209 results on '"Sellers WR"'
Search Results
2. Ascending aortic blood flow dynamics following intense exercise
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Sellers Wr and Kilgour Rd
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Adult ,Male ,medicine.medical_specialty ,Hemodynamics ,Physical Therapy, Sports Therapy and Rehabilitation ,Physical exercise ,Oxygen Consumption ,medicine.artery ,Internal medicine ,Ascending aorta ,medicine ,Humans ,Orthopedics and Sports Medicine ,Respiratory system ,Exercise ,Aorta ,business.industry ,VO2 max ,Blood flow ,Surgery ,medicine.anatomical_structure ,Cardiology ,business ,Anaerobic exercise ,Blood Flow Velocity ,Blood vessel - Abstract
The purpose of this study was to compare and contrast aortic blood flow kinetics during recovery from intense aerobic (maximal oxygen uptake test) and anaerobic (Wingate anaerobic power test) exercise. Fifteen healthy male subjects (VO2max = 56.1 +/- 5.8 mk/kg/min) participated in this study. Beat-to-beat peak aortic blood flow velocity (pkV) and acceleration (pkA) measurements were obtained by placing a 3.0 MHz continuous-wave ultrasonic transducer on the suprasternal notch at rest and during recovery (immediately post-exercise, 2.5 min, and 5.0 min) following the two exercise conditions. Peak velocity and acceleration significantly increased (p less than 0.01) from rest to immediately post-exercise and remained elevated throughout the 5-min recovery period. No differences were observed between the aerobic and anaerobic tests. Stroke distance significantly declined (p less than 0.01) immediately following exercise and progressively rose during the 5-min recovery period. The results indicate that: 1) aortic blood flow kinetics remained elevated during short-term recovery, and 2) intense aerobic and anaerobic exercise exhibit similar post-exercise aortic blood flow kinetics.
- Published
- 1990
3. Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors.
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Mellinghoff IK, Wang MY, Vivanco I, Haas-Kogan DA, Zhu S, Dia EQ, Lu KV, Yoshimoto K, Huang JH, Chute DJ, Riggs BL, Horvath S, Liau LM, Cavenee WK, Rao PN, Beroukhim R, Peck TC, Lee JC, Sellers WR, and Stokoe D
- Abstract
Background: The epidermal growth factor receptor (EGFR) is frequently amplified, overexpressed, or mutated in glioblastomas, but only 10 to 20 percent of patients have a response to EGFR kinase inhibitors. The mechanism of responsiveness of glioblastomas to these inhibitors is unknown.Methods: We sequenced kinase domains in the EGFR and human EGFR type 2 (Her2/neu) genes and analyzed the expression of EGFR, EGFR deletion mutant variant III (EGFRvIII), and the tumor-suppressor protein PTEN in recurrent malignant gliomas from patients who had received EGFR kinase inhibitors. We determined the molecular correlates of clinical response, validated them in an independent data set, and identified effects of the molecular abnormalities in vitro.Results: Of 49 patients with recurrent malignant glioma who were treated with EGFR kinase inhibitors, 9 had tumor shrinkage of at least 25 percent. Pretreatment tissue was available for molecular analysis from 26 patients, 7 of whom had had a response and 19 of whom had rapid progression during therapy. No mutations in EGFR or Her2/neu kinase domains were detected in the tumors. Coexpression of EGFRvIII and PTEN was significantly associated with a clinical response (P<0.001; odds ratio, 51; 95 percent confidence interval, 4 to 669). These findings were validated in 33 patients who received similar treatment for glioblastoma at a different institution (P=0.001; odds ratio, 40; 95 percent confidence interval, 3 to 468). In vitro, coexpression of EGFRvIII and PTEN sensitized glioblastoma cells to erlotinib.Conclusions: Coexpression of EGFRvIII and PTEN by glioblastoma cells is associated with responsiveness to EGFR kinase inhibitors. [ABSTRACT FROM AUTHOR]- Published
- 2005
4. Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates.
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Huang HT, Lumpkin RJ, Tsai RW, Su S, Zhao X, Xiong Y, Chen J, Mageed N, Donovan KA, Fischer ES, and Sellers WR
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- Humans, Substrate Specificity, HEK293 Cells, Von Hippel-Lindau Tumor Suppressor Protein metabolism, Proteolysis, Ubiquitin-Protein Ligases metabolism, Ubiquitin-Protein Ligases chemistry, Ubiquitination, Ubiquitin metabolism, Ubiquitin chemistry, Biotinylation
- Abstract
Protein ubiquitylation controls diverse processes within eukaryotic cells, including protein degradation, and is often dysregulated in disease. Moreover, small-molecule degraders that redirect ubiquitylation activities toward disease targets are an emerging and promising therapeutic class. Over 600 E3 ubiquitin ligases are expressed in humans, but their substrates remain largely elusive, necessitating the development of new methods for their discovery. Here we report the development of E3-substrate tagging by ubiquitin biotinylation (E-STUB), a ubiquitin-specific proximity labeling method that biotinylates ubiquitylated substrates in proximity to an E3 ligase of interest. E-STUB accurately identifies the direct ubiquitylated targets of protein degraders, including collateral targets and ubiquitylation events that do not lead to substrate degradation. It also detects known substrates of E3 ligase CRBN and VHL with high specificity. With the ability to elucidate proximal ubiquitylation events, E-STUB may facilitate the development of proximity-inducing therapeutics and act as a generalizable method for E3-substrate mapping., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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- 2024
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5. Editor's Note: Androgen-Induced Differentiation and Tumorigenicity of Human Prostate Epithelial Cells.
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Berger R, Febbo PG, Majumder PK, Zhao JJ, Mukherjee S, Signoretti S, Thirza Campbell K, Sellers WR, Roberts TM, Loda M, Golub TR, and Hahn WC
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- 2024
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6. Generation of a biliary tract cancer cell line atlas reveals molecular subtypes and therapeutic targets.
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Vijay V, Karisani N, Shi L, Hung YH, Vu P, Kattel P, Kenney L, Merritt J, Adil R, Wu Q, Zhen Y, Morris R, Kreuzer J, Kathiresan M, Herrera Lopez XI, Ellis H, Gritti I, Lecorgne L, Farag I, Popa A, Shen W, Kato H, Xu Q, Balasooriya ER, Wu MJ, Chaturantabut S, Kelley RK, Cleary JM, Lawrence MS, Root D, Benes CH, Deshpande V, Juric D, Sellers WR, Ferrone CR, Haas W, Vazquez F, Getz G, and Bardeesy N
- Abstract
Biliary tract cancers (BTCs) are a group of deadly malignancies encompassing intrahepatic and extrahepatic cholangiocarcinoma, gallbladder carcinoma, and ampullary carcinoma. Here, we present the integrative analysis of 63 BTC cell lines via multi-omics clustering and genome- scale CRISPR screens, providing a platform to illuminate BTC biology and inform therapeutic development. We identify dependencies broadly enriched in BTC compared to other cancers as well as dependencies selective to the anatomic subtypes. Notably, cholangiocarcinoma cell lines are stratified into distinct lineage subtypes based on biliary or dual biliary/hepatocyte marker signatures, associated with dependency on specific lineage survival factors. Transcriptional analysis of patient specimens demonstrates the prognostic significance of these lineage subtypes. Additionally, we delineate strategies to enhance targeted therapies or to overcome resistance in cell lines with key driver gene mutations. Furthermore, clustering based on dependencies and proteomics data elucidates unexpected functional relationships, including a BTC subgroup with partial squamous differentiation. Thus, this cell line atlas reveals potential therapeutic targets in molecularly defined BTCs, unveils biologically distinct disease subtypes, and offers a vital resource for BTC research.
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- 2024
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7. A Prostatic Intraepithelial Neoplasia-Dependent p27Kip1 Checkpoint Induces Senescence and Inhibits Cell Proliferation and Cancer Progression.
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Majumder PK, Grisanzio C, O'Connell F, Barry M, Brito JM, Xu Q, Guney I, Berger R, Herman P, Bikoff R, Fedele G, Baek WK, Wang S, Ellwood-Yen K, Wu H, Sawyers CL, Signoretti S, Hahn WC, Loda M, and Sellers WR
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- Humans, Male, Animals, Disease Progression, Mice, Cell Line, Tumor, Cell Cycle Checkpoints drug effects, Cyclin-Dependent Kinase Inhibitor p27 metabolism, Cyclin-Dependent Kinase Inhibitor p27 genetics, Cell Proliferation drug effects, Prostatic Neoplasms pathology, Prostatic Neoplasms metabolism, Prostatic Neoplasms genetics, Prostatic Neoplasms drug therapy, Cellular Senescence drug effects, Prostatic Intraepithelial Neoplasia pathology, Prostatic Intraepithelial Neoplasia metabolism, Prostatic Intraepithelial Neoplasia genetics
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- 2024
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8. Author Correction: Systematic profiling of conditional pathway activation identifies context-dependent synthetic lethalities.
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Chang L, Jung NY, Atari A, Rodriguez DJ, Kesar D, Song TY, Rees MG, Ronan M, Li R, Ruiz P, Chaturantabut S, Ito T, van Tienen LM, Tseng YY, Roth JA, and Sellers WR
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- 2024
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9. Systematic profiling of conditional pathway activation identifies context-dependent synthetic lethalities.
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Chang L, Jung NY, Atari A, Rodriguez DJ, Kesar D, Song TY, Rees MG, Ronan M, Li R, Ruiz P, Chaturantabut S, Ito T, van Tienen LM, Tseng YY, Roth JA, and Sellers WR
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- Humans, Phosphatidylinositol 3-Kinases, beta Catenin genetics, Wnt Signaling Pathway genetics, Cell Proliferation, Cell Line, Tumor, Colorectal Neoplasms pathology
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The paradigm of cancer-targeted therapies has focused largely on inhibition of critical pathways in cancer. Conversely, conditional activation of signaling pathways as a new source of selective cancer vulnerabilities has not been deeply characterized. In this study, we sought to systematically identify context-specific gene-activation-induced lethalities in cancer. To this end, we developed a method for gain-of-function genetic perturbations simultaneously across ~500 barcoded cancer cell lines. Using this approach, we queried the pan-cancer vulnerability landscape upon activating ten key pathway nodes, revealing selective activation dependencies of MAPK and PI3K pathways associated with specific biomarkers. Notably, we discovered new pathway hyperactivation dependencies in subsets of APC-mutant colorectal cancers where further activation of the WNT pathway by APC knockdown or direct β-catenin overexpression led to robust antitumor effects in xenograft and patient-derived organoid models. Together, this study reveals a new class of conditional gene-activation dependencies in cancer., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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- 2023
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10. Integrated CRISPR screening and drug profiling identifies combination opportunities for EGFR, ALK, and BRAF/MEK inhibitors.
