1
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Izumi M, Costa DB, Kobayashi SS. Targeting of drug-tolerant persister cells as an approach to counter drug resistance in non-small cell lung cancer. Lung Cancer 2024; 194:107885. [PMID: 39002493 PMCID: PMC11305904 DOI: 10.1016/j.lungcan.2024.107885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/15/2024]
Abstract
The advent of targeted therapies revolutionized treatments of advanced oncogene-driven non-small cell lung cancer (NSCLC). Nonetheless, despite initial dramatic responses, development of drug resistance is inevitable. Although mechanisms underlying acquired resistance, such as on-target mutations, bypass pathways, or lineage transformation, have been described, overcoming drug resistance remains challenging. Recent evidence suggests that drug-tolerant persister (DTP) cells, which are tumor cells tolerant to initial drug exposure, give rise to cells that acquire drug resistance. Thus, the possibility of eradicating cancer by targeting DTP cells is under investigation, and various strategies are proposed. Here, we review overall features of DTP cells, current efforts to define DTP markers, and potential therapeutic strategies to target and eradicate DTP cells in oncogene-driven NSCLC. We also discuss future challenges in the field.
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Affiliation(s)
- Motohiro Izumi
- Department of Medicine, Division of Medical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Daniel B Costa
- Department of Medicine, Division of Medical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Susumu S Kobayashi
- Department of Medicine, Division of Medical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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2
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Leighow SM, Reynolds JA, Sokirniy I, Yao S, Yang Z, Inam H, Wodarz D, Archetti M, Pritchard JR. Programming tumor evolution with selection gene drives to proactively combat drug resistance. Nat Biotechnol 2024:10.1038/s41587-024-02271-7. [PMID: 38965430 DOI: 10.1038/s41587-024-02271-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 05/06/2024] [Indexed: 07/06/2024]
Abstract
Most targeted anticancer therapies fail due to drug resistance evolution. Here we show that tumor evolution can be reproducibly redirected to engineer therapeutic opportunity, regardless of the exact ensemble of pre-existing genetic heterogeneity. We develop a selection gene drive system that is stably introduced into cancer cells and is composed of two genes, or switches, that couple an inducible fitness advantage with a shared fitness cost. Using stochastic models of evolutionary dynamics, we identify the design criteria for selection gene drives. We then build prototypes that harness the selective pressure of multiple approved tyrosine kinase inhibitors and employ therapeutic mechanisms as diverse as prodrug catalysis and immune activity induction. We show that selection gene drives can eradicate diverse forms of genetic resistance in vitro. Finally, we demonstrate that model-informed switch engagement effectively targets pre-existing resistance in mouse models of solid tumors. These results establish selection gene drives as a powerful framework for evolution-guided anticancer therapy.
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Affiliation(s)
- Scott M Leighow
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
- Huck Institute For The Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Joshua A Reynolds
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Ivan Sokirniy
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
- Huck Institute For The Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Shun Yao
- Huck Institute For The Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Zeyu Yang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Haider Inam
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Dominik Wodarz
- Department of Biology, University of California San Diego, San Diego, CA, USA
| | - Marco Archetti
- Huck Institute For The Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Justin R Pritchard
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA.
- Huck Institute For The Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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3
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Adnan Awad S, Dufva O, Klievink J, Karjalainen E, Ianevski A, Pietarinen P, Kim D, Potdar S, Wolf M, Lotfi K, Aittokallio T, Wennerberg K, Porkka K, Mustjoki S. Integrated drug profiling and CRISPR screening identify BCR::ABL1-independent vulnerabilities in chronic myeloid leukemia. Cell Rep Med 2024; 5:101521. [PMID: 38653245 PMCID: PMC11148568 DOI: 10.1016/j.xcrm.2024.101521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/10/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024]
Abstract
BCR::ABL1-independent pathways contribute to primary resistance to tyrosine kinase inhibitor (TKI) treatment in chronic myeloid leukemia (CML) and play a role in leukemic stem cell persistence. Here, we perform ex vivo drug screening of CML CD34+ leukemic stem/progenitor cells using 100 single drugs and TKI-drug combinations and identify sensitivities to Wee1, MDM2, and BCL2 inhibitors. These agents effectively inhibit primitive CD34+CD38- CML cells and demonstrate potent synergies when combined with TKIs. Flow-cytometry-based drug screening identifies mepacrine to induce differentiation of CD34+CD38- cells. We employ genome-wide CRISPR-Cas9 screening for six drugs, and mediator complex, apoptosis, and erythroid-lineage-related genes are identified as key resistance hits for TKIs, whereas the Wee1 inhibitor AZD1775 and mepacrine exhibit distinct resistance profiles. KCTD5, a consistent TKI-resistance-conferring gene, is found to mediate TKI-induced BCR::ABL1 ubiquitination. In summary, we delineate potential mechanisms for primary TKI resistance and non-BCR::ABL1-targeting drugs, offering insights for optimizing CML treatment.
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MESH Headings
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Protein Kinase Inhibitors/pharmacology
- CRISPR-Cas Systems/genetics
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/drug effects
- Proto-Oncogene Proteins c-abl/metabolism
- Proto-Oncogene Proteins c-abl/genetics
- Proto-Oncogene Proteins c-abl/antagonists & inhibitors
- Cell Line, Tumor
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Affiliation(s)
- Shady Adnan Awad
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; Foundation for the Finnish Cancer Institute, 00290 Helsinki, Finland; Clinical Pathology Department, National Cancer Institute, Cairo University, 11796 Cairo, Egypt.
| | - Olli Dufva
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland
| | - Jay Klievink
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Ella Karjalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Paavo Pietarinen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland
| | - Daehong Kim
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Maija Wolf
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Kourosh Lotfi
- Department of Medical and Health Sciences, Faculty of Medicine and Health, Linköping University, 58183 Linköping, Sweden
| | - Tero Aittokallio
- Foundation for the Finnish Cancer Institute, 00290 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland; Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, University of Oslo, 0317 Oslo, Norway
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland; Biotech Research & Innovation Centre and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kimmo Porkka
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland.
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4
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Quintero-Ruiz N, Oliveira WDL, Esteca MV, Granato DC, Simabuco FM. Uncovering the bookshelves of CRISPR-based libraries: Advances and applications in cancer studies. Crit Rev Oncol Hematol 2024; 196:104287. [PMID: 38342473 DOI: 10.1016/j.critrevonc.2024.104287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/13/2024] Open
Abstract
The advent of CRISPR/Cas9 technology has revolutionized the genome editing field. CRISPR-based libraries have become powerful tools for high-throughput functional genomics and genetic screening. CRISPR-based libraries can represent a powerful approach to uncovering genes related to chemoresistance and therapy efficacy and to studying cancer cells' fitness. In this review, we conducted an extensive literature search and summarized multiple studies that utilized these libraries in both in vitro and in vivo research, emphasizing their key findings. We provide an overview of the design, construction, and applications of CRISPR-based libraries in different cancer-focused studies and discuss the different types of CRISPR-based libraries. We finally point out the challenges associated with library design, including guide RNA selection, off-target effects, and library complexity. This review provides an overview of the work conducted with CRISPR libraries in the search for new targets that could potentially assist in cancer therapy by contributing to functional approaches.
