1
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Souchek J, Laliwala A, Houser L, Muraskin L, Vu Q, Mohs AM. Fatty Acid Synthase Inhibitors Enhance Microtubule-Stabilizing and Microtubule-Destabilizing Drugs in Taxane-Resistant Prostate Cancer Cells. ACS Pharmacol Transl Sci 2023; 6:1859-1869. [PMID: 38093839 PMCID: PMC10714433 DOI: 10.1021/acsptsci.3c00182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 02/01/2024]
Abstract
Prostate cancer is the third leading cause of cancer-related death in men in the United States. Taxane chemotherapy is a staple therapy for men with metastatic prostate cancer, yet the median survival is less than 2 years in this setting. New strategies are needed to overcome taxane resistance to improve patient survival. Fatty acid synthase (FASN) is overexpressed in many types of cancer, and several inhibitors have been designed in the past 30 years. Previously, we showed that the FASN inhibitor orlistat was able to synergize with taxanes in two established taxane-resistant (TxR) cell lines. In the current study, we investigated five FASN inhibitors-cerulenin, orlistat, triclosan, thiophenopyrimidine fasnall, and pyrazole derivative TVB-3166 for their potential to synergize with docetaxel (a microtubule stabilizer) and vinblastine (a microtubule destabilizer) in TxR cell lines. Orlistat, TVB-3166, and fasnall synergistically inhibited cell viability when combined with docetaxel and vinblastine in PC3-TxR and DU145-TxR cells. Confocal microscopy and immunoblot with an antidetyrosinated tubulin antibody demonstrated that enhanced microtubule stability was induced by the combined treatment of FASN inhibitors and docetaxel compared with docetaxel alone, while combinations of FASN inhibitors with vinblastine diminished microtubule stability compared to vinblastine alone.
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Affiliation(s)
- Joshua
J. Souchek
- Department
of Pharmaceutical Sciences, University of
Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
| | - Aayushi Laliwala
- Department
of Pharmaceutical Sciences, University of
Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
| | - Lucas Houser
- Department
of Pharmaceutical Sciences, University of
Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
| | - Lindsey Muraskin
- Department
of Pharmaceutical Sciences, University of
Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
| | - Quyen Vu
- Department
of Pharmaceutical Sciences, University of
Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
| | - Aaron M. Mohs
- Department
of Pharmaceutical Sciences, University of
Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
- Department
of Biochemistry and Molecular Biology, University
of Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
- Fred
& Pamela Buffet Cancer Center, University
of Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
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2
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Deusenbery C, Carneiro O, Oberkfell C, Shukla A. Synergy of Antibiotics and Antibiofilm Agents against Methicillin-Resistant Staphylococcus aureus Biofilms. ACS Infect Dis 2023; 9:1949-1963. [PMID: 37646612 DOI: 10.1021/acsinfecdis.3c00239] [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] [Indexed: 09/01/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) infections are some of the most common antibiotic-resistant infections, often exacerbated by the formation of biofilms. Here, we evaluated six compounds, three common antibiotics used against MRSA and three antibiofilm compounds, in nine combinations to investigate the mechanisms of synergistic eradication of MRSA biofilms. Using metabolic assessment, colony enumeration, confocal fluorescence microscopy, and scanning electron microscopy, we identified two promising combinations of antibiotics with antibiofilm agents against preformed MRSA biofilms. The broad-spectrum protease, proteinase K, and membrane-targeting antibiotic, daptomycin, worked in synergy against MRSA biofilms by manipulating the protein content, increasing access to the cell membrane of biofilm bacteria. We also found that the combination of cationic peptide, IDR-1018, with the cell wall cross-linking inhibitor, vancomycin, exhibited synergy against MRSA biofilms by causing bacterial damage and preventing repair. Our findings identify synergistic combinations of antibiotics and antibiofilm agents, providing insight into mechanisms that may be explored further for the development of effective treatments against MRSA biofilm.