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Tiedt R, King FJ, Stamm C, Niederst MJ, Delach S, Zumstein-Mecker S, Meltzer J, Mulford IJ, Labrot E, Engstler BS, Baltschukat S, Kerr G, Golji J, Wyss D, Schnell C, Ainscow E, Engelman JA, Sellers WR, Barretina J, Caponigro G, and Porta DG
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- Humans, Proto-Oncogene Proteins B-raf genetics, Clustered Regularly Interspaced Short Palindromic Repeats genetics, Neoplasm Recurrence, Local genetics, Protein Kinase Inhibitors pharmacology, Protein Kinase Inhibitors therapeutic use, ErbB Receptors genetics, Receptor Protein-Tyrosine Kinases genetics, Mitogen-Activated Protein Kinase Kinases genetics, Mutation, Cell Line, Tumor, Carcinoma, Non-Small-Cell Lung drug therapy, Carcinoma, Non-Small-Cell Lung genetics, Carcinoma, Non-Small-Cell Lung pathology, Lung Neoplasms drug therapy, Lung Neoplasms genetics, Lung Neoplasms pathology
- Abstract
Anti-tumor efficacy of targeted therapies is variable across patients and cancer types. Even in patients with initial deep response, tumors are typically not eradicated and eventually relapse. To address these challenges, we present a systematic screen for targets that limit the anti-tumor efficacy of EGFR and ALK inhibitors in non-small cell lung cancer and BRAF/MEK inhibitors in colorectal cancer. Our approach includes genome-wide CRISPR screens with or without drugs targeting the oncogenic driver ("anchor therapy"), and large-scale pairwise combination screens of anchor therapies with 351 other drugs. Interestingly, targeting of a small number of genes, including MCL1, BCL2L1, and YAP1, sensitizes multiple cell lines to the respective anchor therapy. Data from drug combination screens with EGF816 and ceritinib indicate that dasatinib and agents disrupting microtubules act synergistically across many cell lines. Finally, we show that a higher-order-combination screen with 26 selected drugs in two resistant EGFR-mutant lung cancer cell lines identified active triplet combinations., Competing Interests: Declaration of interests All authors are or have been employees and shareholders of Novartis. During the preparation of the manuscript, W.R.S. was a Board or SAB member and equity holder in Peloton Therapeutics, Ideaya Biosciences, Civetta Therapeutics, Scorpion Therapeutics, and Bluebird Bio and has consulted for Array, Astex, Dynamo Therapeutics, Ipsen, PearlRiver Bio, Sanofi, and Servier, and receives research funding from Pfizer Pharmaceuticals, Merck, Ideaya Biosciences, Boehringer-Ingelheim, and Deerfield Management., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)
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- 2023
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11. The next big questions in cancer research.
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Loi S, Settleman J, Joyce JA, Pramesh CS, Bernards R, Fan J, Merchant JL, Moslehi J, and Sellers WR
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- Humans, Carcinogenesis, Quality of Life, Research, Biomarkers, Tumor blood, Neoplasms blood, Neoplasms pathology, Neoplasms therapy, Research Personnel
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Our understanding of tumorigenesis and cancer progression as well as clinical therapies for different cancer types have evolved dramatically in recent years. However, even with this progress, there are big challenges for scientists and oncologists to tackle, ranging from unpacking the molecular and cellular mechanisms involved to therapeutics and biomarker development to quality of life in the aftermath of therapy. In this article, we asked researchers to comment on the questions that they think are important to address in the coming years., Competing Interests: Declaration of interests R.B. is a shareholder of Agendia and Oncosence, is a member of the board of directors for and has received research funding from Lixte Biotechnology holdings, and receives research funding from Heparegenix GmbH. J.A.J. has received honoraria for speaking at research symposia organized by Bristol Meyers Squibb and Glenmark Pharmaceuticals and currently serves on the scientific advisory board of Pionyr Immunotherapeutics. S.L. receives research funding to her institution from Novartis, Bristol Meyers Squibb, Merck, Puma Biotechnology, Eli Lilly, Nektar Therapeutics, Astra Zeneca, and Seattle Genetics; has acted as consultant (not compensated) to Seattle Genetics, Novartis, Bristol Meyers Squibb, Merck, AstraZeneca, Eli Lilly, Pfizer, Gilead Therapeutics, and Roche-Genentech; and has acted as consultant (paid to her institution) to Aduro Biotech, Novartis, GlaxoSmithKline, Roche-Genentech, Astra Zeneca, Silverback Therapeutics, G1 Therapeutics, PUMA Biotechnologies, Pfizer, Gilead Therapeutics, Seattle Genetics, Daiichi Sankyo, Merck, Amunix, Tallac Therapeutics, Eli Lilly, and Bristol Meyers Squibb. S.L. is supported by the National Breast Cancer Foundation of Australia Endowed Chair and the Breast Cancer Research Foundation, New York. J.M. has served on advisory boards for Bristol-Myers Squibb, Takeda, AstraZeneca, Myovant, Kurome Therapeutics, Kiniksa Pharmaceuticals, Daiichi Sankyo, CRC Oncology, BeiGene, Prelude Therapeutics, TransThera Sciences, and Cytokinetics. J.M. is supported by the NIH (R01HL141466, R01HL155990, R01HL156021, and R01HL160688). J.M. has patents pending related to the treatment of immune-related adverse events including ICI-myocarditis. W.R.S. is a Board or SAB member and holds equity in Ideaya Biosciences, Civetta Therapeutics, Red Ridge Bio, 2Seventy Bio, and Scorpion Therapeutics; has consulted for Array, Astex, Epidarex Capital, Ipsen, Merck Pharmaceuticals, Pierre Fabre, Sanofi, Servier, and Syndax Pharmaceuticals; and receives research funding from Pfizer, Merck, Bristol-Myers, Boehringer-Ingelheim, Ideaya Biosciences, Calico Biosciences, and Ridgeline Discovery. W.R.S. is a co-patent holder on EGFR mutation diagnostic patents. J.S. is an employee of Pfizer, Inc., (Copyright © 2023 Elsevier Inc. All rights reserved.)
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- 2023
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12. Systematic profiling of conditional degron tag technologies for target validation studies.
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Bondeson DP, Mullin-Bernstein Z, Oliver S, Skipper TA, Atack TC, Bick N, Ching M, Guirguis AA, Kwon J, Langan C, Millson D, Paolella BR, Tran K, Wie SJ, Vazquez F, Tothova Z, Golub TR, Sellers WR, and Ianari A
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- Kinetics, Proteolysis
- Abstract
Conditional degron tags (CDTs) are a powerful tool for target validation that combines the kinetics and reversible action of pharmacological agents with the generalizability of genetic manipulation. However, successful design of a CDT fusion protein often requires a prolonged, ad hoc cycle of construct design, failure, and re-design. To address this limitation, we report here a system to rapidly compare the activity of five unique CDTs: AID/AID2, IKZF3d, dTAG, HaloTag, and SMASh. We demonstrate the utility of this system against 16 unique protein targets. We find that expression and degradation are highly dependent on the specific CDT, the construct design, and the target. None of the CDTs leads to efficient expression and/or degradation across all targets; however, our systematic approach enables the identification of at least one optimal CDT fusion for each target. To enable the adoption of CDT strategies more broadly, we have made these reagents, and a detailed protocol, available as a community resource., (© 2022. The Author(s).)
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- 2022
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13. Comparative optimization of combinatorial CRISPR screens.
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Li R, Klingbeil O, Monducci D, Young MJ, Rodriguez DJ, Bayyat Z, Dempster JM, Kesar D, Yang X, Zamanighomi M, Vakoc CR, Ito T, and Sellers WR
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- RNA, Guide, CRISPR-Cas Systems genetics, Staphylococcus aureus genetics, Streptococcus pyogenes genetics, Acidaminococcus genetics, CRISPR-Cas Systems genetics
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Combinatorial CRISPR technologies have emerged as a transformative approach to systematically probe genetic interactions and dependencies of redundant gene pairs. However, the performance of different functional genomic tools for multiplexing sgRNAs vary widely. Here, we generate and benchmark ten distinct pooled combinatorial CRISPR libraries targeting paralog pairs to optimize digenic knockout screens. Libraries composed of dual Streptococcus pyogenes Cas9 (spCas9), orthogonal spCas9 and Staphylococcus aureus (saCas9), and enhanced Cas12a from Acidaminococcus were evaluated. We demonstrate a combination of alternative tracrRNA sequences from spCas9 consistently show superior effect size and positional balance between the sgRNAs as a robust combinatorial approach to profile genetic interactions of multiple genes., (© 2022. The Author(s).)
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- 2022
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14. Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers.
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Ito T, Young MJ, Li R, Jain S, Wernitznig A, Krill-Burger JM, Lemke CT, Monducci D, Rodriguez DJ, Chang L, Dutta S, Pal D, Paolella BR, Rothberg MV, Root DE, Johannessen CM, Parida L, Getz G, Vazquez F, Doench JG, Zamanighomi M, and Sellers WR
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- Cell Line, Tumor, Clustered Regularly Interspaced Short Palindromic Repeats, Enzyme Activation, GTP Phosphohydrolases genetics, Gene Knockout Techniques, Humans, Melanoma, Experimental genetics, Melanoma, Experimental therapy, Membrane Proteins genetics, Neoplasms enzymology, Neoplasms metabolism, Neoplasms therapy, Proto-Oncogene Proteins B-raf genetics, Dual Specificity Phosphatase 6 genetics, Dual-Specificity Phosphatases genetics, MAP Kinase Signaling System, Mitogen-Activated Protein Kinase Phosphatases genetics, Neoplasms genetics
- Abstract
Although single-gene perturbation screens have revealed a number of new targets, vulnerabilities specific to frequently altered drivers have not been uncovered. An important question is whether the compensatory relationship between functionally redundant genes masks potential therapeutic targets in single-gene perturbation studies. To identify digenic dependencies, we developed a CRISPR paralog targeting library to investigate the viability effects of disrupting 3,284 genes, 5,065 paralog pairs and 815 paralog families. We identified that dual inactivation of DUSP4 and DUSP6 selectively impairs growth in NRAS and BRAF mutant cells through the hyperactivation of MAPK signaling. Furthermore, cells resistant to MAPK pathway therapeutics become cross-sensitized to DUSP4 and DUSP6 perturbations such that the mechanisms of resistance to the inhibitors reinforce this mechanism of vulnerability. Together, multigene perturbation technologies unveil previously unrecognized digenic vulnerabilities that may be leveraged as new therapeutic targets in cancer., (© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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- 2021
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15. Are CRISPR Screens Providing the Next Generation of Therapeutic Targets?
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Vazquez F and Sellers WR
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- Humans, Neoplasm Proteins genetics, Neoplasms genetics, Neoplasms pathology, CRISPR-Cas Systems, Molecular Targeted Therapy, Neoplasm Proteins antagonists & inhibitors, Neoplasms therapy
- Abstract
CRISPR screens combined with molecular and genetic profiling of large panels of cell lines are helping to systematically identify cancer vulnerabilities. These large-scale screens, together with focused in vivo and isogenic cell line screens, have identified a growing number of promising targets and led directly to numerous target-specific drug discovery programs, several of which have reached clinical testing. However, systematic loss-of-function studies are still in their early stages. Genetic redundancy, the limitation of cell line models for many cancer types, and the difficulty of conducting complex in vitro and in vivo screens remain opportunities for discovery. We expect that over the next few years, efforts like the Cancer Dependency Map along with more focused screens will play a significant role in the creation of a roadmap of oncology therapeutic targets., (©2021 American Association for Cancer Research.)
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- 2021
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16. Molecular basis for substrate recruitment to the PRMT5 methylosome.