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Affiliation(s)
- Nathalia Quintero-Ruiz
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil
| | - Wesley de Lima Oliveira
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil; Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa Em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Marcos Vinicius Esteca
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil
| | - Daniela Campos Granato
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa Em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Fernando Moreira Simabuco
- Multidisciplinary Laboratory of Food and Health (LabMAS), School of Applied Sciences (FCA), University of Campinas (UNICAMP), Limeira, SP 13484-350, Brazil; Department of Biochemistry, Federal University of São Paulo, São Paulo, SP 04044-020, Brazil.
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5
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Kumarasamy V, Wang J, Frangou C, Wan Y, Dynka A, Rosenheck H, Dey P, Abel EV, Knudsen ES, Witkiewicz AK. The Extracellular Niche and Tumor Microenvironment Enhance KRAS Inhibitor Efficacy in Pancreatic Cancer. Cancer Res 2024; 84:1115-1132. [PMID: 38294344 PMCID: PMC10982648 DOI: 10.1158/0008-5472.can-23-2504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/28/2023] [Accepted: 01/25/2024] [Indexed: 02/01/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease that lacks effective treatment options, highlighting the need for developing new therapeutic interventions. Here, we assessed the response to pharmacologic inhibition of KRAS, the central oncogenic driver of PDAC. In a panel of PDAC cell lines, inhibition of KRASG12D with MRTX1133 yielded variable efficacy in suppressing cell growth and downstream gene expression programs in 2D cultures. On the basis of CRISPR-Cas9 loss-of-function screens, ITGB1 was identified as a target to enhance the therapeutic response to MRTX1133 by regulating mechanotransduction signaling and YAP/TAZ expression, which was confirmed by gene-specific knockdown and combinatorial drug synergy. Interestingly, MRTX1133 was considerably more efficacious in 3D cell cultures. Moreover, MRTX1133 elicited a pronounced cytostatic effect in vivo and controlled tumor growth in PDAC patient-derived xenografts. In syngeneic models, KRASG12D inhibition led to tumor regression that did not occur in immune-deficient hosts. Digital spatial profiling on tumor tissues indicated that MRTX1133-mediated KRAS inhibition enhanced IFNγ signaling and induced antigen presentation that modulated the tumor microenvironment. Further investigation of the immunologic response using single-cell sequencing and multispectral imaging revealed that tumor regression was associated with suppression of neutrophils and influx of effector CD8+ T cells. Together, these findings demonstrate that both tumor cell-intrinsic and -extrinsic events contribute to response to MRTX1133 and credential KRASG12D inhibition as a promising therapeutic strategy for a large percentage of patients with PDAC. SIGNIFICANCE Pharmacologic inhibition of KRAS elicits varied responses in pancreatic cancer 2D cell lines, 3D organoid cultures, and xenografts, underscoring the importance of mechanotransduction and the tumor microenvironment in regulating therapeutic responses.
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Affiliation(s)
- Vishnu Kumarasamy
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Jianxin Wang
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Costakis Frangou
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Yin Wan
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Andrew Dynka
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Hanna Rosenheck
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Prasenjit Dey
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Ethan V. Abel
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Erik S. Knudsen
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Agnieszka K. Witkiewicz
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
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6
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Dziubańska-Kusibab PJ, Nevedomskaya E, Haendler B. Preclinical Anticipation of On- and Off-Target Resistance Mechanisms to Anti-Cancer Drugs: A Systematic Review. Int J Mol Sci 2024; 25:705. [PMID: 38255778 PMCID: PMC10815614 DOI: 10.3390/ijms25020705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
The advent of targeted therapies has led to tremendous improvements in treatment options and their outcomes in the field of oncology. Yet, many cancers outsmart precision drugs by developing on-target or off-target resistance mechanisms. Gaining the ability to resist treatment is the rule rather than the exception in tumors, and it remains a major healthcare challenge to achieve long-lasting remission in most cancer patients. Here, we discuss emerging strategies that take advantage of innovative high-throughput screening technologies to anticipate on- and off-target resistance mechanisms before they occur in treated cancer patients. We divide the methods into non-systematic approaches, such as random mutagenesis or long-term drug treatment, and systematic approaches, relying on the clustered regularly interspaced short palindromic repeats (CRISPR) system, saturated mutagenesis, or computational methods. All these new developments, especially genome-wide CRISPR-based screening platforms, have significantly accelerated the processes for identification of the mechanisms responsible for cancer drug resistance and opened up new avenues for future treatments.
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Affiliation(s)
| | | | - Bernard Haendler
- Research and Early Development Oncology, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany; (P.J.D.-K.); (E.N.)
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7
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Schröder M, Renatus M, Liang X, Meili F, Zoller T, Ferrand S, Gauter F, Li X, Sigoillot F, Gleim S, Stachyra TM, Thomas JR, Begue D, Khoshouei M, Lefeuvre P, Andraos-Rey R, Chung B, Ma R, Pinch B, Hofmann A, Schirle M, Schmiedeberg N, Imbach P, Gorses D, Calkins K, Bauer-Probst B, Maschlej M, Niederst M, Maher R, Henault M, Alford J, Ahrne E, Tordella L, Hollingworth G, Thomä NH, Vulpetti A, Radimerski T, Holzer P, Carbonneau S, Thoma CR. DCAF1-based PROTACs with activity against clinically validated targets overcoming intrinsic- and acquired-degrader resistance. Nat Commun 2024; 15:275. [PMID: 38177131 PMCID: PMC10766610 DOI: 10.1038/s41467-023-44237-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Targeted protein degradation (TPD) mediates protein level through small molecule induced redirection of E3 ligases to ubiquitinate neo-substrates and mark them for proteasomal degradation. TPD has recently emerged as a key modality in drug discovery. So far only a few ligases have been utilized for TPD. Interestingly, the workhorse ligase CRBN has been observed to be downregulated in settings of resistance to immunomodulatory inhibitory drugs (IMiDs). Here we show that the essential E3 ligase receptor DCAF1 can be harnessed for TPD utilizing a selective, non-covalent DCAF1 binder. We confirm that this binder can be functionalized into an efficient DCAF1-BRD9 PROTAC. Chemical and genetic rescue experiments validate specific degradation via the CRL4DCAF1 E3 ligase. Additionally, a dasatinib-based DCAF1 PROTAC successfully degrades cytosolic and membrane-bound tyrosine kinases. A potent and selective DCAF1-BTK-PROTAC (DBt-10) degrades BTK in cells with acquired resistance to CRBN-BTK-PROTACs while the DCAF1-BRD9 PROTAC (DBr-1) provides an alternative strategy to tackle intrinsic resistance to VHL-degrader, highlighting DCAF1-PROTACS as a promising strategy to overcome ligase mediated resistance in clinical settings.
