JR, Hug CB, Coy S, Chen YA, de Bruijn I, Shih N, Jung E, Pelletier RJ, Lopez Leon M, Mingo G, Omran DK, Lee JS, Yapp C, Satravada BA, Kundra R, Xu Y, Chan S, Tefft JB, Muhlich JL, Kim SH, Gysler SM, Agudo J, Heath JR, Schultz N, Drescher CW, Sorger PK, Drapkin R, Santagata S. Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma. Cancer Discov. 2024 Dec 20; PMID: 39704522
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Girnius N, Henstridge AZ, Marks B, Yu JK, Gray GK, Sander C, Zervantonakis IK, Luna A. Cilengitide sensitivity is predicted by overall integrin expression in breast cancer. Breast Cancer Res. 2024 Dec 20;26(1):187. PMCID: PMC11660856
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Letai A, de The H. Conventional chemotherapy: millions of cures, unresolved therapeutic index. Nat Rev Cancer. 2024 Dec 16; PMID: 39681637
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Yu WW, Barrett JNP, Tong J, Lin MJ, Marohn M, Devlin JC, Herrera A, Remark J, Levine J, Liu PK, Fang V, Zellmer AM, Oldridge DA, Wherry EJ, Lin JR, Chen JY, Sorger P, Santagata S, Krueger JG, Ruggles KV, Wang F, Su C, Koralov SB, Wang J, Chiu ES, Lu CP. Skin immune-mesenchymal interplay within tertiary lymphoid structures promotes autoimmunepathogenesis in hidradenitis suppurativa. Immunity. 2024 Dec 10;57(12):2827-2842.e5. PMID: 39662091
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Launonen IM, Niemiec I, Hincapié-Otero M, Erkan EP, Junquera A, Afenteva D, Falco MM, Liang Z, Salko M, Chamchougia F, Szabo A, Perez-Villatoro F, Li Y, Micoli G, Nagaraj A, Haltia UM, Kahelin E, Oikkonen J, Hynninen J, Virtanen A, Nirmal AJ, Vallius T, Hautaniemi S, Sorger PK, Vähärautio A, Färkkilä A. Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer. Cancer Cell. 2024 Dec 9;42(12):2045-2063.e10. PMID: 39658541
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Loi P, Schade AE, Rodriguez CL, Krishnan A, Perurena N, Nguyen VTM, Xu Y, Watanabe M, Davis RA, Gardner A, Pilla NF, Mattioli K, Popow O, Gunduz N, Lannagan TRM, Fitzgerald S, Sicinska ET, Lin JR, Tan W, Brais LK, Haigis KM, Giannakis M, Ng K, Santagata S, Helin K, Sansom OJ, Cichowski K. Epigenetic and Oncogenic Inhibitors Cooperatively Drive Differentiation and Kill KRAS-Mutant Colorectal Cancers. Cancer Discov. 2024 Dec 2;14(12):2430–2449. PMCID: PMC11609823
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Tobochnik S, Regan MS, Dorotan MKC, Reich D, Lapinskas E, Hossain MA, Stopka S, Meredith DM, Santagata S, Murphy MM, Arnaout O, Bi WL, Chiocca EA, Golby AJ, Mooney MA, Smith TR, Ligon KL, Wen PY, Agar NYR, Lee JW. Pilot Trial of Perampanel on Peritumoral Hyperexcitability in Newly Diagnosed High-grade Glioma. Clin Cancer Res. 2024 Dec 2;30(23):5365–5373. PMCID: PMC11611619
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Baker GJ, Novikov E, Zhao Z, Vallius T, Davis JA, Lin JR, Muhlich JL, Mittendorf EA, Santagata S, Guerriero JL, Sorger PK. Quality control for single-cell analysis of high-plex tissue profiles using CyLinter. Nat Methods. 2024 Dec;21(12):2248–2259. PMCID: PMC11621021
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Shimada K, Michaud DE, Cui YX, Zheng K, Goldberg J, Ju Z, Schnitt SJ, Pastorello R, Kania LD, Hoffer J, Muhlich JL, Hyun N, Krueger R, Gottlieb A, Nelson A, Wanderley CW, Antonellis G, McAllister SS, Tolaney SM, Waks AG, Jeselsohn R, Sorger PK, Agudo J, Mittendorf EA, Guerriero JL. An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer. bioRxiv; 2024. PMCID: PMC11623498
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Rand EA, Owen SV, Quinones-Olvera N, Jean KDC, Hernandez-Perez C, Baym M. Phage DisCo: targeted discovery of bacteriophages by co-culture [Internet]. bioRxiv; 2024 [cited 2024 Dec 5]. Available from: https://www.biorxiv.org/content/10.1101/2024.11.22.624878v1
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Vaelli P, Fujita A, Jo S, Zhang HXB, Osorno T, Ma X, Bean BP. State-Dependent Inhibition of Nav1.8 Sodium Channels by VX-150 and VX-548. Mol Pharmacol. 2024 Nov 18;106(6):298–308. PMCID: PMC11585256