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Mulvaney KM, Blomquist C, Acharya N, Li R, Ranaghan MJ, O'Keefe M, Rodriguez DJ, Young MJ, Kesar D, Pal D, Stokes M, Nelson AJ, Jain SS, Yang A, Mullin-Bernstein Z, Columbus J, Bozal FK, Skepner A, Raymond D, LaRussa S, McKinney DC, Freyzon Y, Baidi Y, Porter D, Aguirre AJ, Ianari A, McMillan B, and Sellers WR
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- Animals, Cell Line, Tumor, Cytoplasm metabolism, Female, HCT116 Cells, HEK293 Cells, Histones metabolism, Humans, Intracellular Signaling Peptides and Proteins metabolism, Ion Channels metabolism, Male, Methylation, Mice, Mice, Nude, Nuclear Proteins metabolism, Peptides genetics, Protein Binding, Protein Processing, Post-Translational, Protein Serine-Threonine Kinases metabolism, Protein-Arginine N-Methyltransferases genetics, Spliceosomes metabolism, Protein-Arginine N-Methyltransferases metabolism, Protein-Arginine N-Methyltransferases physiology
- Abstract
PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP-null cancers. PRMT5 uses adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1, and COPR5) and show that it is necessary and sufficient for interaction with PRMT5. We demonstrate that PRMT5 uses modular adaptor proteins containing a common binding motif for substrate recruitment, comparable with other enzyme classes such as kinases and E3 ligases. We structurally resolve the interface with PRMT5 and show via genetic perturbation that it is required for methylation of adaptor-recruited substrates including the spliceosome, histones, and ribosomal complexes. Furthermore, disruption of this site affects Sm spliceosome activity, leading to intron retention. Genetic disruption of the PRMT5-substrate adaptor interface impairs growth of MTAP-null tumor cells and is thus a site for development of therapeutic inhibitors of PRMT5., Competing Interests: Declaration of interests Materials related to this article are in a provisional patent application by the Broad Institute. W.R.S. is a board or scientific advisory board (SAB) member and holds equity in Peloton Therapeutics, Ideaya Biosciences, Civetta Therapeutics, and Bluebird bio; has consulted for Array, Astex, Dynamo Therapeutics, Ipsen, Merck Pharmaceuticals, PearlRiver Therapeutics, Sanofi, Scorpion Therapeutics, and Servier; and receives research funding from Pfizer Pharmaceuticals, Merck Pharmaceuticals, Ideaya Biosciences, and Deerfield Management. B.J.M. is an employee and equity holder of Tango Therapeutics. D. Porter is an employee and equity holder of Cedilla Therapeutics. A.J.A. has consulted for Oncorus Inc., Arrakis Therapeutics, and Merck & Company and has research funding from Mirati Therapeutics and Deerfield Management., (Copyright © 2021 Elsevier Inc. All rights reserved.)
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- 2021
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17. A highly multiplexed quantitative phosphosite assay for biology and preclinical studies.
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Keshishian H, McDonald ER 3rd, Mundt F, Melanson R, Krug K, Porter DA, Wallace L, Forestier D, Rabasha B, Marlow SE, Jane-Valbuena J, Todres E, Specht H, Robinson ML, Jean Beltran PM, Babur O, Olive ME, Golji J, Kuhn E, Burgess M, MacMullan MA, Rejtar T, Wang K, Mani DR, Satpathy S, Gillette MA, Sellers WR, and Carr SA
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- Humans, Mass Spectrometry, Phosphorylation, Signal Transduction, Phosphoproteins genetics, Phosphoproteins metabolism, Proteomics
- Abstract
Reliable methods to quantify dynamic signaling changes across diverse pathways are needed to better understand the effects of disease and drug treatment in cells and tissues but are presently lacking. Here, we present SigPath, a targeted mass spectrometry (MS) assay that measures 284 phosphosites in 200 phosphoproteins of biological interest. SigPath probes a broad swath of signaling biology with high throughput and quantitative precision. We applied the assay to investigate changes in phospho-signaling in drug-treated cancer cell lines, breast cancer preclinical models, and human medulloblastoma tumors. In addition to validating previous findings, SigPath detected and quantified a large number of differentially regulated phosphosites newly associated with disease models and human tumors at baseline or with drug perturbation. Our results highlight the potential of SigPath to monitor phosphoproteomic signaling events and to nominate mechanistic hypotheses regarding oncogenesis, response, and resistance to therapy., (© 2021 The Authors. Published under the terms of the CC BY 4.0 license.)
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- 2021
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18. Discovery of a First-in-Class Inhibitor of the PRMT5-Substrate Adaptor Interaction.
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McKinney DC, McMillan BJ, Ranaghan MJ, Moroco JA, Brousseau M, Mullin-Bernstein Z, O'Keefe M, McCarren P, Mesleh MF, Mulvaney KM, Robinson F, Singh R, Bajrami B, Wagner FF, Hilgraf R, Drysdale MJ, Campbell AJ, Skepner A, Timm DE, Porter D, Kaushik VK, Sellers WR, and Ianari A
- Subjects
- Adaptor Proteins, Signal Transducing metabolism, Dose-Response Relationship, Drug, Humans, Models, Molecular, Molecular Structure, Protein-Arginine N-Methyltransferases metabolism, Pyridazines chemical synthesis, Pyridazines chemistry, Structure-Activity Relationship, Adaptor Proteins, Signal Transducing antagonists & inhibitors, Drug Discovery, Protein-Arginine N-Methyltransferases antagonists & inhibitors, Pyridazines pharmacology
- Abstract
PRMT5 and its substrate adaptor proteins (SAPs), pICln and Riok1, are synthetic lethal dependencies in MTAP-deleted cancer cells. SAPs share a conserved PRMT5 binding motif (PBM) which mediates binding to a surface of PRMT5 distal to the catalytic site. This interaction is required for methylation of several PRMT5 substrates, including histone and spliceosome complexes. We screened for small molecule inhibitors of the PRMT5-PBM interaction and validated a compound series which binds to the PRMT5-PBM interface and directly inhibits binding of SAPs. Mode of action studies revealed the formation of a covalent bond between a halogenated pyridazinone group and cysteine 278 of PRMT5. Optimization of the starting hit produced a lead compound, BRD0639, which engages the target in cells, disrupts PRMT5-RIOK1 complexes, and reduces substrate methylation. BRD0639 is a first-in-class PBM-competitive inhibitor that can support studies of PBM-dependent PRMT5 activities and the development of novel PRMT5 inhibitors that selectively target these functions.
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- 2021
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19. Targeting pan-essential genes in cancer: Challenges and opportunities.
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Chang L, Ruiz P, Ito T, and Sellers WR
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- Drug Therapy, Humans, Treatment Outcome, Antineoplastic Agents therapeutic use, Genes, Essential genetics, Molecular Targeted Therapy methods, Neoplasms genetics, Neoplasms therapy
- Abstract
Despite remarkable successes in the clinic, cancer targeted therapy development remains challenging and the failure rate is disappointingly high. This problem is partly due to the misapplication of the targeted therapy paradigm to therapeutics targeting pan-essential genes, which can result in therapeutics whereby efficacy is attenuated by dose-limiting toxicity. Here we summarize the key features of successful chemotherapy and targeted therapy agents, and use case studies to outline recurrent challenges to drug development efforts targeting pan-essential genes. Finally, we suggest strategies to avoid previous pitfalls for ongoing and future development of pan-essential therapeutics., Competing Interests: Declaration of interests W.R.S. is a board or SAB member and holds equity in Ideaya Biosciences, Civetta Therapeutics, and Bluebird bio and has consulted for Array, Astex, Dynamo Therapeutics, Epidarex Capital, Ipsen, PearlRiver Therapeutics, Sanofi, Servier and Syndax Pharmaceuticals, and receives research funding from Pfizer Pharmaceuticals, Merck Pharmaceuticals, Ideaya Biosciences and Ridgeline Discovery. W.R.S. is a co-patent holder on EGFR mutation diagnostic patents. T.I. is an employee and shareholder of Scorpion Therapeutics., (Copyright © 2020 Elsevier Inc. All rights reserved.)
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- 2021
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20. Distinct CDK6 complexes determine tumor cell response to CDK4/6 inhibitors and degraders.
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Wu X, Yang X, Xiong Y, Li R, Ito T, Ahmed TA, Karoulia Z, Adamopoulos C, Wang H, Wang L, Xie L, Liu J, Ueberheide B, Aaronson SA, Chen X, Buchanan SG, Sellers WR, Jin J, and Poulikakos PI
- Subjects
- Cell Line, Tumor, Cyclin-Dependent Kinase 4 metabolism, Cyclin-Dependent Kinase 6, Female, HSP90 Heat-Shock Proteins, Humans, Breast Neoplasms drug therapy
- Abstract
CDK4/6 inhibitors (CDK4/6i) are effective in metastatic breast cancer, but they have been only modestly effective in most other tumor types. Here we show that tumors expressing low CDK6 rely on CDK4 function, and are exquisitely sensitive to CDK4/6i. In contrast, tumor cells expressing both CDK4 and CDK6 have increased reliance on CDK6 to ensure cell cycle progression. We discovered that CDK4/6i and CDK4/6 degraders potently bind and inhibit CDK6 selectively in tumors in which CDK6 is highly thermo-unstable and strongly associated with the HSP90/CDC37 complex. In contrast, CDK4/6i and CDK4/6 degraders are ineffective in antagonizing tumor cells expressing thermostable CDK6, due to their weaker binding to CDK6 in these cells. Thus, we uncover a general mechanism of intrinsic resistance to CDK4/6i and CDK4/6i-derived degraders and the need for novel inhibitors targeting the CDK4/6i-resistant, thermostable form of CDK6 for application as cancer therapeutics.
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- 2021
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21. Identification of TNO155, an Allosteric SHP2 Inhibitor for the Treatment of Cancer.
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LaMarche MJ, Acker M, Argintaru A, Bauer D, Boisclair J, Chan H, Chen CH, Chen YN, Chen Z, Deng Z, Dore M, Dunstan D, Fan J, Fekkes P, Firestone B, Fodor M, Garcia-Fortanet J, Fortin PD, Fridrich C, Giraldes J, Glick M, Grunenfelder D, Hao HX, Hentemann M, Ho S, Jouk A, Kang ZB, Karki R, Kato M, Keen N, Koenig R, LaBonte LR, Larrow J, Liu G, Liu S, Majumdar D, Mathieu S, Meyer MJ, Mohseni M, Ntaganda R, Palermo M, Perez L, Pu M, Ramsey T, Reilly J, Sarver P, Sellers WR, Sendzik M, Shultz MD, Slisz J, Slocum K, Smith T, Spence S, Stams T, Straub C, Tamez V Jr, Toure BB, Towler C, Wang P, Wang H, Williams SL, Yang F, Yu B, Zhang JH, and Zhu S
- Subjects
- Allosteric Regulation drug effects, Allosteric Regulation physiology, Animals, Antineoplastic Agents therapeutic use, Dogs, Enzyme Inhibitors chemistry, Enzyme Inhibitors pharmacology, Enzyme Inhibitors therapeutic use, Humans, Macaca fascicularis, Mice, Neoplasms drug therapy, Neoplasms pathology, Rats, Tumor Cells, Cultured, Xenograft Model Antitumor Assays methods, Antineoplastic Agents chemistry, Antineoplastic Agents pharmacology, Neoplasms enzymology, Protein Tyrosine Phosphatase, Non-Receptor Type 11 antagonists & inhibitors, Protein Tyrosine Phosphatase, Non-Receptor Type 11 metabolism
- Abstract
SHP2 is a nonreceptor protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also plays an important role in the programed cell death pathway (PD-1/PD-L1). As an oncoprotein as well as a potential immunomodulator, controlling SHP2 activity is of high therapeutic interest. As part of our comprehensive program targeting SHP2, we identified multiple allosteric binding modes of inhibition and optimized numerous chemical scaffolds in parallel. In this drug annotation report, we detail the identification and optimization of the pyrazine class of allosteric SHP2 inhibitors. Structure and property based drug design enabled the identification of protein-ligand interactions, potent cellular inhibition, control of physicochemical, pharmaceutical and selectivity properties, and potent in vivo antitumor activity. These studies culminated in the discovery of TNO155, (3 S ,4 S )-8-(6-amino-5-((2-amino-3-chloropyridin-4-yl)thio)pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine ( 1 ), a highly potent, selective, orally efficacious, and first-in-class SHP2 inhibitor currently in clinical trials for cancer.
- Published
- 2020
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22. A Proof of Concept for Biomarker-Guided Targeted Therapy against Ovarian Cancer Based on Patient-Derived Tumor Xenografts.