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Affiliation(s)
- Martin Schröder
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Basel, Switzerland
- Ridgeline Discovery, Basel, Switzerland
| | - Xiaoyou Liang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Fabian Meili
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Thomas Zoller
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Francois Gauter
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Xiaoyan Li
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Jason R Thomas
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Damien Begue
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Peggy Lefeuvre
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - BoYee Chung
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Renate Ma
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Benika Pinch
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Andreas Hofmann
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Patricia Imbach
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Delphine Gorses
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Keith Calkins
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Matt Niederst
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Rob Maher
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Martin Henault
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John Alford
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Erik Ahrne
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Luca Tordella
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Anna Vulpetti
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Thomas Radimerski
- Novartis Institutes for BioMedical Research, Basel, Switzerland
- Ridgeline Discovery, Basel, Switzerland
| | - Philipp Holzer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Seth Carbonneau
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Claudio R Thoma
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
- Ridgeline Discovery, Basel, Switzerland.
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8
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Kondo N, Utsumi T, Shimizu Y, Takemoto A, Oh-hara T, Uchibori K, Subat-Motoshi S, Ninomiya H, Takeuchi K, Nishio M, Miyazaki Y, Katayama R. MIG6 loss confers resistance to ALK/ROS1 inhibitors in NSCLC through EGFR activation by low-dose EGF. JCI Insight 2023; 8:e173688. [PMID: 37917191 PMCID: PMC10807714 DOI: 10.1172/jci.insight.173688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023] Open
Abstract
Although tyrosine kinase inhibitor (TKI) therapy shows marked clinical efficacy in patients with anaplastic lymphoma kinase-positive (ALK+) and ROS proto-oncogene 1-positive (ROS1+) non-small cell lung cancer (NSCLC), most of these patients eventually relapse with acquired resistance. Therefore, genome-wide CRISPR/Cas9 knockout screening was performed using an ALK+ NSCLC cell line established from pleural effusion without ALK-TKI treatment. After 9 days of ALK-TKI therapy, sequencing analysis was performed, which identified several tumor suppressor genes, such as NF2 or MED12, and multiple candidate genes. Among them, this study focused on ERRFI1, which is known as MIG6 and negatively regulates EGFR signaling. Interestingly, MIG6 loss induced resistance to ALK-TKIs by treatment with quite a low dose of EGF, which is equivalent to plasma concentration, through the upregulation of MAPK and PI3K/AKT/mTOR pathways. Combination therapy with ALK-TKIs and anti-EGFR antibodies could overcome the acquired resistance in both in vivo and in vitro models. In addition, this verified that MIG6 loss induces resistance to ROS1-TKIs in ROS1+ cell lines. This study found a potentially novel factor that plays a role in ALK and ROS1-TKI resistance by activating the EGFR pathway with low-dose ligands.
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Affiliation(s)
- Nobuyuki Kondo
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiro Utsumi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuki Shimizu
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
- Department of Computational Biology and Medical Science, Graduate School of Frontier Science, The University of Tokyo, Tokyo, Japan
| | - Ai Takemoto
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Tomoko Oh-hara
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Ken Uchibori
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital
| | - Sophia Subat-Motoshi
- Department of Pathology, the Cancer Institute Hospital, and
- Pathology Project for Molecular Targets, Cancer Institute, JFCR, Tokyo, Japan
| | | | - Kengo Takeuchi
- Department of Pathology, the Cancer Institute Hospital, and
- Pathology Project for Molecular Targets, Cancer Institute, JFCR, Tokyo, Japan
| | - Makoto Nishio
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
- Department of Computational Biology and Medical Science, Graduate School of Frontier Science, The University of Tokyo, Tokyo, Japan
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9
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Prahallad A, Weiss A, Voshol H, Kerr G, Sprouffske K, Yuan T, Ruddy D, Meistertzheim M, Kazic-Legueux M, Kottarathil T, Piquet M, Cao Y, Martinuzzi-Duboc L, Buhles A, Adler F, Mannino S, Tordella L, Sansregret L, Maira SM, Graus Porta D, Fedele C, Brachmann SM. CRISPR Screening Identifies Mechanisms of Resistance to KRASG12C and SHP2 Inhibitor Combinations in Non-Small Cell Lung Cancer. Cancer Res 2023; 83:4130-4141. [PMID: 37934115 PMCID: PMC10722132 DOI: 10.1158/0008-5472.can-23-1127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/08/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Although KRASG12C inhibitors show clinical activity in patients with KRAS G12C mutated non-small cell lung cancer (NSCLC) and other solid tumor malignancies, response is limited by multiple mechanisms of resistance. The KRASG12C inhibitor JDQ443 shows enhanced preclinical antitumor activity combined with the SHP2 inhibitor TNO155, and the combination is currently under clinical evaluation. To identify rational combination strategies that could help overcome or prevent some types of resistance, we evaluated the duration of tumor responses to JDQ443 ± TNO155, alone or combined with the PI3Kα inhibitor alpelisib and/or the cyclin-dependent kinase 4/6 inhibitor ribociclib, in xenograft models derived from a KRASG12C-mutant NSCLC line and investigated the genetic mechanisms associated with loss of response to combined KRASG12C/SHP2 inhibition. Tumor regression by single-agent JDQ443 at clinically relevant doses lasted on average 2 weeks and was increasingly extended by the double, triple, or quadruple combinations. Growth resumption was accompanied by progressively increased KRAS G12C amplification. Functional genome-wide CRISPR screening in KRASG12C-dependent NSCLC lines with distinct mutational profiles to identify adaptive mechanisms of resistance revealed sensitizing and rescuing genetic interactions with KRASG12C/SHP2 coinhibition; FGFR1 loss was the strongest sensitizer, and PTEN loss the strongest rescuer. Consistently, the antiproliferative activity of KRASG12C/SHP2 inhibition was strongly enhanced by PI3K inhibitors. Overall, KRAS G12C amplification and alterations of the MAPK/PI3K pathway were predominant mechanisms of resistance to combined KRASG12C/SHP2 inhibitors in preclinical settings. The biological nodes identified by CRISPR screening might provide additional starting points for effective combination treatments. SIGNIFICANCE Identification of resistance mechanisms to KRASG12C/SHP2 coinhibition highlights the need for additional combination therapies for lung cancer beyond on-pathway combinations and offers the basis for development of more effective combination approaches. See related commentary by Johnson and Haigis, p. 4005.