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Souque C, González Ojeda I, Baym M. From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance. Annu Rev Microbiol. 2024 Nov;78(1):361–382. PMID: 39141706
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Schade AE, Perurena N, Yang Y, Rodriguez CL, Krishnan A, Gardner A, Loi P, Xu Y, Nguyen VTM, Mastellone GM, Pilla NF, Watanabe M, Ota K, Davis RA, Mattioli K, Xiang D, Zoeller JJ, Lin JR, Morganti S, Garrido-Castro AC, Tolaney SM, Li Z, Barbie DA, Sorger PK, Helin K, Santagata S, Knott SRV, Cichowski K. AKT and EZH2 inhibitors kill TNBCs by hijacking mechanisms of involution. Nature. 2024 Nov;635(8039):755–763. PMCID: PMC11578877
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Lu D, Faizi M, Drown B, Simerzin A, François J, Bradshaw G, Kelleher N, Jambhekar A, Gunawardena J, Lahav G. Temporal regulation of gene expression through integration of p53 dynamics and modifications. Sci Adv. 2024 Oct 25;10(43):eadp2229. PMCID: PMC11506164
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Ji W, Du G, Jiang J, Lu W, Mills CE, Yuan L, Jiang F, He Z, Bradshaw GA, Chung M, Jiang Z, Byun WS, Hinshaw SM, Zhang T, Gray NS. Discovery of bivalent small molecule degraders of cyclin-dependent kinase 7 (CDK7). Eur J Med Chem. 2024 Oct 5;276:116613. PMCID: PMC11316633
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Wala J, de Bruijn I, Coy S, Gagné A, Chan S, Chen YA, Hoffer J, Muhlich J, Schultz N, Santagata S, Sorger PK. Integrating spatial profiles and cancer genomics to identify immune-infiltrated mismatch repair proficient colorectal cancers. bioRxiv; 2024. PMCID: PMC11463659
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Minichetti DG, Boyd A, Lemire E, Hacker J, Haber AL, Roditi RE, Albers MW, Lee S, Buchheit KM, Laidlaw TM, Bankova LG. Determinants of Persistence and Recovery of Chronic COVID19 Chemosensory Dysfunction. J Allergy Clin Immunol. 2024 Sep 11;S0091-6749(24)00913–8. PMID: 39270802
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Conger KO, Chidley C, Ozgurses ME, Zhao H, Kim Y, Semina SE, Burns P, Rawat V, Lietuvninkas L, Sheldon R, Ben-Sahra I, Frasor J, Sorger PK, DeNicola GM, Coloff JL. ASCT2 is a major contributor to serine uptake in cancer cells. Cell Rep. 2024 Aug 27;43(8):114552. PMCID: PMC11406281
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Ghosh HS, Patel RV, Woodward E, Greenwald NF, Bhave VM, Maury EA, Cello G, Hoffman SE, Li Y, Gupta H, Youssef G, Spurr LF, Vogelzang J, Touat M, Dubois F, Cherniack AD, Guo X, Tavakol S, Cioffi G, Lindeman NI, Ligon AH, Chiocca EA, Reardon DA, Wen PY, Meredith D, Santagata S, Barnholtz-Sloan JS, Ligon KL, Beroukhim R, Bi WL. Contemporary Prognostic Signatures and Refined Risk Stratification of Gliomas: An Analysis of 4,400 Tumors. Neuro Oncol. 2024 Aug 21;noae164. PMID: 39164213
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Do BT, Hsu PP, Vermeulen SY, Wang Z, Hirz T, Abbott KL, Aziz N, Replogle JM, Bjelosevic S, Paolino J, Nelson SA, Block S, Darnell AM, Ferreira R, Zhang H, Milosevic J, Schmidt DR, Chidley C, Harris IS, Weissman JS, Pikman Y, Stegmaier K, Cheloufi S, Su XA, Sykes DB, Vander Heiden MG. Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress. Dev Cell. 2024 Aug 19;59(16):2203-2221.e15. PMID: 38823395
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Sarfraz I, Wang Y, Shastry A, Teh WK, Sokolov A, Herb BR, Creasy HH, Virshup I, Dries R, Degatano K, Mahurkar A, Schnell DJ, Madrigal P, Hilton J, Gehlenborg N, Tickle T, Campbell JD. MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data. Genome Biol. 2024 Aug 1;25(1):205. PMCID: PMC11292877
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Ahdritz G, Bouatta N, Floristean C, Kadyan S, Xia Q, Gerecke W, O’Donnell TJ, Berenberg D, Fisk I, Zanichelli N, Zhang B, Nowaczynski A, Wang B, Stepniewska-Dziubinska MM, Zhang S, Ojewole A, Guney ME, Biderman S, Watkins AM, Ra S, Lorenzo PR, Nivon L, Weitzner B, Ban YEA, Chen S, Zhang M, Li C, Song SL, He Y, Sorger PK, Mostaque E, Zhang Z, Bonneau R, AlQuraishi M. OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization. Nat Methods. 2024 Aug;21(8):1514–1524. PMCID: PMC11645889