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Palmer AC, Plana D, Gao H, Korn JM, Yang G, Green J, Zhang X, Velazquez R, McLaughlin ME, Ruddy DA, Kowal C, Muszynski J, Bullock C, Rivera S, Rakiec DP, Elliott G, Fordjour P, Meyer R, Loo A, Kurth E, Engelman JA, Bitter H, Sellers WR, Williams JA, and Sorger PK
- Subjects
- Antineoplastic Agents pharmacology, Carcinoma, Ovarian Epithelial drug therapy, Carcinoma, Ovarian Epithelial genetics, Carcinoma, Ovarian Epithelial mortality, Carcinoma, Ovarian Epithelial pathology, Drug Resistance, Neoplasm drug effects, Drug Resistance, Neoplasm genetics, Female, Gene Expression Regulation, Neoplastic, Humans, Kaplan-Meier Estimate, Molecular Targeted Therapy methods, Ovarian Neoplasms genetics, Ovarian Neoplasms mortality, Ovarian Neoplasms pathology, Precision Medicine, Proof of Concept Study, Antineoplastic Combined Chemotherapy Protocols pharmacology, Biomarkers, Tumor genetics, Ovarian Neoplasms drug therapy, Xenograft Model Antitumor Assays methods
- Abstract
Advanced ovarian cancers are a leading cause of cancer-related death in women and are currently treated with surgery and chemotherapy. This standard of care is often temporarily successful but exhibits a high rate of relapse, after which, treatment options are few. Here we investigate whether biomarker-guided use of multiple targeted therapies, including small molecules and antibody-drug conjugates, is a viable alternative. A panel of patient-derived ovarian cancer xenografts (PDX), similar in genetics and chemotherapy responsiveness to human tumors, was exposed to 21 monotherapies and combination therapies. Three monotherapies and one combination were found to be active in different subsets of PDX. Analysis of gene expression data identified biomarkers associated with responsiveness to each of the three targeted therapies, none of which directly inhibits an oncogenic driver. While no single treatment had as high a response rate as chemotherapy, nearly 90% of PDXs were eligible for and responded to at least one biomarker-guided treatment, including tumors resistant to standard chemotherapy. The distribution of biomarker positivity in The Cancer Genome Atlas data suggests the potential for a similar precision approach in human patients. SIGNIFICANCE: This study exploits a panel of patient-derived xenografts to demonstrate that most ovarian tumors can be matched to effective biomarker-guided treatments., (©2020 American Association for Cancer Research.)
- Published
- 2020
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23. Targeted Covalent Inhibition of Plasmodium FK506 Binding Protein 35.
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Atack TC, Raymond DD, Blomquist CA, Pasaje CF, McCarren PR, Moroco J, Befekadu HB, Robinson FP, Pal D, Esherick LY, Ianari A, Niles JC, and Sellers WR
- Abstract
FK506-binding protein 35, FKBP35, has been implicated as an essential malarial enzyme. Rapamycin and FK506 exhibit antiplasmodium activity in cultured parasites. However, due to the highly conserved nature of the binding pockets of FKBPs and the immunosuppressive properties of these drugs, there is a need for compounds that selectively inhibit FKBP35 and lack the undesired side effects. In contrast to human FKBPs, FKBP35 contains a cysteine, C106, adjacent to the rapamycin binding pocket, providing an opportunity to develop targeted covalent inhibitors of Plasmodium FKBP35. Here, we synthesize inhibitors of FKBP35, show that they directly bind FKBP35 in a model cellular setting, selectively covalently modify C106, and exhibit antiplasmodium activity in blood-stage cultured parasites., Competing Interests: The authors declare the following competing financial interest(s): W.R.S. is a Board or SAB member and holds equity in Peloton Therapeutics, Ideaya Biosciences, Civetta Therapeutics, and Bluebird and has consulted for Array, Astex, Dynamo Therapeutics, Ipsen, PearlRiver Therapeutics, Sanofi, and Servier and receives research funding from Pfizer Pharmaceuticals and Deerfield Management.
- Published
- 2020
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24. Correction: The potent and selective cyclin-dependent kinases 4 and 6 inhibitor ribociclib (LEE011) is a versatile combination partner in preclinical cancer models.
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Kim S, Tiedt R, Loo A, Horn T, Delach S, Kovats S, Haas K, Engstler BS, Cao A, Pinzon-Ortiz M, Mulford I, Acker MG, Chopra R, Brain C, Tomaso ED, Sellers WR, and Caponigro G
- Abstract
[This corrects the article DOI: 10.18632/oncotarget.26215.]., (Copyright: © 2019 Kim et al.)
- Published
- 2020
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25. Design and Discovery of N -(3-(2-(2-Hydroxyethoxy)-6-morpholinopyridin-4-yl)-4-methylphenyl)-2-(trifluoromethyl)isonicotinamide, a Selective, Efficacious, and Well-Tolerated RAF Inhibitor Targeting RAS Mutant Cancers: The Path to the Clinic.
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Ramurthy S, Taft BR, Aversa RJ, Barsanti PA, Burger MT, Lou Y, Nishiguchi GA, Rico A, Setti L, Smith A, Subramanian S, Tamez V, Tanner H, Wan L, Hu C, Appleton BA, Mamo M, Tandeske L, Tellew JE, Huang S, Yue Q, Chaudhary A, Tian H, Iyer R, Hassan AQ, Mathews Griner LA, La Bonte LR, Cooke VG, Van Abbema A, Merritt H, Gampa K, Feng F, Yuan J, Mishina Y, Wang Y, Haling JR, Vaziri S, Hekmat-Nejad M, Polyakov V, Zang R, Sethuraman V, Amiri P, Singh M, Sellers WR, Lees E, Shao W, Dillon MP, and Stuart DD
- Subjects
- Animals, Antineoplastic Agents pharmacology, Drug Design, Drug Discovery trends, Humans, Molecular Docking Simulation methods, Molecular Docking Simulation trends, Mutation drug effects, Protein Kinase Inhibitors pharmacology, Xenograft Model Antitumor Assays methods, Antineoplastic Agents chemistry, Drug Discovery methods, Mutation genetics, Protein Kinase Inhibitors chemistry, Proto-Oncogene Proteins B-raf antagonists & inhibitors, Proto-Oncogene Proteins B-raf genetics
- Abstract
Direct pharmacological inhibition of RAS has remained elusive, and efforts to target CRAF have been challenging due to the complex nature of RAF signaling, downstream of activated RAS, and the poor overall kinase selectivity of putative RAF inhibitors. Herein, we describe 15 (LXH254, Aversa, R.; et al. Int. Patent WO2014151616A1, 2014), a selective B/C RAF inhibitor, which was developed by focusing on drug-like properties and selectivity. Our previous tool compound, 3 (RAF709; Nishiguchi, G. A.; et al. J. Med. Chem. 2017 , 60 , 4969), was potent, selective, efficacious, and well tolerated in preclinical models, but the high human intrinsic clearance precluded further development and prompted further investigation of close analogues. A structure-based approach led to a pyridine series with an alcohol side chain that could interact with the DFG loop and significantly improved cell potency. Further mitigation of human intrinsic clearance and time-dependent inhibition led to the discovery of 15 . Due to its excellent properties, it was progressed through toxicology studies and is being tested in phase 1 clinical trials.
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- 2020
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26. Quantitative Proteomics of the Cancer Cell Line Encyclopedia.
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Nusinow DP, Szpyt J, Ghandi M, Rose CM, McDonald ER 3rd, Kalocsay M, Jané-Valbuena J, Gelfand E, Schweppe DK, Jedrychowski M, Golji J, Porter DA, Rejtar T, Wang YK, Kryukov GV, Stegmeier F, Erickson BK, Garraway LA, Sellers WR, and Gygi SP
- Subjects
- Cell Line, Tumor, Gene Expression Profiling methods, Humans, Mass Spectrometry methods, Microsatellite Instability, Mutation genetics, Proteomics methods, Gene Expression Regulation, Neoplastic genetics, Neoplasms metabolism, Proteome metabolism
- Abstract
Proteins are essential agents of biological processes. To date, large-scale profiling of cell line collections including the Cancer Cell Line Encyclopedia (CCLE) has focused primarily on genetic information whereas deep interrogation of the proteome has remained out of reach. Here, we expand the CCLE through quantitative profiling of thousands of proteins by mass spectrometry across 375 cell lines from diverse lineages to reveal information undiscovered by DNA and RNA methods. We observe unexpected correlations within and between pathways that are largely absent from RNA. An analysis of microsatellite instable (MSI) cell lines reveals the dysregulation of specific protein complexes associated with surveillance of mutation and translation. These and other protein complexes were associated with sensitivity to knockdown of several different genes. These data in conjunction with the wider CCLE are a broad resource to explore cellular behavior and facilitate cancer research., (Copyright © 2020 Elsevier Inc. All rights reserved.)
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- 2020
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27. FGF401, A First-In-Class Highly Selective and Potent FGFR4 Inhibitor for the Treatment of FGF19-Driven Hepatocellular Cancer.
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Weiss A, Adler F, Buhles A, Stamm C, Fairhurst RA, Kiffe M, Sterker D, Centeleghe M, Wartmann M, Kinyamu-Akunda J, Schadt HS, Couttet P, Wolf A, Wang Y, Barzaghi-Rinaudo P, Murakami M, Kauffmann A, Knoepfel T, Buschmann N, Leblanc C, Mah R, Furet P, Blank J, Hofmann F, Sellers WR, and Graus Porta D
- Subjects
- Animals, Humans, Liver Neoplasms pathology, Mice, Mice, Nude, Signal Transduction, Fibroblast Growth Factors genetics, Liver Neoplasms genetics, Liver Neoplasms therapy, Receptor, Fibroblast Growth Factor, Type 4 antagonists & inhibitors
- Abstract
Hepatocellular carcinoma (HCC) is the most common primary malignancy of the liver and it is the third leading cause of cancer-related deaths worldwide. Recently, aberrant signaling through the FGF19/FGFR4 axis has been implicated in HCC. Here, we describe the development of FGF401, a highly potent and selective, first in class, reversible-covalent small-molecule inhibitor of the kinase activity of FGFR4. FGF401 is exquisitely selective for FGFR4 versus the other FGFR paralogues FGFR1, FGFR2, FGFR3, and all other kinases in the kinome. FGF401 has excellent drug-like properties showing a robust pharmacokinetic/pharmacodynamics/efficacy relationship, driven by a fraction of time above the phospho-FGFR4 IC
90 value. FGF401 has remarkable antitumor activity in mice bearing HCC tumor xenografts and patient-derived xenograft models that are positive for FGF19, FGFR4, and KLB. FGF401 is the first FGFR4 inhibitor to enter clinical trials, and a phase I/II study is currently ongoing in HCC and other solid malignancies., (©2019 American Association for Cancer Research.)- Published
- 2019
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28. Metabolomic adaptations and correlates of survival to immune checkpoint blockade.
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Li H, Bullock K, Gurjao C, Braun D, Shukla SA, Bossé D, Lalani AA, Gopal S, Jin C, Horak C, Wind-Rotolo M, Signoretti S, McDermott DF, Freeman GJ, Van Allen EM, Schreiber SL, Stephen Hodi F, Sellers WR, Garraway LA, Clish CB, Choueiri TK, and Giannakis M
- Subjects
- Adaptation, Physiological drug effects, Aged, Antineoplastic Agents therapeutic use, Carcinoma, Renal Cell blood, Carcinoma, Renal Cell metabolism, Clinical Trials as Topic, Female, Humans, Kaplan-Meier Estimate, Kidney Neoplasms blood, Kidney Neoplasms metabolism, Kynurenine blood, Male, Melanoma blood, Melanoma metabolism, Middle Aged, Programmed Cell Death 1 Receptor antagonists & inhibitors, Programmed Cell Death 1 Receptor metabolism, Treatment Outcome, Tryptophan blood, Carcinoma, Renal Cell drug therapy, Everolimus therapeutic use, Kidney Neoplasms drug therapy, Melanoma drug therapy, Metabolomics, Nivolumab therapeutic use
- Abstract
Despite remarkable success of immune checkpoint inhibitors, the majority of cancer patients have yet to receive durable benefits. Here, in order to investigate the metabolic alterations in response to immune checkpoint blockade, we comprehensively profile serum metabolites in advanced melanoma and renal cell carcinoma patients treated with nivolumab, an antibody against programmed cell death protein 1 (PD1). We identify serum kynurenine/tryptophan ratio increases as an adaptive resistance mechanism associated with worse overall survival. This advocates for patient stratification and metabolic monitoring in immunotherapy clinical trials including those combining PD1 blockade with indoleamine 2,3-dioxygenase/tryptophan 2,3-dioxygenase (IDO/TDO) inhibitors.