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Affiliation(s)
| | - Andreas Weiss
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Hans Voshol
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Grainne Kerr
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Tina Yuan
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - David Ruddy
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | | | | | | | - Michelle Piquet
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Yichen Cao
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | | | | | - Flavia Adler
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Luca Tordella
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | | | - Carmine Fedele
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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10
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Guna A, Page KR, Replogle JM, Esantsi TK, Wang ML, Weissman JS, Voorhees RM. A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens. BMC Genomics 2023; 24:651. [PMID: 37904134 PMCID: PMC10614335 DOI: 10.1186/s12864-023-09754-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Mapping genetic interactions is essential for determining gene function and defining novel biological pathways. We report a simple to use CRISPR interference (CRISPRi) based platform, compatible with Fluorescence Activated Cell Sorting (FACS)-based reporter screens, to query epistatic relationships at scale. This is enabled by a flexible dual-sgRNA library design that allows for the simultaneous delivery and selection of a fixed sgRNA and a second randomized guide, comprised of a genome-wide library, with a single transduction. We use this approach to identify epistatic relationships for a defined biological pathway, showing both increased sensitivity and specificity than traditional growth screening approaches.
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Affiliation(s)
- Alina Guna
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Katharine R Page
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Maxine L Wang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA.
- Howard Hughes Medical Institute Freeman Hrabowski Scholar, California Institute of Technology, Pasadena, CA, 91125, USA.
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11
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Guna A, Page KR, Replogle JM, Esantsi TK, Wang ML, Weissman JS, Voorhees RM. A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525086. [PMID: 36711738 PMCID: PMC9882262 DOI: 10.1101/2023.01.22.525086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mapping genetic interactions is essential for determining gene function and defining novel biological pathways. We report a simple to use CRISPR interference (CRISPRi) based platform, compatible with Fluorescence Activated Cell Sorting (FACS)-based reporter screens, to query epistatic relationships at scale. This is enabled by a flexible dual-sgRNA library design that allows for the simultaneous delivery and selection of a fixed sgRNA and a second randomized guide, comprised of a genome-wide library, with a single transduction. We use this approach to identify epistatic relationships for a defined biological pathway, showing both increased sensitivity and specificity than traditional growth screening approaches.
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Affiliation(s)
- Alina Guna
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Katharine R Page
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maxine L Wang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA,02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
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12
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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, Porta DG. Integrated CRISPR screening and drug profiling identifies combination opportunities for EGFR, ALK, and BRAF/MEK inhibitors. Cell Rep 2023; 42:112297. [PMID: 36961816 DOI: 10.1016/j.celrep.2023.112297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 01/11/2022] [Accepted: 03/03/2023] [Indexed: 03/25/2023] Open
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.
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Affiliation(s)
- Ralph Tiedt
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Frederick J King
- Novartis Institutes for BioMedical Research, Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - Christelle Stamm
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Matthew J Niederst
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA.
| | - Scott Delach
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | | | - Jodi Meltzer
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Iain J Mulford
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Emma Labrot
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | | | - Sabrina Baltschukat
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Grainne Kerr
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Javad Golji
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Daniel Wyss
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Christian Schnell
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
| | - Edward Ainscow
- Novartis Institutes for BioMedical Research, Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - Jeffrey A Engelman
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - William R Sellers
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Jordi Barretina
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Giordano Caponigro
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Cambridge, MA, USA
| | - Diana Graus Porta
- Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland
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13
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Kumarasamy V, Frangou C, Wang J, Wan Y, Dynka A, Rosenheck H, Dey P, Abel EV, Knudsen ES, Witkiewicz AK. Pharmacologically targeting KRAS G12D in PDAC models: tumor cell intrinsic and extrinsic impact. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.533261. [PMID: 37162905 PMCID: PMC10168422 DOI: 10.1101/2023.03.18.533261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease for which new therapeutic interventions are needed. Here we assessed the cellular response to pharmacological KRAS inhibition, which target the central oncogenic factor in PDAC. In a panel of PDAC cell lines, pharmaceutical inhibition of KRAS G12D allele, with MRTX1133 yields variable efficacy in the suppression of cell growth and downstream gene expression programs in 2D culture. CRISPR screens identify new drivers for enhanced therapeutic response that regulate focal adhesion and signaling cascades, which were confirmed by gene specific knockdowns and combinatorial drug synergy. Interestingly, MRTX1133 is considerably more efficacious in the context of 3D cell cultures and in vivo PDAC patient-derived xenografts. In syngeneic models, KRAS G12D inhibition elicits potent tumor regression that did not occur in immune-deficient hosts. Digital spatial profiling on tumor tissues indicates that MRTX1133 activates interferon-γ signaling and induces antigen presentation that modulate the tumor microenvironment. Further investigation on the immunological response using single cell sequencing and multispectral imaging reveals that tumor regression is associated with suppression of neutrophils and influx of effector CD8 + T-cells. Thus, both tumor cell intrinsic and extrinsic events contribute to response and credential KRAS G12D inhibition as promising strategy for a large percentage of PDAC tumors.
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14
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Zhou Z, Zheng J, Lin D, Xu R, Chen Y, Hu X. Exosomes derived from dental pulp stem cells accelerate cutaneous wound healing by enhancing angiogenesis via the Cdc42/p38 MAPK pathway. Int J Mol Med 2022; 50:143. [PMID: 36321793 PMCID: PMC9662140 DOI: 10.3892/ijmm.2022.5199] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/18/2022] [Indexed: 11/22/2022] Open
Abstract
Skin wound healing is a common challenging clinical issue which requires advanced treatment strategies. The present study investigated the therapeutic effects of exosomes derived from dental pulp stem cells (DPSC‑Exos) on cutaneous wound healing and the underlying mechanisms. The effects of DPSC‑Exos on cutaneous wound healing in mice were examined by measuring wound closure rates, and using histological and immunohistochemical analysis. A series of functional assays were performed to evaluate the effects of DPSC‑Exos on the angiogenic activities of human umbilical vein endothelial cells (HUVECs) <i>in vitro</i>. Tandem mass tag‑based quantitative proteomics analysis of DPSCs and DPSC‑Exos was performed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were used to evaluate the biological functions and pathways for the differentially expressed proteins in DPSC‑Exos. Western blot analysis was used to assess the protein levels of cell division control protein 42 (Cdc42) and p38 in DPSC‑Exos and in HUVECs subjected to DPSC‑Exos‑induced angiogenesis. SB203580, a p38 mitogen‑activated protein kinase (MAPK) signaling pathway inhibitor, was employed to verify the role of the p38 MAPK pathway <i>in vitro</i> and <i>in vivo</i>. Histological and immunohistochemical staining revealed that the DPSC‑Exos accelerated wound healing by promoting neovascularization. The DPSC‑Exos promoted the migration, proliferation and capillary formation capacity of HUVECs. Proteomics data demonstrated that proteins contained in DPSC‑Exos regulated vasculature development and angiogenesis. Pathway analysis revealed that proteins expressed in DPSC‑Exos were involved in several pathways, including MAPK pathway. Western blot analysis demonstrated that the DPSC‑Exos increased the protein levels of Cdc42 and phosphorylation of p38 in HUVECs. SB203580 suppressed the angiogenesis induced by DPSC‑Exos. On the whole, the present study demonstrates that DPSC‑Exos accelerate cutaneous wound healing by enhancing the angiogenic properties of HUVECs via the Cdc42/p38 MAPK signaling pathway.