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Affiliation(s)
- Carly Deusenbery
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Olivia Carneiro
- Therapeutic Sciences Graduate Program, Division of Biology and Medicine, Brown University, Providence, Rhode Island 02912, United States
| | - Carleigh Oberkfell
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Anita Shukla
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
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3
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Flanary VL, Fisher JL, Wilk EJ, Howton TC, Lasseigne BN. Computational Advancements in Cancer Combination Therapy Prediction. JCO Precis Oncol 2023; 7:e2300261. [PMID: 37824797 DOI: 10.1200/po.23.00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/20/2023] [Accepted: 08/15/2023] [Indexed: 10/14/2023] Open
Abstract
Given the high attrition rate of de novo drug discovery and limited efficacy of single-agent therapies in cancer treatment, combination therapy prediction through in silico drug repurposing has risen as a time- and cost-effective alternative for identifying novel and potentially efficacious therapies for cancer. The purpose of this review is to provide an introduction to computational methods for cancer combination therapy prediction and to summarize recent studies that implement each of these methods. A systematic search of the PubMed database was performed, focusing on studies published within the past 10 years. Our search included reviews and articles of ongoing and retrospective studies. We prioritized articles with findings that suggest considerations for improving combination therapy prediction methods over providing a meta-analysis of all currently available cancer combination therapy prediction methods. Computational methods used for drug combination therapy prediction in cancer research include networks, regression-based machine learning, classifier machine learning models, and deep learning approaches. Each method class has its own advantages and disadvantages, so careful consideration is needed to determine the most suitable class when designing a combination therapy prediction method. Future directions to improve current combination therapy prediction technology include incorporation of disease pathobiology, drug characteristics, patient multiomics data, and drug-drug interactions to determine maximally efficacious and tolerable drug regimens for cancer. As computational methods improve in their capability to integrate patient, drug, and disease data, more comprehensive models can be developed to more accurately predict safe and efficacious combination drug therapies for cancer and other complex diseases.
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Affiliation(s)
- Victoria L Flanary
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL
| | - Jennifer L Fisher
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL
| | - Elizabeth J Wilk
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL
| | - Timothy C Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL
| | - Brittany N Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL
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4
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Nair NU, Greninger P, Zhang X, Friedman AA, Amzallag A, Cortez E, Sahu AD, Lee JS, Dastur A, Egan RK, Murchie E, Ceribelli M, Crowther GS, Beck E, McClanaghan J, Klump-Thomas C, Boisvert JL, Damon LJ, Wilson KM, Ho J, Tam A, McKnight C, Michael S, Itkin Z, Garnett MJ, Engelman JA, Haber DA, Thomas CJ, Ruppin E, Benes CH. A landscape of response to drug combinations in non-small cell lung cancer. Nat Commun 2023; 14:3830. [PMID: 37380628 PMCID: PMC10307832 DOI: 10.1038/s41467-023-39528-9] [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: 01/31/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023] Open
Abstract
Combination of anti-cancer drugs is broadly seen as way to overcome the often-limited efficacy of single agents. The design and testing of combinations are however very challenging. Here we present a uniquely large dataset screening over 5000 targeted agent combinations across 81 non-small cell lung cancer cell lines. Our analysis reveals a profound heterogeneity of response across the tumor models. Notably, combinations very rarely result in a strong gain in efficacy over the range of response observable with single agents. Importantly, gain of activity over single agents is more often seen when co-targeting functionally proximal genes, offering a strategy for designing more efficient combinations. Because combinatorial effect is strongly context specific, tumor specificity should be achievable. The resource provided, together with an additional validation screen sheds light on major challenges and opportunities in building efficacious combinations against cancer and provides an opportunity for training computational models for synergy prediction.