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- 2019
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29. GEMINI: a variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens.
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Zamanighomi M, Jain SS, Ito T, Pal D, Daley TP, and Sellers WR
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- Bayes Theorem, Epistasis, Genetic, Clustered Regularly Interspaced Short Palindromic Repeats, Genetic Techniques, Software
- Abstract
Systems for CRISPR-based combinatorial perturbation of two or more genes are emerging as powerful tools for uncovering genetic interactions. However, systematic identification of these relationships is complicated by sample, reagent, and biological variability. We develop a variational Bayes approach (GEMINI) that jointly analyzes all samples and reagents to identify genetic interactions in pairwise knockout screens. The improved accuracy and scalability of GEMINI enables the systematic analysis of combinatorial CRISPR knockout screens, regardless of design and dimension. GEMINI is available as an open source R package on GitHub at https://github.com/sellerslab/gemini .
- Published
- 2019
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30. Capmatinib (INC280) Is Active Against Models of Non-Small Cell Lung Cancer and Other Cancer Types with Defined Mechanisms of MET Activation.
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Baltschukat S, Engstler BS, Huang A, Hao HX, Tam A, Wang HQ, Liang J, DiMare MT, Bhang HC, Wang Y, Furet P, Sellers WR, Hofmann F, Schoepfer J, and Tiedt R
- Subjects
- Animals, Benzamides, Carcinoma, Non-Small-Cell Lung genetics, Carcinoma, Non-Small-Cell Lung metabolism, Carcinoma, Non-Small-Cell Lung pathology, Cell Line, Tumor, Drug Resistance, Neoplasm drug effects, Enzyme Activation drug effects, Glioblastoma drug therapy, Glioblastoma genetics, Glioblastoma metabolism, Glioblastoma pathology, Hepatocyte Growth Factor genetics, Hepatocyte Growth Factor metabolism, Humans, Lung Neoplasms genetics, Lung Neoplasms metabolism, Lung Neoplasms pathology, Mice, Proto-Oncogene Proteins c-met antagonists & inhibitors, Proto-Oncogene Proteins c-met genetics, Stomach Neoplasms drug therapy, Stomach Neoplasms genetics, Stomach Neoplasms metabolism, Stomach Neoplasms pathology, Xenograft Model Antitumor Assays, Carcinoma, Non-Small-Cell Lung drug therapy, Drug Evaluation, Preclinical methods, Imidazoles pharmacology, Lung Neoplasms drug therapy, Protein Kinase Inhibitors pharmacology, Proto-Oncogene Proteins c-met metabolism, Triazines pharmacology
- Abstract
Purpose: The selective MET inhibitor capmatinib is being investigated in multiple clinical trials, both as a single agent and in combination. Here, we describe the preclinical data of capmatinib, which supported the clinical biomarker strategy for rational patient selection., Experimental Design: The selectivity and cellular activity of capmatinib were assessed in large cellular screening panels. Antitumor efficacy was quantified in a large set of cell line- or patient-derived xenograft models, testing single-agent or combination treatment depending on the genomic profile of the respective models., Results: Capmatinib was found to be highly selective for MET over other kinases. It was active against cancer models that are characterized by MET amplification, marked MET overexpression, MET exon 14 skipping mutations, or MET activation via expression of the ligand hepatocyte growth factor (HGF). In cancer models where MET is the dominant oncogenic driver, anticancer activity could be further enhanced by combination treatments, for example, by the addition of apoptosis-inducing BH3 mimetics. The combinations of capmatinib and other kinase inhibitors resulted in enhanced anticancer activity against models where MET activation co-occurred with other oncogenic drivers, for example EGFR activating mutations., Conclusions: Activity of capmatinib in preclinical models is associated with a small number of plausible genomic features. The low fraction of cancer models that respond to capmatinib as a single agent suggests that the implementation of patient selection strategies based on these biomarkers is critical for clinical development. Capmatinib is also a rational combination partner for other kinase inhibitors to combat MET-driven resistance., (©2019 American Association for Cancer Research.)
- Published
- 2019
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31. The landscape of cancer cell line metabolism.
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Li H, Ning S, Ghandi M, Kryukov GV, Gopal S, Deik A, Souza A, Pierce K, Keskula P, Hernandez D, Ann J, Shkoza D, Apfel V, Zou Y, Vazquez F, Barretina J, Pagliarini RA, Galli GG, Root DE, Hahn WC, Tsherniak A, Giannakis M, Schreiber SL, Clish CB, Garraway LA, and Sellers WR
- Subjects
- Animals, Asparaginase therapeutic use, Asparagine metabolism, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor antagonists & inhibitors, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor genetics, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor metabolism, Cell Line, Tumor, DNA Methylation, Female, Gene Knockdown Techniques, Humans, Kynurenine metabolism, Liver Neoplasms genetics, Liver Neoplasms metabolism, Liver Neoplasms therapy, Metabolome, Mice, Mice, Nude, Neoplasms genetics, Neoplasms therapy, Stomach Neoplasms genetics, Stomach Neoplasms metabolism, Stomach Neoplasms therapy, Neoplasms metabolism
- Abstract
Despite considerable efforts to identify cancer metabolic alterations that might unveil druggable vulnerabilities, systematic characterizations of metabolism as it relates to functional genomic features and associated dependencies remain uncommon. To further understand the metabolic diversity of cancer, we profiled 225 metabolites in 928 cell lines from more than 20 cancer types in the Cancer Cell Line Encyclopedia (CCLE) using liquid chromatography-mass spectrometry (LC-MS). This resource enables unbiased association analysis linking the cancer metabolome to genetic alterations, epigenetic features and gene dependencies. Additionally, by screening barcoded cell lines, we demonstrated that aberrant ASNS hypermethylation sensitizes subsets of gastric and hepatic cancers to asparaginase therapy. Finally, our analysis revealed distinct synthesis and secretion patterns of kynurenine, an immune-suppressive metabolite, in model cancer cell lines. Together, these findings and related methodology provide comprehensive resources that will help clarify the landscape of cancer metabolism.
- Published
- 2019
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32. Next-generation characterization of the Cancer Cell Line Encyclopedia.
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Ghandi M, Huang FW, Jané-Valbuena J, Kryukov GV, Lo CC, McDonald ER 3rd, Barretina J, Gelfand ET, Bielski CM, Li H, Hu K, Andreev-Drakhlin AY, Kim J, Hess JM, Haas BJ, Aguet F, Weir BA, Rothberg MV, Paolella BR, Lawrence MS, Akbani R, Lu Y, Tiv HL, Gokhale PC, de Weck A, Mansour AA, Oh C, Shih J, Hadi K, Rosen Y, Bistline J, Venkatesan K, Reddy A, Sonkin D, Liu M, Lehar J, Korn JM, Porter DA, Jones MD, Golji J, Caponigro G, Taylor JE, Dunning CM, Creech AL, Warren AC, McFarland JM, Zamanighomi M, Kauffmann A, Stransky N, Imielinski M, Maruvka YE, Cherniack AD, Tsherniak A, Vazquez F, Jaffe JD, Lane AA, Weinstock DM, Johannessen CM, Morrissey MP, Stegmeier F, Schlegel R, Hahn WC, Getz G, Mills GB, Boehm JS, Golub TR, Garraway LA, and Sellers WR
- Subjects
- Antineoplastic Agents pharmacology, Biomarkers, Tumor, DNA Methylation, Drug Resistance, Neoplasm, Ethnicity genetics, Gene Editing, Histones metabolism, Humans, MicroRNAs genetics, Molecular Targeted Therapy, Neoplasms metabolism, Protein Array Analysis, RNA Splicing, Cell Line, Tumor, Neoplasms genetics, Neoplasms pathology
- Abstract
Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets, and small-molecule and biological therapeutics and to identify new marker-driven cancer dependencies. To improve our understanding of the molecular features that contribute to cancer phenotypes, including drug responses, here we have expanded the characterizations of cancer cell lines to include genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cell lines from individuals of various lineages and ethnicities. Integration of these data with functional characterizations such as drug-sensitivity, short hairpin RNA knockdown and CRISPR-Cas9 knockout data reveals potential targets for cancer drugs and associated biomarkers. Together, this dataset and an accompanying public data portal provide a resource for the acceleration of cancer research using model cancer cell lines.
- Published
- 2019
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33. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P Jr, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, and Garraway LA
- Published
- 2019
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34. Dose and Schedule Determine Distinct Molecular Mechanisms Underlying the Efficacy of the p53-MDM2 Inhibitor HDM201.
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Jeay S, Ferretti S, Holzer P, Fuchs J, Chapeau EA, Wartmann M, Sterker D, Romanet V, Murakami M, Kerr G, Durand EY, Gaulis S, Cortes-Cros M, Ruetz S, Stachyra TM, Kallen J, Furet P, Würthner J, Guerreiro N, Halilovic E, Jullion A, Kauffmann A, Kuriakose E, Wiesmann M, Jensen MR, Hofmann F, and Sellers WR
- Subjects
- Animals, Antineoplastic Agents pharmacology, Apoptosis, Area Under Curve, Cell Line, Tumor, Cyclin-Dependent Kinase Inhibitor p21 metabolism, Drug Screening Assays, Antitumor, Humans, Imidazoles pharmacology, Kaplan-Meier Estimate, Maximum Tolerated Dose, Mice, Neoplasm Transplantation, Pyrimidines pharmacology, Pyrroles pharmacology, RNA, Small Interfering metabolism, Time Factors, bcl-X Protein metabolism, Antineoplastic Agents administration & dosage, Imidazoles administration & dosage, Neoplasms drug therapy, Neoplasms metabolism, Proto-Oncogene Proteins c-mdm2 antagonists & inhibitors, Pyrimidines administration & dosage, Pyrroles administration & dosage, Tumor Suppressor Protein p53 antagonists & inhibitors
- Abstract
Activation of p53 by inhibitors of the p53-MDM2 interaction is being pursued as a therapeutic strategy in p53 wild-type cancers. Here, we report distinct mechanisms by which the novel, potent, and selective inhibitor of the p53-MDM2 interaction HDM201 elicits therapeutic efficacy when applied at various doses and schedules. Continuous exposure of HDM201 led to induction of p21 and delayed accumulation of apoptotic cells. By comparison, high-dose pulses of HDM201 were associated with marked induction of PUMA and a rapid onset of apoptosis. shRNA screens identified PUMA as a mediator of the p53 response specifically in the pulsed regimen. Consistent with this, the single high-dose HDM201 regimen resulted in rapid and marked induction of PUMA expression and apoptosis together with downregulation of Bcl-xL in vivo Knockdown of Bcl-xL was identified as the top sensitizer to HDM201 in vitro , and Bcl-xL was enriched in relapsing tumors from mice treated with intermittent high doses of HDM201. These findings define a regimen-dependent mechanism by which disruption of MDM2-p53 elicits therapeutic efficacy when given with infrequent dosing. In an ongoing HDM201 trial, the observed exposure-response relationship indicates that the molecular mechanism elicited by pulse dosing is likely reproducible in patients. These data support the clinical comparison of daily and intermittent regimens of p53-MDM2 inhibitors. Significance: Pulsed high doses versus sustained low doses of the p53-MDM2 inhibitor HDM201 elicit a proapoptotic response from wild-type p53 cancer cells, offering guidance to current clinical trials with this and other drugs that exploit the activity of p53. Cancer Res; 78(21); 6257-67. ©2018 AACR ., (©2018 American Association for Cancer Research.)