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Affiliation(s)
| | - Jianmao Zheng
- Correspondence to: Dr Jianmao Zheng or Professor Xiaoli Hu, Department of Operative Dentistry and Endodontics, Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Lingyuan West Road, Guangzhou, Guangdong 510055, P.R. China, E-mail: , E-mail:
| | | | | | | | - Xiaoli Hu
- Correspondence to: Dr Jianmao Zheng or Professor Xiaoli Hu, Department of Operative Dentistry and Endodontics, Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Lingyuan West Road, Guangzhou, Guangdong 510055, P.R. China, E-mail: , E-mail:
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15
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Wang Z, Hou X, Li M, Ji R, Li Z, Wang Y, Guo Y, Liu D, Huang B, Du H. Active fractions of golden-flowered tea ( Camellia nitidissima Chi) inhibit epidermal growth factor receptor mutated non-small cell lung cancer via multiple pathways and targets in vitro and in vivo. Front Nutr 2022; 9:1014414. [PMID: 36386893 PMCID: PMC9649924 DOI: 10.3389/fnut.2022.1014414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/29/2022] [Indexed: 08/13/2023] Open
Abstract
As a medicine-food homology (MFH) plant, golden-flowered tea (Camellia nitidissima Chi, CNC) has many different pharmacologic activities and is known as "the queen of the tea family" and "the Panda of the Plant world". Several studies have revealed the pharmacologic effects of CNC crude extract, including anti-tumor, anti-oxidative and hepatoprotective activity. However, there are few studies on the anti-tumor active fractions and components of CNC, yet the underlying mechanism has not been investigated. Thus, we sought to verify the anti-non-small cell lung cancer (NSCLC) effects of four active fractions of CNC. Firstly, we determined the pharmacodynamic material basis of the four active fractions of CNC (Camellia. leave. saponins, Camellia. leave. polyphenols, Camellia. flower. saponins, Camellia. flower. polyphenols) by UPLC-Q-TOF-MS/MS and confirmed the differences in their specific compound contents. Then, MTT, colony formation assay and EdU incorporation assay confirmed that all fractions of CNC exhibit significant inhibitory on NSCLC, especially the Camellia. leave. saponins (CLS) fraction on EGFR mutated NSCLC cell lines. Moreover, transcriptome analysis revealed that the inhibition of NSCLC cell growth by CLS may be via three pathways, including "Cytokine-cytokine receptor interaction," "PI3K-Akt signaling pathway" and "MAPK signaling pathway." Subsequently, quantitative real-time PCR (RT-qPCR) and Western blot (WB) revealed TGFB2, INHBB, PIK3R3, ITGB8, TrkB and CACNA1D as the critical targets for the anti-tumor effects of CLS in vitro. Finally, the xenograft models confirmed that CLS treatment effectively suppressed tumor growth, and the key targets were also verified in vivo. These observations suggest that golden-flowered tea could be developed as a functional tea drink with anti-cancer ability, providing an essential molecular mechanism foundation for MFH medicine treating NSCLC.
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Affiliation(s)
- Ziling Wang
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xiaoying Hou
- School of Medicine, Wuhan Institutes of Biomedical Sciences, Jianghan University, Wuhan, China
| | - Min Li
- Shenzhen Luohu Hospital Group Luohu People’s Hospital, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Rongsheng Ji
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Zhouyuan Li
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yuqiao Wang
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yujie Guo
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Dahui Liu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Bisheng Huang
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Hongzhi Du
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
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16
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Ding H, Wang Y, Cui Y, Chen Z, Li Y, Yang J, Yang Y, Chen T, Xia D, Li C, Xu C, Ding C, Zhao J. Comprehensive analysis of the expression and prognosis for RBR E3 ubiquitin ligases in lung adenocarcinoma. Thorac Cancer 2022; 13:2459-2472. [PMID: 35820682 PMCID: PMC9436683 DOI: 10.1111/1759-7714.14577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/25/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the most common subtype of non‐small cell lung cancer and has a poor prognosis. RBR E3 ubiquitin ligases are a special class of E3 ubiquitin ligases which contain three zinc‐bing domains that catalyze ubiquitin to substrate proteins. The RBR family of E3 ubiquitin ligases has been reported in various human malignancies, but the roles of RBR E3 ubiquitin ligases in LUAD remain unclear. Methods By using TCGA and Kaplan–Meier plotter databases, we examined the expression and prognostic value of RBR E3 ubiquitin ligases. cBioPortal was used to analyze genetic mutations. The STRING database was used to build a protein interactive network. GO, KEGG, and GSEA were performed to investigate the potential biological functions of RBR E3 ubiquitin ligases. Results The expression of ARIH2, RNF144B, RNF216, and RNF217 was significantly related to the clinicopathological parameters and prognosis in LUAD patients. GSEA enrichment result showed ARIH2, RNF144B, RNF216, and RNF217 were all associated with NADH dehydrogenase complex assembly. GO functional enrichment analysis revealed that four RBR E3 ubiquitin ligases and their interactors were most correlated with ubiquitin‐protein transferase activity. KEGG pathway analysis indicated they were associated with cytosolic DNA‐sensing pathway, RIG‐I‐like receptor signaling pathway and NF‐kappa B signaling pathway. Conclusions Our comprehensive bioinformatic analysis revealed that ARIH2, RNF144B, RNF216, and RNF217 may be new prognostic biomarkers and these findings will help to better understand the distinct roles of RBR E3 ubiquitin ligases in LUAD.
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Affiliation(s)
- Hao Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuxin Wang
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, Suzhou, China
| | - Yuan Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhike Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yu Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yang Yang
- Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, School of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Tengfei Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Dian Xia
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, Xuzhou, China
| | - Chang Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chun Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Cheng Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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17
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Wang Y, Huang C, Zhao W. Recent advances of the biological and biomedical applications of CRISPR/Cas systems. Mol Biol Rep 2022; 49:7087-7100. [PMID: 35705772 PMCID: PMC9199458 DOI: 10.1007/s11033-022-07519-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/19/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022]
Abstract
The clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated endonuclease (Cas) system, referred to as CRISPR/Cas system, has attracted significant interest in scientific community due to its great potential in translating into versatile therapeutic tools in biomedical field. For instance, a myriad of studies has demonstrated that the CRISPR/Cas system is capable of detecting various types of viruses, killing antibiotic-resistant bacteria, treating inherited genetic diseases, and providing new strategies for cancer therapy. Furthermore, CRISPR/Cas systems are also exploited as research tools such as genome engineering tool that allows researchers to interrogate the biological roles of unexplored genes or uncover novel functions of known genes. Additionally, the CRISPR/Cas system has been employed to edit the genome of a wide range of eukaryotic, prokaryotic organisms and experimental models, including but not limited to mammalian cells, mice, zebrafish, plants, yeast, and Escherichia coli. The present review mainly focuses on summarizing recent discoveries regarding the type II CRISPR/Cas9 and type VI CRISPR/Cas13a systems to give researchers a glimpse of their potential applications in the biological and biomedical field.