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Affiliation(s)
- Nishanth Ulhas Nair
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xiaohu Zhang
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Adam A Friedman
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Arnaud Amzallag
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eliane Cortez
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Avinash Das Sahu
- University of New Mexico, Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Joo Sang Lee
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Anahita Dastur
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Regina K Egan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ellen Murchie
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Erin Beck
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | | | | | | | - Leah J Damon
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jeffrey Ho
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Angela Tam
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Sam Michael
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Zina Itkin
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Mathew J Garnett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | | | - Daniel A Haber
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institute of Health, Rockville, MD, 20850, USA
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Cyril H Benes
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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5
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Dhungel L, Harris C, Romine L, Sarkaria J, Raucher D. Targeted c-Myc Inhibition and Systemic Temozolomide Therapy Extend Survival in Glioblastoma Xenografts. Bioengineering (Basel) 2023; 10:718. [PMID: 37370649 DOI: 10.3390/bioengineering10060718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/26/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Glioblastoma is a highly aggressive disease with poor patient outcomes despite current treatment options, which consist of surgery, radiation, and chemotherapy. However, these strategies present challenges such as resistance development, damage to healthy tissue, and complications due to the blood-brain barrier. There is therefore a critical need for new treatment modalities that can selectively target tumor cells, minimize resistance development, and improve patient survival. Temozolomide is the current standard chemotherapeutic agent for glioblastoma, yet its use is hindered by drug resistance and severe side effects. Combination therapy using multiple drugs acting synergistically to kill cancer cells and with multiple targets can provide increased efficacy at lower drug concentrations and reduce side effects. In our previous work, we designed a therapeutic peptide (Bac-ELP1-H1) targeting the c-myc oncogene and demonstrated its ability to reduce tumor size, delay neurological deficits, and improve survival in a rat glioblastoma model. In this study, we expanded our research to the U87 glioblastoma cell line and investigated the efficacy of Bac-ELP1-H1/hyperthermia treatment, as well as the combination treatment of temozolomide and Bac-ELP1-H1, in suppressing tumor growth and extending survival in athymic mice. Our experiments revealed that the combination treatment of Bac-ELP1-H1 and temozolomide acted synergistically to enhance survival in mice and was more effective in reducing tumor progression than the single components. Additionally, our study demonstrated the effectiveness of hyperthermia in facilitating the accumulation of the Bac-ELP1-H1 protein at the tumor site. Our findings suggest that the combination of targeted c-myc inhibitory biopolymer with systemic temozolomide therapy may represent a promising alternative treatment option for glioblastoma patients.
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Affiliation(s)
- Laxmi Dhungel
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
| | - Cayla Harris
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
| | - Lauren Romine
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
| | - Jan Sarkaria
- Division of Radiation Oncology, Mayo Clinic and Foundation, 200 First Street, SW, Rochester, MN 55905, USA
| | - Drazen Raucher
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
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6
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Wang Q, Hsiao JC, Yardeny N, Huang HC, O’Mara CM, Orth-He EL, Ball DP, Zhang Z, Bachovchin DA. The NLRP1 and CARD8 inflammasomes detect reductive stress. Cell Rep 2023; 42:111966. [PMID: 36649710 PMCID: PMC9942139 DOI: 10.1016/j.celrep.2022.111966] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/25/2022] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
The danger signals that activate the related nucleotide-binding domain leucine-rich repeat pyrin domain-containing 1 (NLRP1) and caspase activation and recruitment domain-containing 8 (CARD8) inflammasomes have not been fully established. We recently reported that the oxidized form of TRX1 binds to NLRP1 and represses inflammasome activation. These findings suggested that intracellular reductive stress, which would reduce oxidized TRX1 and thereby abrogate the NLRP1-TRX1 interaction, is an NLRP1 inflammasome-activating danger signal. However, no agents that induce reductive stress were known to test this premise. Here, we identify and characterize several radical-trapping antioxidants, including JSH-23, that induce reductive stress. We show that these compounds accelerate the proteasome-mediated degradation of the repressive N-terminal fragments of both NLRP1 and CARD8, releasing the inflammasome-forming C-terminal fragments from autoinhibition. Overall, this work validates chemical probes that induce reductive stress and establishes reductive stress as a danger signal sensed by both the NLRP1 and CARD8 inflammasomes.