- Published
- 2018
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35. TRPS1 Is a Lineage-Specific Transcriptional Dependency in Breast Cancer.
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Witwicki RM, Ekram MB, Qiu X, Janiszewska M, Shu S, Kwon M, Trinh A, Frias E, Ramadan N, Hoffman G, Yu K, Xie Y, McAllister G, McDonald R, Golji J, Schlabach M, deWeck A, Keen N, Chan HM, Ruddy D, Rejtar T, Sovath S, Silver S, Sellers WR, Jagani Z, Hogarty MD, Roberts C, Brown M, Stegmaier K, Long H, Shivdasani RA, Pellman D, and Polyak K
- Subjects
- Cell Line, Tumor, Cell Survival genetics, Female, HEK293 Cells, Humans, Mi-2 Nucleosome Remodeling and Deacetylase Complex metabolism, Protein Binding, RNA, Small Interfering metabolism, Repressor Proteins metabolism, Triple Negative Breast Neoplasms metabolism, Triple Negative Breast Neoplasms pathology, Breast Neoplasms genetics, Breast Neoplasms pathology, Cell Lineage, DNA-Binding Proteins metabolism, Transcription Factors metabolism, Transcription, Genetic
- Abstract
Perturbed epigenomic programs play key roles in tumorigenesis, and chromatin modulators are candidate therapeutic targets in various human cancer types. To define singular and shared dependencies on DNA and histone modifiers and transcription factors in poorly differentiated adult and pediatric cancers, we conducted a targeted shRNA screen across 59 cell lines of 6 cancer types. Here, we describe the TRPS1 transcription factor as a strong breast cancer-specific hit, owing largely to lineage-restricted expression. Knockdown of TRPS1 resulted in perturbed mitosis, apoptosis, and reduced tumor growth. Integrated analysis of TRPS1 transcriptional targets, chromatin binding, and protein interactions revealed that TRPS1 is associated with the NuRD repressor complex. These findings uncover a transcriptional network that is essential for breast cancer cell survival and propagation., (Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2018
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36. The potent and selective cyclin-dependent kinases 4 and 6 inhibitor ribociclib (LEE011) is a versatile combination partner in preclinical cancer models.
- Author
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Kim S, Tiedt R, Loo A, Horn T, Delach S, Kovats S, Haas K, Engstler BS, Cao A, Pinzon-Ortiz M, Mulford I, Acker MG, Chopra R, Brain C, di Tomaso E, Sellers WR, and Caponigro G
- Abstract
Inhibition of cyclin-dependent kinases 4 and 6 (CDK4/6) is associated with robust antitumor activity. Ribociclib (LEE011) is an orally bioavailable CDK4/6 inhibitor that is approved for the treatment of hormone receptor-positive, human epidermal growth factor receptor 2-negative advanced breast cancer, in combination with an aromatase inhibitor, and is currently being evaluated in several additional trials. Here, we report the preclinical profile of ribociclib. When tested across a large panel of kinase active site binding assays, ribociclib and palbociclib were highly selective for CDK4, while abemaciclib showed affinity to several other kinases. Both ribociclib and abemaciclib showed slightly higher potency in CDK4 -dependent cells than in CDK6 -dependent cells, while palbociclib did not show such a difference. Profiling CDK4/6 inhibitors in large-scale cancer cell line screens in vitro confirmed that RB1 loss of function is a negative predictor of sensitivity. We also found that routinely used cellular viability assays measuring adenosine triphosphate levels as a proxy for cell numbers underestimated the effects of CDK4/6 inhibition, which contrasts with assays that assess cell number more directly. Robust antitumor efficacy and combination benefit was detected when ribociclib was added to encorafenib, nazartinib, or endocrine therapies in patient-derived xenografts., Competing Interests: CONFLICTS OF INTEREST All authors are current or previous employees and stockholders of Novartis.
- Published
- 2018
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37. Preclinical Antitumor Activity of a Novel Anti-c-KIT Antibody-Drug Conjugate against Mutant and Wild-type c-KIT-Positive Solid Tumors.
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Abrams T, Connor A, Fanton C, Cohen SB, Huber T, Miller K, Hong EE, Niu X, Kline J, Ison-Dugenny M, Harris S, Walker D, Krauser K, Galimi F, Wang Z, Ghoddusi M, Mansfield K, Lee-Hoeflich ST, Holash J, Pryer N, Kluwe W, Ettenberg SA, Sellers WR, Lees E, Kwon P, Abraham JA, and Schleyer SC
- Subjects
- Animals, Antibodies, Anti-Idiotypic pharmacology, Cell Line, Tumor, Cell Proliferation drug effects, Drug Resistance, Neoplasm immunology, Heterografts, Humans, Imatinib Mesylate pharmacology, Immunoconjugates immunology, Mice, Mutation, Neoplasms classification, Neoplasms immunology, Neoplasms pathology, Protein Kinase Inhibitors pharmacology, Proto-Oncogene Proteins c-kit immunology, Drug Resistance, Neoplasm drug effects, Immunoconjugates pharmacology, Neoplasms drug therapy, Proto-Oncogene Proteins c-kit genetics
- Abstract
Purpose: c-KIT overexpression is well recognized in cancers such as gastrointestinal stromal tumors (GIST), small cell lung cancer (SCLC), melanoma, non-small cell lung cancer (NSCLC), and acute myelogenous leukemia (AML). Treatment with the small-molecule inhibitors imatinib, sunitinib, and regorafenib resulted in resistance (c-KIT mutant tumors) or limited activity (c-KIT wild-type tumors). We selected an anti-c-KIT ADC approach to evaluate the anticancer activity in multiple disease models. Experimental Design: A humanized anti-c-KIT antibody LMJ729 was conjugated to the microtubule destabilizing maytansinoid, DM1, via a noncleavable linker (SMCC). The activity of the resulting ADC, LOP628, was evaluated in vitro against GIST, SCLC, and AML models and in vivo against GIST and SCLC models. Results: LOP628 exhibited potent antiproliferative activity on c-KIT-positive cell lines, whereas LMJ729 displayed little to no effect. At exposures predicted to be clinically achievable, LOP628 demonstrated single administration regressions or stasis in GIST and SCLC xenograft models in mice. LOP628 also displayed superior efficacy in an imatinib-resistant GIST model. Further, LOP628 was well tolerated in monkeys with an adequate therapeutic index several fold above efficacious exposures. Safety findings were consistent with the pharmacodynamic effect of neutropenia due to c-KIT-directed targeting. Additional toxicities were considered off-target and were consistent with DM1, such as effects in the liver and hematopoietic/lymphatic system. Conclusions: The preclinical findings suggest that the c-KIT-directed ADC may be a promising therapeutic for the treatment of mutant and wild-type c-KIT-positive cancers and supported the clinical evaluation of LOP628 in GIST, AML, and SCLC patients. Clin Cancer Res; 24(17); 4297-308. ©2018 AACR ., (©2018 American Association for Cancer Research.)
- Published
- 2018
- Full Text
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38. Big Data Approaches for Modeling Response and Resistance to Cancer Drugs.
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Jiang P, Sellers WR, and Liu XS
- Abstract
Despite significant progress in cancer research, current standard-of-care drugs fail to cure many types of cancers. Hence, there is an urgent need to identify better predictive biomarkers and treatment regimes. Conventionally, insights from hypothesis-driven studies are the primary force for cancer biology and therapeutic discoveries. Recently, the rapid growth of big data resources, catalyzed by breakthroughs in high-throughput technologies, has resulted in a paradigm shift in cancer therapeutic research. The combination of computational methods and genomics data has led to several successful clinical applications. In this review, we focus on recent advances in data-driven methods to model anticancer drug efficacy, and we present the challenges and opportunities for data science in cancer therapeutic research.
- Published
- 2018
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39. Antitumor Properties of RAF709, a Highly Selective and Potent Inhibitor of RAF Kinase Dimers, in Tumors Driven by Mutant RAS or BRAF.
- Author
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Shao W, Mishina YM, Feng Y, Caponigro G, Cooke VG, Rivera S, Wang Y, Shen F, Korn JM, Mathews Griner LA, Nishiguchi G, Rico A, Tellew J, Haling JR, Aversa R, Polyakov V, Zang R, Hekmat-Nejad M, Amiri P, Singh M, Keen N, Dillon MP, Lees E, Ramurthy S, Sellers WR, and Stuart DD
- Subjects
- 2,2'-Dipyridyl pharmacology, Animals, Cell Line, Tumor, Cell Proliferation drug effects, Drug Resistance, Neoplasm drug effects, Female, Humans, MAP Kinase Kinase Kinases antagonists & inhibitors, Mice, Nude, Mutation, Protein Kinase Inhibitors pharmacology, Protein Multimerization, Xenograft Model Antitumor Assays, raf Kinases metabolism, 2,2'-Dipyridyl analogs & derivatives, Antineoplastic Agents pharmacology, Benzamides pharmacology, Proto-Oncogene Proteins B-raf genetics, raf Kinases antagonists & inhibitors, ras Proteins genetics
- Abstract
Resistance to the RAF inhibitor vemurafenib arises commonly in melanomas driven by the activated BRAF oncogene. Here, we report antitumor properties of RAF709, a novel ATP-competitive kinase inhibitor with high potency and selectivity against RAF kinases. RAF709 exhibited a mode of RAF inhibition distinct from RAF monomer inhibitors such as vemurafenib, showing equal activity against both RAF monomers and dimers. As a result, RAF709 inhibited MAPK signaling activity in tumor models harboring either BRAF
V600 alterations or mutant N- and KRAS-driven signaling, with minimal paradoxical activation of wild-type RAF. In cell lines and murine xenograft models, RAF709 demonstrated selective antitumor activity in tumor cells harboring BRAF or RAS mutations compared with cells with wild-type BRAF and RAS genes. RAF709 demonstrated a direct pharmacokinetic/pharmacodynamic relationship in in vivo tumor models harboring KRAS mutation. Furthermore, RAF709 elicited regression of primary human tumor-derived xenograft models with BRAF, NRAS, or KRAS mutations with excellent tolerability. Our results support further development of inhibitors like RAF709, which represents a next-generation RAF inhibitor with unique biochemical and cellular properties that enables antitumor activities in RAS-mutant tumors. Significance: In an effort to develop RAF inhibitors with the appropriate pharmacological properties to treat RAS mutant tumors, RAF709, a compound with potency, selectivity, and in vivo properties, was developed that will allow preclinical therapeutic hypothesis testing, but also provide an excellent probe to further unravel the complexities of RAF kinase signaling. Cancer Res; 78(6); 1537-48. ©2018 AACR ., (©2018 American Association for Cancer Research.)- Published
- 2018
- Full Text
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40. Mechanism of Action and Clinical Impact of Ribociclib-Response.