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Affiliation(s)
- Yaya Wang
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, 58 Yanta Zhonglu, 710054, Xi'an, Shaanxi, China.
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Air Force Medical University, Xi'an, China.
| | - Chun Huang
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, 58 Yanta Zhonglu, 710054, Xi'an, Shaanxi, China
| | - Weiqin Zhao
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, 58 Yanta Zhonglu, 710054, Xi'an, Shaanxi, China
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18
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Tang Y, Guo Y. A Ubiquitin-Proteasome Gene Signature for Predicting Prognosis in Patients With Lung Adenocarcinoma. Front Genet 2022; 13:893511. [PMID: 35711913 PMCID: PMC9194557 DOI: 10.3389/fgene.2022.893511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Dysregulation of the ubiquitin-proteasome system (UPS) can lead to instability in the cell cycle and may act as a crucial factor in both tumorigenesis and tumor progression. However, there is no established prognostic signature based on UPS genes (UPSGs) for lung adenocarcinoma (LUAD) despite their value in other cancers. Methods: We retrospectively evaluated a total of 703 LUAD patients through multivariate Cox and Lasso regression analyses from two datasets, the Cancer Genome Atlas (n = 477) and GSE31210 (n = 226). An independent dataset (GSE50081) containing 128 LUAD samples were used for validation. Results: An eight-UPSG signature, including ARIH2, FBXO9, KRT8, MYLIP, PSMD2, RNF180, TRIM28, and UBE2V2, was established. Kaplan-Meier survival analysis and time-receiver operating characteristic curves for the training and validation datasets revealed that this risk signature presented with good performance in predicting overall and relapsed-free survival. Based on the signature and its associated clinical features, a nomogram and corresponding web-based calculator for predicting survival were established. Calibration plot and decision curve analyses showed that this model was clinically useful for both the training and validation datasets. Finally, a web-based calculator (https://ostool.shinyapps.io/lungcancer) was built to facilitate convenient clinical application of the signature. Conclusion: An UPSG based model was developed and validated in this study, which may be useful as a novel prognostic predictor for LUAD.
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Affiliation(s)
- Yunliang Tang
- Department of Rehabilitation Medicine, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yinhong Guo
- Department of Oncology, Zhuji People's Hospital of Zhejiang Province, Zhuji, China
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19
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miR-6077 promotes cisplatin/pemetrexed resistance in lung adenocarcinoma via CDKN1A/cell cycle arrest and KEAP1/ferroptosis pathways. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:366-386. [PMID: 35505963 PMCID: PMC9035384 DOI: 10.1016/j.omtn.2022.03.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/27/2022] [Indexed: 01/18/2023]
Abstract
Lung adenocarcinoma (LUAD) is one of the most common malignancies worldwide. Combination chemotherapy with cisplatin (CDDP) plus pemetrexed (PEM) remains the predominant therapeutic regimen; however, chemoresistance greatly limits its curative potential. Here, through CRISPR-Cas9 screening, we identified miR-6077 as a key driver of CDDP/PEM resistance in LUAD. Functional experiments verified that ectopic overexpression of miR-6077 desensitized LUAD cells to CDDP/PEM in both cell lines and patient-derived xenograft models. Through RNA sequencing in cells and single-cell sequencing of samples from patients with CDDP/PEM treatments, we observed CDDP/PEM-induced upregulation of CDKN1A and KEAP1, which in turn activated cell-cycle arrest and ferroptosis, respectively, thus leading to cell death. Through miRNA pull-down, we identified and validated that miR-6077 targets CDKN1A and KEAP1. Furthermore, we demonstrated that miR-6077 protects LUAD cells from cell death induced by CDDP/PEM via CDKN1A-CDK1-mediated cell-cycle arrest and KEAP1-NRF2-SLC7A11/NQO1-mediated ferroptosis, thus resulting in chemoresistance in multiple LUAD cells both in vitro and in vivo. Moreover, we found that GMDS-AS1 and LINC01128 sensitized LUAD cells to CDDP/PEM by sponging miR-6077. Collectively, these results imply the critical role of miR-6077 in LUAD’s sensitivity to CDDP/PEM, thus providing a novel therapeutic strategy for overcoming chemoresistance in clinical practice.
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20
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Coker EA, Stewart A, Ozer B, Minchom A, Pickard L, Ruddle R, Carreira S, Popat S, O'Brien M, Raynaud F, de Bono J, Al-Lazikani B, Banerji U. Individualized Prediction of Drug Response and Rational Combination Therapy in NSCLC Using Artificial Intelligence-Enabled Studies of Acute Phosphoproteomic Changes. Mol Cancer Ther 2022; 21:1020-1029. [PMID: 35368084 PMCID: PMC9381105 DOI: 10.1158/1535-7163.mct-21-0442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/15/2021] [Accepted: 03/11/2022] [Indexed: 01/07/2023]
Abstract
We hypothesize that the study of acute protein perturbation in signal transduction by targeted anticancer drugs can predict drug sensitivity of these agents used as single agents and rational combination therapy. We assayed dynamic changes in 52 phosphoproteins caused by an acute exposure (1 hour) to clinically relevant concentrations of seven targeted anticancer drugs in 35 non-small cell lung cancer (NSCLC) cell lines and 16 samples of NSCLC cells isolated from pleural effusions. We studied drug sensitivities across 35 cell lines and synergy of combinations of all drugs in six cell lines (252 combinations). We developed orthogonal machine-learning approaches to predict drug response and rational combination therapy. Our methods predicted the most and least sensitive quartiles of drug sensitivity with an AUC of 0.79 and 0.78, respectively, whereas predictions based on mutations in three genes commonly known to predict response to the drug studied, for example, EGFR, PIK3CA, and KRAS, did not predict sensitivity (AUC of 0.5 across all quartiles). The machine-learning predictions of combinations that were compared with experimentally generated data showed a bias to the highest quartile of Bliss synergy scores (P = 0.0243). We confirmed feasibility of running such assays on 16 patient samples of freshly isolated NSCLC cells from pleural effusions. We have provided proof of concept for novel methods of using acute ex vivo exposure of cancer cells to targeted anticancer drugs to predict response as single agents or combinations. These approaches could complement current approaches using gene mutations/amplifications/rearrangements as biomarkers and demonstrate the utility of proteomics data to inform treatment selection in the clinic.