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Affiliation(s)
- Qinghui Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jeffrey C. Hsiao
- Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Noah Yardeny
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hsin-Che Huang
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claire M. O’Mara
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elizabeth L. Orth-He
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel P. Ball
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ze Zhang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel A. Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Lead contact,Correspondence:
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7
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Ianevski A, Giri AK, Aittokallio T. SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples. Nucleic Acids Res 2022; 50:W739-W743. [PMID: 35580060 PMCID: PMC9252834 DOI: 10.1093/nar/gkac382] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/16/2022] [Accepted: 04/29/2022] [Indexed: 11/26/2022] Open
Abstract
SynergyFinder (https://synergyfinder.fimm.fi) is a free web-application for interactive analysis and visualization of multi-drug combination response data. Since its first release in 2017, SynergyFinder has become a popular tool for multi-dose combination data analytics, partly because the development of its functionality and graphical interface has been driven by a diverse user community, including both chemical biologists and computational scientists. Here, we describe the latest upgrade of this community-effort, SynergyFinder release 3.0, introducing a number of novel features that support interactive multi-sample analysis of combination synergy, a novel consensus synergy score that combines multiple synergy scoring models, and an improved outlier detection functionality that eliminates false positive results, along with many other post-analysis options such as weighting of synergy by drug concentrations and distinguishing between different modes of synergy (potency and efficacy). Based on user requests, several additional improvements were also implemented, including new data visualizations and export options for multi-drug combinations. With these improvements, SynergyFinder 3.0 supports robust identification of consistent combinatorial synergies for multi-drug combinatorial discovery and clinical translation.
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Affiliation(s)
- Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland.,Helsinki Institute for Information Technology (HIIT), Aalto University, Finland
| | - Anil K Giri
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland.,Foundation for the Finnish Cancer Institute (FCI), University of Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland.,Helsinki Institute for Information Technology (HIIT), Aalto University, Finland.,Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Norway.,Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Norway
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8
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Wu Q, Zhen Y, Shi L, Vu P, Greninger P, Adil R, Merritt J, Egan R, Wu MJ, Yin X, Ferrone CR, Deshpande V, Baiev I, Pinto CJ, McLoughlin DE, Walmsley CS, Stone JR, Gordan JD, Zhu AX, Juric D, Goyal L, Benes CH, Bardeesy N. EGFR Inhibition Potentiates FGFR Inhibitor Therapy and Overcomes Resistance in FGFR2 Fusion-Positive Cholangiocarcinoma. Cancer Discov 2022; 12:1378-1395. [PMID: 35420673 PMCID: PMC9064956 DOI: 10.1158/2159-8290.cd-21-1168] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/10/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022]
Abstract
FGFR inhibitors are approved for the treatment of advanced cholangiocarcinoma harboring FGFR2 fusions. However, the response rate is moderate, and resistance emerges rapidly due to acquired secondary FGFR2 mutations or due to other less-defined mechanisms. Here, we conducted high-throughput combination drug screens, biochemical analysis, and therapeutic studies using patient-derived models of FGFR2 fusion-positive cholangiocarcinoma to gain insight into these clinical profiles and uncover improved treatment strategies. We found that feedback activation of EGFR signaling limits FGFR inhibitor efficacy, restricting cell death induction in sensitive models and causing resistance in insensitive models lacking secondary FGFR2 mutations. Inhibition of wild-type EGFR potentiated responses to FGFR inhibitors in both contexts, durably suppressing MEK/ERK and mTOR signaling, increasing apoptosis, and causing marked tumor regressions in vivo. Our findings reveal EGFR-dependent adaptive signaling as an important mechanism limiting FGFR inhibitor efficacy and driving resistance and support clinical testing of FGFR/EGFR inhibitor therapy for FGFR2 fusion-positive cholangiocarcinoma. SIGNIFICANCE We demonstrate that feedback activation of EGFR signaling limits the effectiveness of FGFR inhibitor therapy and drives adaptive resistance in patient-derived models of FGFR2 fusion-positive cholangiocarcinoma. These studies support the potential of combination treatment with FGFR and EGFR inhibitors as an improved treatment for patients with FGFR2-driven cholangiocarcinoma.