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Tripathy D, Bardia A, and Sellers WR
- Subjects
- Aminopyridines, Humans, Purines, Cyclin-Dependent Kinase 4 antagonists & inhibitors, Neoplasms
- Published
- 2017
- Full Text
- View/download PDF
41. Discovery and Optimization of HKT288, a Cadherin-6-Targeting ADC for the Treatment of Ovarian and Renal Cancers.
- Author
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Bialucha CU, Collins SD, Li X, Saxena P, Zhang X, Dürr C, Lafont B, Prieur P, Shim Y, Mosher R, Lee D, Ostrom L, Hu T, Bilic S, Rajlic IL, Capka V, Jiang W, Wagner JP, Elliott G, Veloso A, Piel JC, Flaherty MM, Mansfield KG, Meseck EK, Rubic-Schneider T, London AS, Tschantz WR, Kurz M, Nguyen D, Bourret A, Meyer MJ, Faris JE, Janatpour MJ, Chan VW, Yoder NC, Catcott KC, McShea MA, Sun X, Gao H, Williams J, Hofmann F, Engelman JA, Ettenberg SA, Sellers WR, and Lees E
- Subjects
- Animals, Antineoplastic Agents pharmacology, Cadherins genetics, Cadherins metabolism, Female, Humans, Kidney Neoplasms genetics, Kidney Neoplasms metabolism, Macaca fascicularis, Mice, Nude, Ovarian Neoplasms genetics, Ovarian Neoplasms metabolism, Rats, Xenograft Model Antitumor Assays, Antineoplastic Agents therapeutic use, Cadherins antagonists & inhibitors, Kidney Neoplasms drug therapy, Ovarian Neoplasms drug therapy
- Abstract
Despite an improving therapeutic landscape, significant challenges remain in treating the majority of patients with advanced ovarian or renal cancer. We identified the cell-cell adhesion molecule cadherin-6 ( CDH6 ) as a lineage gene having significant differential expression in ovarian and kidney cancers. HKT288 is an optimized CDH6-targeting DM4-based antibody-drug conjugate (ADC) developed for the treatment of these diseases. Our study provides mechanistic evidence supporting the importance of linker choice for optimal antitumor activity and highlights CDH6 as an antigen for biotherapeutic development. To more robustly predict patient benefit of targeting CDH6, we incorporate a population-based patient-derived xenograft (PDX) clinical trial (PCT) to capture the heterogeneity of response across an unselected cohort of 30 models-a novel preclinical approach in ADC development. HKT288 induces durable tumor regressions of ovarian and renal cancer models in vivo , including 40% of models on the PCT, and features a preclinical safety profile supportive of progression toward clinical evaluation. Significance: We identify CDH6 as a target for biotherapeutics development and demonstrate how an integrated pharmacology strategy that incorporates mechanistic pharmacodynamics and toxicology studies provides a rich dataset for optimizing the therapeutic format. We highlight how a population-based PDX clinical trial and retrospective biomarker analysis can provide correlates of activity and response to guide initial patient selection for first-in-human trials of HKT288. Cancer Discov; 7(9); 1030-45. ©2017 AACR. This article is highlighted in the In This Issue feature, p. 920 ., (©2017 American Association for Cancer Research.)
- Published
- 2017
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42. Project DRIVE: A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening.
- Author
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McDonald ER 3rd, de Weck A, Schlabach MR, Billy E, Mavrakis KJ, Hoffman GR, Belur D, Castelletti D, Frias E, Gampa K, Golji J, Kao I, Li L, Megel P, Perkins TA, Ramadan N, Ruddy DA, Silver SJ, Sovath S, Stump M, Weber O, Widmer R, Yu J, Yu K, Yue Y, Abramowski D, Ackley E, Barrett R, Berger J, Bernard JL, Billig R, Brachmann SM, Buxton F, Caothien R, Caushi JX, Chung FS, Cortés-Cros M, deBeaumont RS, Delaunay C, Desplat A, Duong W, Dwoske DA, Eldridge RS, Farsidjani A, Feng F, Feng J, Flemming D, Forrester W, Galli GG, Gao Z, Gauter F, Gibaja V, Haas K, Hattenberger M, Hood T, Hurov KE, Jagani Z, Jenal M, Johnson JA, Jones MD, Kapoor A, Korn J, Liu J, Liu Q, Liu S, Liu Y, Loo AT, Macchi KJ, Martin T, McAllister G, Meyer A, Mollé S, Pagliarini RA, Phadke T, Repko B, Schouwey T, Shanahan F, Shen Q, Stamm C, Stephan C, Stucke VM, Tiedt R, Varadarajan M, Venkatesan K, Vitari AC, Wallroth M, Weiler J, Zhang J, Mickanin C, Myer VE, Porter JA, Lai A, Bitter H, Lees E, Keen N, Kauffmann A, Stegmeier F, Hofmann F, Schmelzle T, and Sellers WR
- Subjects
- Cell Line, Tumor, Gene Library, Gene Regulatory Networks, Humans, Multiprotein Complexes metabolism, Neoplasms metabolism, Oncogenes, RNA, Small Interfering, Signal Transduction, Transcription Factors metabolism, Neoplasms genetics, Neoplasms pathology, RNA Interference
- Abstract
Elucidation of the mutational landscape of human cancer has progressed rapidly and been accompanied by the development of therapeutics targeting mutant oncogenes. However, a comprehensive mapping of cancer dependencies has lagged behind and the discovery of therapeutic targets for counteracting tumor suppressor gene loss is needed. To identify vulnerabilities relevant to specific cancer subtypes, we conducted a large-scale RNAi screen in which viability effects of mRNA knockdown were assessed for 7,837 genes using an average of 20 shRNAs per gene in 398 cancer cell lines. We describe findings of this screen, outlining the classes of cancer dependency genes and their relationships to genetic, expression, and lineage features. In addition, we describe robust gene-interaction networks recapitulating both protein complexes and functional cooperation among complexes and pathways. This dataset along with a web portal is provided to the community to assist in the discovery and translation of new therapeutic approaches for cancer., (Copyright © 2017 Elsevier Inc. All rights reserved.)
- Published
- 2017
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43. Ribociclib (LEE011): Mechanism of Action and Clinical Impact of This Selective Cyclin-Dependent Kinase 4/6 Inhibitor in Various Solid Tumors.
- Author
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Tripathy D, Bardia A, and Sellers WR
- Subjects
- Aminopyridines pharmacokinetics, Cell Cycle drug effects, Cell Proliferation drug effects, Cyclin-Dependent Kinase 4 genetics, Cyclin-Dependent Kinase 6 genetics, Humans, Neoplasms genetics, Neoplasms pathology, Protein Kinase Inhibitors therapeutic use, Purines pharmacokinetics, Signal Transduction drug effects, Treatment Outcome, Aminopyridines therapeutic use, Cyclin-Dependent Kinase 4 antagonists & inhibitors, Cyclin-Dependent Kinase 6 antagonists & inhibitors, Neoplasms drug therapy, Purines therapeutic use
- Abstract
The cyclin D-cyclin-dependent kinase (CDK) 4/6-p16-retinoblastoma (Rb) pathway is commonly disrupted in cancer, leading to abnormal cell proliferation. Therapeutics targeting this pathway have demonstrated antitumor effects in preclinical and clinical studies. Ribociclib is a selective, orally bioavailable inhibitor of CDK4 and CDK6, which received FDA approval in March 2017 and is set to enter the treatment landscape alongside other CDK4/6 inhibitors, including palbociclib and abemaciclib. Here, we describe the mechanism of action of ribociclib and review preclinical and clinical data from phase I, II, and III trials of ribociclib across different tumor types, within the context of other selective CDK4/6 inhibitors. The pharmacokinetics, pharmacodynamics, safety, tolerability, and clinical responses with ribociclib as a single agent or in combination with other therapies are discussed, and an overview of the broad portfolio of ongoing clinical trials with ribociclib across a wide range of indications is presented. On the basis of the available data, ribociclib has a manageable tolerability profile and therapeutic potential for a variety of cancer types. Its high selectivity makes it an important partner drug for other targeted therapies, and it has been shown to enhance the clinical activity of existing anticancer therapies and delay the development of treatment resistance, without markedly increasing toxicity. Ongoing trials of doublet and triplet targeted therapies containing ribociclib seek to identify optimal CDK4/6-based targeted combination regimens for various tumor types and advance the field of precision therapeutics in oncology. Clin Cancer Res; 23(13); 3251-62. ©2017 AACR ., (©2017 American Association for Cancer Research.)
- Published
- 2017
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44. Complementary activities of DOT1L and Menin inhibitors in MLL-rearranged leukemia.
- Author
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Dafflon C, Craig VJ, Méreau H, Gräsel J, Schacher Engstler B, Hoffman G, Nigsch F, Gaulis S, Barys L, Ito M, Aguadé-Gorgorió J, Bornhauser B, Bourquin JP, Proske A, Stork-Fux C, Murakami M, Sellers WR, Hofmann F, Schwaller J, and Tiedt R
- Subjects
- Animals, Apoptosis, Cell Proliferation, Drug Resistance, Neoplasm drug effects, Female, Gene Expression Regulation, Leukemic, Histone-Lysine N-Methyltransferase metabolism, Humans, Leukemia genetics, Leukemia pathology, Methyltransferases genetics, Mice, Mice, Inbred C57BL, Mice, Nude, Myeloid-Lymphoid Leukemia Protein metabolism, Tumor Cells, Cultured, Drug Resistance, Neoplasm genetics, Enzyme Inhibitors pharmacology, Gene Rearrangement, Histone-Lysine N-Methyltransferase genetics, Leukemia drug therapy, Methyltransferases metabolism, Myeloid-Lymphoid Leukemia Protein genetics, Proto-Oncogene Proteins antagonists & inhibitors, RNA, Small Interfering genetics
- Abstract
Chromosomal rearrangements of the mixed lineage leukemia (MLL/KMT2A) gene leading to oncogenic MLL-fusion proteins occur in ~10% of acute leukemias and are associated with poor clinical outcomes, emphasizing the need for new treatment modalities. Inhibition of the DOT1-like histone H3K79 methyltransferase (DOT1L) is a specific therapeutic approach for such leukemias that is currently being tested in clinical trials. However, in most MLL-rearranged leukemia models responses to DOT1L inhibitors are limited. Here, we performed deep-coverage short hairpin RNA sensitizer screens in DOT1L inhibitor-treated MLL-rearranged leukemia cell lines and discovered that targeting additional nodes of MLL complexes concomitantly with DOT1L inhibition bears great potential for superior therapeutic results. Most notably, combination of a DOT1L inhibitor with an inhibitor of the MLL-Menin interaction markedly enhanced induction of differentiation and cell killing in various MLL disease models including primary leukemia cells, while sparing normal hematopoiesis and leukemias without MLL rearrangements. Gene expression analysis on human and murine leukemic cells revealed that target genes of MLL-fusion proteins and MYC were suppressed more profoundly upon combination treatment. Our findings provide a strong rationale for a novel targeted combination therapy that is expected to improve therapeutic outcomes in patients with MLL-rearranged leukemia.
- Published
- 2017
- Full Text
- View/download PDF
45. Combined ALK and MDM2 inhibition increases antitumor activity and overcomes resistance in human ALK mutant neuroblastoma cell lines and xenograft models.
- Author
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Wang HQ, Halilovic E, Li X, Liang J, Cao Y, Rakiec DP, Ruddy DA, Jeay S, Wuerthner JU, Timple N, Kasibhatla S, Li N, Williams JA, Sellers WR, Huang A, and Li F
- Subjects
- Anaplastic Lymphoma Kinase, Animals, Antineoplastic Agents pharmacology, Cell Line, Tumor, Disease Models, Animal, Heterografts, Humans, Mice, Nude, Neoplasm Transplantation, Pyrimidines pharmacology, Pyrimidines therapeutic use, Sulfones pharmacology, Sulfones therapeutic use, Antineoplastic Agents therapeutic use, Drug Resistance, Neoplasm, Neuroblastoma drug therapy, Neuroblastoma pathology, Proto-Oncogene Proteins c-mdm2 antagonists & inhibitors, Receptor Protein-Tyrosine Kinases antagonists & inhibitors
- Abstract
The efficacy of ALK inhibitors in patients with ALK -mutant neuroblastoma is limited, highlighting the need to improve their effectiveness in these patients. To this end, we sought to develop a combination strategy to enhance the antitumor activity of ALK inhibitor monotherapy in human neuroblastoma cell lines and xenograft models expressing activated ALK. Herein, we report that combined inhibition of ALK and MDM2 induced a complementary set of anti-proliferative and pro-apoptotic proteins. Consequently, this combination treatment synergistically inhibited proliferation of TP53 wild-type neuroblastoma cells harboring ALK amplification or mutations in vitro, and resulted in complete and durable responses in neuroblastoma xenografts derived from these cells. We further demonstrate that concurrent inhibition of MDM2 and ALK was able to overcome ceritinib resistance conferred by MYCN upregulation in vitro and in vivo. Together, combined inhibition of ALK and MDM2 may provide an effective treatment for TP53 wild-type neuroblastoma with ALK aberrations.