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Affiliation(s)
- Elizabeth A. Coker
- Department of Data Science, The Institute of Cancer Research, London, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Healx Ltd., Cambridge, United Kingdom
| | - Adam Stewart
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Bugra Ozer
- Department of Data Science, The Institute of Cancer Research, London, United Kingdom
- Healx Ltd., Cambridge, United Kingdom
| | - Anna Minchom
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Lisa Pickard
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Ruth Ruddle
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Suzanne Carreira
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Sanjay Popat
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Mary O'Brien
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Florence Raynaud
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Johann de Bono
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Bissan Al-Lazikani
- Department of Data Science, The Institute of Cancer Research, London, United Kingdom
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Udai Banerji
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
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21
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Huang L, Liao Z, Liu Z, Chen Y, Huang T, Xiao H. Application and Prospect of CRISPR/Cas9 Technology in Reversing Drug Resistance of Non-Small Cell Lung Cancer. Front Pharmacol 2022; 13:900825. [PMID: 35620280 PMCID: PMC9127258 DOI: 10.3389/fphar.2022.900825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer drug resistance has always been a major factor affecting the treatment of non-small cell lung cancer, which reduces the quality of life of patients. The clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) technology, as an efficient and convenient new gene-editing technology, has provided a lot of help to the clinic and accelerated the research of cancer and drug resistance. In this review, we introduce the mechanisms of drug resistance in non-small cell lung cancer (NSCLC), discuss how the CRISPR/Cas9 system can reverse multidrug resistance in NSCLC, and focus on drug resistance gene mutations. To improve the prognosis of NSCLC patients and further improve patients' quality of life, it is necessary to utilize the CRISPR/Cas9 system in systematic research on cancer drug resistance.
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Affiliation(s)
- Lu Huang
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Zhi Liao
- Department of Gynecology and Obstetrics, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Zhixi Liu
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Yan Chen
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China
| | - Tingwenli Huang
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Hongtao Xiao
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
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22
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Das S, Bano S, Kapse P, Kundu GC. CRISPR based therapeutics: a new paradigm in cancer precision medicine. Mol Cancer 2022; 21:85. [PMID: 35337340 PMCID: PMC8953071 DOI: 10.1186/s12943-022-01552-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/24/2022] [Indexed: 02/08/2023] Open
Abstract
Background Clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) systems are the latest addition to the plethora of gene-editing tools. These systems have been repurposed from their natural counterparts by means of both guide RNA and Cas nuclease engineering. These RNA-guided systems offer greater programmability and multiplexing capacity than previous generation gene editing tools based on zinc finger nucleases and transcription activator like effector nucleases. CRISPR-Cas systems show great promise for individualization of cancer precision medicine. Main body The biology of Cas nucleases and dead Cas based systems relevant for in vivo gene therapy applications has been discussed. The CRISPR knockout, CRISPR activation and CRISPR interference based genetic screens which offer opportunity to assess functions of thousands of genes in massively parallel assays have been also highlighted. Single and combinatorial gene knockout screens lead to identification of drug targets and synthetic lethal genetic interactions across different cancer phenotypes. There are different viral and non-viral (nanoformulation based) modalities that can carry CRISPR-Cas components to different target organs in vivo. Conclusion The latest developments in the field in terms of optimization of performance of the CRISPR-Cas elements should fuel greater application of the latter in the realm of precision medicine. Lastly, how the already available knowledge can help in furtherance of use of CRISPR based tools in personalized medicine has been discussed.
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Affiliation(s)
- Sumit Das
- National Centre for Cell Science, S P Pune University Campus, Pune, 411007, India
| | - Shehnaz Bano
- National Centre for Cell Science, S P Pune University Campus, Pune, 411007, India
| | - Prachi Kapse
- School of Basic Medical Sciences, S P Pune University, Pune, 411007, India
| | - Gopal C Kundu
- Kalinga Institute of Medical Sciences (KIMS), KIIT Deemed To Be University, Bhubaneswar, 751024, India. .,School of Biotechnology, KIIT Deemed To Be University, Bhubaneswar, 751024, India.
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23
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Hou J, He Z, Liu T, Chen D, Wang B, Wen Q, Zheng X. Evolution of Molecular Targeted Cancer Therapy: Mechanisms of Drug Resistance and Novel Opportunities Identified by CRISPR-Cas9 Screening. Front Oncol 2022; 12:755053. [PMID: 35372044 PMCID: PMC8970599 DOI: 10.3389/fonc.2022.755053] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/17/2022] [Indexed: 12/14/2022] Open
Abstract
Molecular targeted therapy has revolutionized the landscape of cancer treatment due to better therapeutic responses and less systemic toxicity. However, therapeutic resistance is a major challenge in clinical settings that hinders continuous clinical benefits for cancer patients. In this regard, unraveling the mechanisms of drug resistance may identify new druggable genetic alterations for molecularly targeted therapies, thus contributing to improved therapeutic efficacies. The recent rapid development of novel methodologies including CRISPR-Cas9 screening technology and patient-derived models provides powerful tools to dissect the underlying mechanisms of resistance to targeted cancer therapies. In this review, we updated therapeutic targets undergoing preclinical and clinical evaluation for various cancer types. More importantly, we provided comprehensive elaboration of high throughput CRISPR-Cas9 screening in deciphering potential mechanisms of unresponsiveness to molecularly targeted therapies, which will shed light on the discovery of novel opportunities for designing next-generation anti-cancer drugs.
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Affiliation(s)
- Jue Hou
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zongsheng He
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Tian Liu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Dongfeng Chen
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Bin Wang
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xi Zheng
- Department of Gastroenterology, Chongqing University Cancer Hospital, Chongqing, China
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24
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MacLeod G, Rajakulendran N, Angers S. Identification of Drug Resistance Mechanisms Using Genome-Wide CRISPR-Cas9 Screens. Methods Mol Biol 2022; 2535:141-156. [PMID: 35867229 DOI: 10.1007/978-1-0716-2513-2_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
CRISPR-Cas9 genome editing provides a means for simple and scalable production of gene knockouts in mammalian cell lines. The development of guide RNA (gRNA) libraries targeting tens of thousands of genes has allowed researchers to produce pools of cells, each containing a single gene knockout for use in genetic screens. In addition to assessing the effect of gene knockout on cell proliferation, CRISPR-Cas9 genetic screens can be used to assess gene-drug interactions. Here, we outline a protocol for performing positive and negative selection genome-wide CRISPR-Cas9 screens for identifying gene knockouts that cause drug resistance and hypersensitivity. This protocol is designed for the use of the TKOv3 library in human cell lines, but can be readily adapted for different libraries.
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Affiliation(s)
- Graham MacLeod
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
| | | | - Stephane Angers
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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25
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Emerging Molecular Dependencies of Mutant EGFR-Driven Non-Small Cell Lung Cancer. Cells 2021; 10:cells10123553. [PMID: 34944063 PMCID: PMC8699920 DOI: 10.3390/cells10123553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) mutations are the molecular driver of a subset of non-small cell lung cancers (NSCLC); tumors that harbor these mutations are often dependent on sustained oncogene signaling for survival, a concept known as “oncogene addiction”. Inhibiting EGFR with tyrosine kinase inhibitors has improved clinical outcomes for patients; however, successive generations of inhibitors have failed to prevent the eventual emergence of resistance to targeted agents. Although these tumors have a well-established dependency on EGFR signaling, there remain questions about the underlying genetic mechanisms necessary for EGFR-driven oncogenesis and the factors that allow tumor cells to escape EGFR dependence. In this review, we highlight the latest findings on mutant EGFR dependencies, co-operative drivers, and molecular mechanisms that underlie sensitivity to EGFR inhibitors. Additionally, we offer perspective on how these discoveries may inform novel combination therapies tailored to EGFR mutant NSCLC.