- Published
- 2017
- Full Text
- View/download PDF
46. The allosteric inhibitor ABL001 enables dual targeting of BCR-ABL1.
- Author
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Wylie AA, Schoepfer J, Jahnke W, Cowan-Jacob SW, Loo A, Furet P, Marzinzik AL, Pelle X, Donovan J, Zhu W, Buonamici S, Hassan AQ, Lombardo F, Iyer V, Palmer M, Berellini G, Dodd S, Thohan S, Bitter H, Branford S, Ross DM, Hughes TP, Petruzzelli L, Vanasse KG, Warmuth M, Hofmann F, Keen NJ, and Sellers WR
- Subjects
- Allosteric Regulation drug effects, Animals, Catalytic Domain drug effects, Cell Proliferation drug effects, Dasatinib therapeutic use, Drug Resistance, Neoplasm drug effects, Drug Resistance, Neoplasm genetics, Drug Therapy, Combination, Fusion Proteins, bcr-abl chemistry, Fusion Proteins, bcr-abl genetics, Humans, Leukemia, Myelogenous, Chronic, BCR-ABL Positive enzymology, Leukemia, Myelogenous, Chronic, BCR-ABL Positive genetics, Leukemia, Myelogenous, Chronic, BCR-ABL Positive pathology, Mice, Mutation, Niacinamide pharmacology, Niacinamide therapeutic use, Pyrazoles therapeutic use, Pyrimidines pharmacology, Pyrimidines therapeutic use, Xenograft Model Antitumor Assays, Allosteric Site drug effects, Fusion Proteins, bcr-abl antagonists & inhibitors, Leukemia, Myelogenous, Chronic, BCR-ABL Positive drug therapy, Niacinamide analogs & derivatives, Pyrazoles pharmacology
- Abstract
Chronic myeloid leukaemia (CML) is driven by the activity of the BCR-ABL1 fusion oncoprotein. ABL1 kinase inhibitors have improved the clinical outcomes for patients with CML, with over 80% of patients treated with imatinib surviving for more than 10 years. Second-generation ABL1 kinase inhibitors induce more potent molecular responses in both previously untreated and imatinib-resistant patients with CML. Studies in patients with chronic-phase CML have shown that around 50% of patients who achieve and maintain undetectable BCR-ABL1 transcript levels for at least 2 years remain disease-free after the withdrawal of treatment. Here we characterize ABL001 (asciminib), a potent and selective allosteric ABL1 inhibitor that is undergoing clinical development testing in patients with CML and Philadelphia chromosome-positive (Ph
+ ) acute lymphoblastic leukaemia. In contrast to catalytic-site ABL1 kinase inhibitors, ABL001 binds to the myristoyl pocket of ABL1 and induces the formation of an inactive kinase conformation. ABL001 and second-generation catalytic inhibitors have similar cellular potencies but distinct patterns of resistance mutations, with genetic barcoding studies revealing pre-existing clonal populations with no shared resistance between ABL001 and the catalytic inhibitor nilotinib. Consistent with this profile, acquired resistance was observed with single-agent therapy in mice; however, the combination of ABL001 and nilotinib led to complete disease control and eradicated CML xenograft tumours without recurrence after the cessation of treatment.- Published
- 2017
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47. Resistance mechanisms to TP53-MDM2 inhibition identified by in vivo piggyBac transposon mutagenesis screen in an Arf -/- mouse model.
- Author
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Chapeau EA, Gembarska A, Durand EY, Mandon E, Estadieu C, Romanet V, Wiesmann M, Tiedt R, Lehar J, de Weck A, Rad R, Barys L, Jeay S, Ferretti S, Kauffmann A, Sutter E, Grevot A, Moulin P, Murakami M, Sellers WR, Hofmann F, and Jensen MR
- Subjects
- Allografts, Animals, Antineoplastic Agents pharmacology, Biomarkers, Tumor, Cell Transformation, Neoplastic genetics, Cell Transformation, Neoplastic metabolism, Disease Models, Animal, Genetic Drift, Humans, Kaplan-Meier Estimate, Mice, Mice, Knockout, Neoplasms genetics, Neoplasms metabolism, Neoplasms mortality, Neoplasms pathology, Proto-Oncogene Proteins c-mdm2 antagonists & inhibitors, Proto-Oncogene Proteins c-mdm2 metabolism, Tumor Suppressor Protein p53 antagonists & inhibitors, Tumor Suppressor Protein p53 metabolism, bcl-X Protein genetics, bcl-X Protein metabolism, DNA Transposable Elements, Drug Resistance, Neoplasm genetics, Genetic Vectors genetics, Mutagenesis, Insertional, Proto-Oncogene Proteins c-mdm2 genetics, Tumor Suppressor Protein p53 genetics
- Abstract
Inhibitors of double minute 2 protein (MDM2)-tumor protein 53 (TP53) interaction are predicted to be effective in tumors in which the TP53 gene is wild type, by preventing TP53 protein degradation. One such setting is represented by the frequent CDKN2A deletion in human cancer that, through inactivation of p14ARF , activates MDM2 protein, which in turn degrades TP53 tumor suppressor. Here we used piggyBac (PB) transposon insertional mutagenesis to anticipate resistance mechanisms occurring during treatment with the MDM2-TP53 inhibitor HDM201. Constitutive PB mutagenesis in Arf
- /- mice provided a collection of spontaneous tumors with characterized insertional genetic landscapes. Tumors were allografted in large cohorts of mice to assess the pharmacologic effects of HDM201. Sixteen out of 21 allograft models were sensitive to HDM201 but ultimately relapsed under treatment. A comparison of tumors with acquired resistance to HDM201 and untreated tumors identified 87 genes that were differentially and significantly targeted by the PB transposon. Resistant tumors displayed a complex clonality pattern suggesting the emergence of several resistant subclones. Among the most frequent alterations conferring resistance, we observed somatic and insertional loss-of-function mutations in transformation-related protein 53 ( Trp53 ) in 54% of tumors and transposon-mediated gain-of-function alterations in B-cell lymphoma-extra large ( Bcl-xL ), Mdm4 , and two TP53 family members, resulting in expression of the TP53 dominant negative truncations ΔNTrp63 and ΔNTrp73. Enhanced BCL-xL and MDM4 protein expression was confirmed in resistant tumors, as well as in HDM201-resistant patient-derived tumor xenografts. Interestingly, concomitant inhibition of MDM2 and BCL-xL demonstrated significant synergy in p53 wild-type cell lines in vitro. Collectively, our findings identify several potential mechanisms by which TP53 wild-type tumors may escape MDM2-targeted therapy.- Published
- 2017
- Full Text
- View/download PDF
48. High-Order Drug Combinations Are Required to Effectively Kill Colorectal Cancer Cells.
- Author
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Horn T, Ferretti S, Ebel N, Tam A, Ho S, Harbinski F, Farsidjani A, Zubrowski M, Sellers WR, Schlegel R, Porter D, Morris E, Wuerthner J, Jeay S, Greshock J, Halilovic E, Garraway LA, Caponigro G, and Lehár J
- Subjects
- Animals, Cell Proliferation, Colorectal Neoplasms genetics, Female, Humans, Mice, Signal Transduction, Antineoplastic Combined Chemotherapy Protocols therapeutic use, Colorectal Neoplasms drug therapy
- Abstract
Like classical chemotherapy regimens used to treat cancer, targeted therapies will also rely upon polypharmacology, but tools are still lacking to predict which combinations of molecularly targeted drugs may be most efficacious. In this study, we used image-based proliferation and apoptosis assays in colorectal cancer cell lines to systematically investigate the efficacy of combinations of two to six drugs that target critical oncogenic pathways. Drug pairs targeting key signaling pathways resulted in synergies across a broad spectrum of genetic backgrounds but often yielded only cytostatic responses. Enhanced cytotoxicity was observed when additional processes including apoptosis and cell cycle were targeted as part of the combination. In some cases, where cell lines were resistant to paired and tripled drugs, increased expression of antiapoptotic proteins was observed, requiring a fourth-order combination to induce cytotoxicity. Our results illustrate how high-order drug combinations are needed to kill drug-resistant cancer cells, and they also show how systematic drug combination screening together with a molecular understanding of drug responses may help define optimal cocktails to overcome aggressive cancers. Cancer Res; 76(23); 6950-63. ©2016 AACR., (©2016 American Association for Cancer Research.)
- Published
- 2016
- Full Text
- View/download PDF
49. Correction: A distinct p53 target gene set predicts for response to the selective p53-HDM2 inhibitor NVP-CGM097.
- Author
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Jeay S, Gaulis S, Ferretti S, Bitter H, Ito M, Valat T, Murakami M, Ruetz S, Guthy DA, Rynn C, Jensen MR, Wiesmann M, Kallen J, Furet P, Gessier F, Holzer P, Masuya K, Würthner J, Halilovic E, Hofmann F, Sellers WR, and Graus Porta D
- Published
- 2016
- Full Text
- View/download PDF
50. Allosteric Inhibition of SHP2: Identification of a Potent, Selective, and Orally Efficacious Phosphatase Inhibitor.
- Author
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Garcia Fortanet J, Chen CH, Chen YN, Chen Z, Deng Z, Firestone B, Fekkes P, Fodor M, Fortin PD, Fridrich C, Grunenfelder D, Ho S, Kang ZB, Karki R, Kato M, Keen N, LaBonte LR, Larrow J, Lenoir F, Liu G, Liu S, Lombardo F, Majumdar D, Meyer MJ, Palermo M, Perez L, Pu M, Ramsey T, Sellers WR, Shultz MD, Stams T, Towler C, Wang P, Williams SL, Zhang JH, and LaMarche MJ
- Subjects
- Administration, Oral, Allosteric Regulation, Allosteric Site, Animals, Antineoplastic Agents chemical synthesis, Antineoplastic Agents pharmacokinetics, Antineoplastic Agents pharmacology, Cell Line, Tumor, Crystallography, X-Ray, Drug Design, Female, Heterografts, High-Throughput Screening Assays, Humans, Male, Mice, Inbred C57BL, Mice, Nude, Models, Molecular, Neoplasm Transplantation, Piperidines chemical synthesis, Piperidines pharmacokinetics, Piperidines pharmacology, Protein Conformation, Protein Tyrosine Phosphatase, Non-Receptor Type 11 chemistry, Pyrazines chemical synthesis, Pyrazines pharmacokinetics, Pyrazines pharmacology, Pyrimidines chemical synthesis, Pyrimidines pharmacokinetics, Pyrimidines pharmacology, Structure-Activity Relationship, Antineoplastic Agents chemistry, Piperidines chemistry, Protein Tyrosine Phosphatase, Non-Receptor Type 11 antagonists & inhibitors, Pyrazines chemistry, Pyrimidines chemistry
- Abstract
SHP2 is a nonreceptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also purportedly plays an important role in the programmed cell death pathway (PD-1/PD-L1). Because it is an oncoprotein associated with multiple cancer-related diseases, as well as a potential immunomodulator, controlling SHP2 activity is of significant therapeutic interest. Recently in our laboratories, a small molecule inhibitor of SHP2 was identified as an allosteric modulator that stabilizes the autoinhibited conformation of SHP2. A high throughput screen was performed to identify progressable chemical matter, and X-ray crystallography revealed the location of binding in a previously undisclosed allosteric binding pocket. Structure-based drug design was employed to optimize for SHP2 inhibition, and several new protein-ligand interactions were characterized. These studies culminated in the discovery of 6-(4-amino-4-methylpiperidin-1-yl)-3-(2,3-dichlorophenyl)pyrazin-2-amine (SHP099, 1), a potent, selective, orally bioavailable, and efficacious SHP2 inhibitor.
- Published
- 2016
- Full Text
- View/download PDF
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