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26
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Banerjee A, Malonia SK, Dutta S. Frontiers of CRISPR-Cas9 for Cancer Research and Therapy. JOURNAL OF EXPLORATORY RESEARCH IN PHARMACOLOGY 2021; 000:000-000. [DOI: 10.14218/jerp.2020.00033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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27
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CRISPR-Cas systems for genome editing of mammalian cells. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:15-30. [PMID: 34127192 DOI: 10.1016/bs.pmbts.2021.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the past decade, ZFNs and TALENs have been used for targeted genome engineering and have gained scientific attention. It has demonstrated huge potential for gene knockout, knock-in, and indels in desired locations of genomes to understand molecular mechanism of diseases and also discover therapy. However, both the genome engineering techniques are still suffering from design, screening and validation in cell and higher organisms. CRISPR-Cas9 is a rapid, simple, specific, and versatile technology and it has been applied in many organisms including mammalian cells. CRISPR-Cas9 has been used for animal models to modify animal cells for understanding human disease for novel drug discovery and therapy. Additionally, base editing has also been discussed herewith for conversion of C/G-to-T/A or A/T-to-G/C without DNA cleavage or donor DNA templates for correcting mutations or altering gene functions. In this chapter, we highlight CRISPR-Cas9 and base editing for desired genome editing in mammalian cells for a better understanding of molecular mechanisms, and biotechnological and therapeutic applications.
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28
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Wang P, Dai X, Jiang W, Li Y, Wei W. RBR E3 ubiquitin ligases in tumorigenesis. Semin Cancer Biol 2020; 67:131-144. [PMID: 32442483 DOI: 10.1016/j.semcancer.2020.05.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/28/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023]
Abstract
RING-in-between-RING (RBR) E3 ligases are one class of E3 ligases that is characterized by the unique RING-HECT hybrid mechanism to function with E2s to transfer ubiquitin to target proteins for degradation. Emerging evidence has demonstrated that RBR E3 ligases play essential roles in neurodegenerative diseases, infection, inflammation and cancer. Accumulated evidence has revealed that RBR E3 ligases exert their biological functions in various types of cancers by modulating the degradation of tumor promoters or suppressors. Hence, we summarize the differential functions of RBR E3 ligases in a variety of human cancers. In general, ARIH1, RNF14, RNF31, RNF144B, RNF216, and RBCK1 exhibit primarily oncogenic roles, whereas ARIH2, PARC and PARK2 mainly have tumor suppressive functions. Moreover, the underlying mechanisms by which different RBR E3 ligases are involved in tumorigenesis and progression are also described. We discuss the further investigation is required to comprehensively understand the critical role of RBR E3 ligases in carcinogenesis. We hope our review can stimulate the researchers to deeper explore the mechanism of RBR E3 ligases-mediated carcinogenesis and to develop useful inhibitors of these oncogenic E3 ligases for cancer therapy.
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Affiliation(s)
- Peter Wang
- School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Xiaoming Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA, USA
| | - Wenxiao Jiang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Yuyun Li
- School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA, USA.
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29
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Zeng H, Castillo-Cabrera J, Manser M, Lu B, Yang Z, Strande V, Begue D, Zamponi R, Qiu S, Sigoillot F, Wang Q, Lindeman A, Reece-Hoyes JS, Russ C, Bonenfant D, Jiang X, Wang Y, Cong F. Genome-wide CRISPR screening reveals genetic modifiers of mutant EGFR dependence in human NSCLC. eLife 2019; 8:50223. [PMID: 31741433 PMCID: PMC6927754 DOI: 10.7554/elife.50223] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/04/2019] [Indexed: 12/24/2022] Open
Abstract
EGFR-mutant NSCLCs frequently respond to EGFR tyrosine kinase inhibitors (TKIs). However, the responses are not durable, and the magnitude of tumor regression is variable, suggesting the existence of genetic modifiers of EGFR dependency. Here, we applied a genome-wide CRISPR-Cas9 screening to identify genetic determinants of EGFR TKI sensitivity and uncovered putative candidates. We show that knockout of RIC8A, essential for G-alpha protein activation, enhanced EGFR TKI-induced cell death. Mechanistically, we demonstrate that RIC8A is a positive regulator of YAP signaling, activation of which rescued the EGFR TKI sensitizing phenotype resulting from RIC8A knockout. We also show that knockout of ARIH2, or other components in the Cullin-5 E3 complex, conferred resistance to EGFR inhibition, in part by promoting nascent protein synthesis through METAP2. Together, these data uncover a spectrum of previously unidentified regulators of EGFR TKI sensitivity in EGFR-mutant human NSCLC, providing insights into the heterogeneity of EGFR TKI treatment responses. Cancer is caused by cells growing and dividing uncontrollably as a result of mutations in certain genes. Many human lung cancers have a mutation in the gene that makes the protein EGFR. In healthy cells, EGFR allows a cell to respond to chemical signals that encourage healthy growth. In cancer, the altered EGFR is always on, which allows the cell to rapidly grow without any control, resulting in cancer. One approach to treating these cancers is with drugs that block the activity of mutant EGFR. Although these drugs have been very successful, they do not always succeed in completely treating the cancer. This is because over time the cancer cells can become resistant to the drug and start forming new tumors. One way that this can happen is if random mutations lead to changes in other proteins that make the drug less effective or stop it from accessing the EGFR proteins. However, it is unclear how other proteins in cancer cells affect the response to these EGFR inhibiting drugs. Now, Zeng et al. have used gene editing to systematically remove every protein from human lung cancer cells grown in the laboratory to see how this affects resistance to EGFR inhibitor treatment. This revealed that a number of different proteins could change how cancer cells responded to the drug. For instance, cells lacking the protein RIC8A were more sensitive to EGFR inhibitors and less likely to develop resistance. This is because loss of RIC8A turns down a key cell survival pathway in cancer cells. Whereas, cancer cells lacking the ARIH2 protein were able to produce more proteins that are needed for cancer cell growth, which resulted in them having increased resistance to EGFR inhibitors. The proteins identified in this study could be used to develop new drugs that improve the effectiveness of EGFR inhibitors. Understanding how cancer cells respond to EGFR inhibitor treatment could help determine how likely a patient is to develop resistance to these drugs.
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Affiliation(s)
- Hao Zeng
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Johnny Castillo-Cabrera
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Mika Manser
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Bo Lu
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Zinger Yang
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Vaik Strande
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Damien Begue
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Raffaella Zamponi
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Shumei Qiu
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Frederic Sigoillot
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Qiong Wang
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Alicia Lindeman
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - John S Reece-Hoyes
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Carsten Russ
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Debora Bonenfant
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Xiaomo Jiang
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Youzhen Wang
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Feng Cong
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, United States
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