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Affiliation(s)
- Qibiao Wu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yuanli Zhen
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lei Shi
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Phuong Vu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Patricia Greninger
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ramzi Adil
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Joshua Merritt
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Regina Egan
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Meng-Ju Wu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xunqin Yin
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cristina R Ferrone
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Islam Baiev
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christopher J Pinto
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel E McLoughlin
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charlotte S Walmsley
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - James R Stone
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - John D Gordan
- Helen Diller Family Comprehensive Cancer Center and Quantitative Biosciences Institute, University of California, San Francisco
| | - Andrew X Zhu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.,Jiahui International Cancer Center, Jiahui Health, Shanghai, China
| | - Dejan Juric
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lipika Goyal
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cyril H Benes
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nabeel Bardeesy
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
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9
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Lu X, Hackman GL, Saha A, Rathore AS, Collins M, Friedman C, Yi SS, Matsuda F, DiGiovanni J, Lodi A, Tiziani S. Metabolomics-based phenotypic screens for evaluation of drug synergy via direct-infusion mass spectrometry. iScience 2022; 25:104221. [PMID: 35494234 PMCID: PMC9046262 DOI: 10.1016/j.isci.2022.104221] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/22/2022] [Accepted: 04/05/2022] [Indexed: 12/15/2022] Open
Abstract
Drugs used in combination can synergize to increase efficacy, decrease toxicity, and prevent drug resistance. While conventional high-throughput screens that rely on univariate data are incredibly valuable to identify promising drug candidates, phenotypic screening methodologies could be beneficial to provide deep insight into the molecular response of drug combination with a likelihood of improved clinical outcomes. We developed a high-content metabolomics drug screening platform using stable isotope-tracer direct-infusion mass spectrometry that informs an algorithm to determine synergy from multivariate phenomics data. Using a cancer drug library, we validated the drug screening, integrating isotope-enriched metabolomics data and computational data mining, on a panel of prostate cell lines and verified the synergy between CB-839 and docetaxel both in vitro (three-dimensional model) and in vivo. The proposed unbiased metabolomics screening platform can be used to rapidly generate phenotype-informed datasets and quantify synergy for combinatorial drug discovery.
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Affiliation(s)
- Xiyuan Lu
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA,Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX 78723, USA
| | - G. Lavender Hackman
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA,Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX 78723, USA
| | - Achinto Saha
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin,TX 78712, USA
| | - Atul Singh Rathore
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA,Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX 78723, USA
| | - Meghan Collins
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA,Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX 78723, USA
| | - Chelsea Friedman
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin,TX 78712, USA
| | - S. Stephen Yi
- Department of Oncology, Dell Medical School, Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX 78723, USA,Institute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA,Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712, USA,Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX 78712, USA
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - John DiGiovanni
- Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX 78723, USA,Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin,TX 78712, USA,Department of Oncology, Dell Medical School, Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX 78723, USA
| | - Alessia Lodi
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA,Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX 78723, USA,Corresponding author
| | - Stefano Tiziani
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA,Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX 78723, USA,Department of Oncology, Dell Medical School, Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX 78723, USA,Institute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA,Corresponding author
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10
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Rønneberg L, Cremaschi A, Hanes R, Enserink JM, Zucknick M. bayesynergy: flexible Bayesian modelling of synergistic interaction effects in in vitro drug combination experiments. Brief Bioinform 2021; 22:bbab251. [PMID: 34308471 PMCID: PMC8575029 DOI: 10.1093/bib/bbab251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/26/2021] [Accepted: 06/14/2021] [Indexed: 11/24/2022] Open
Abstract
The effect of cancer therapies is often tested pre-clinically via in vitro experiments, where the post-treatment viability of the cancer cell population is measured through assays estimating the number of viable cells. In this way, large libraries of compounds can be tested, comparing the efficacy of each treatment. Drug interaction studies focus on the quantification of the additional effect encountered when two drugs are combined, as opposed to using the treatments separately. In the bayesynergy R package, we implement a probabilistic approach for the description of the drug combination experiment, where the observed dose response curve is modelled as a sum of the expected response under a zero-interaction model and an additional interaction effect (synergistic or antagonistic). Although the model formulation makes use of the Bliss independence assumption, we note that the posterior estimates of the dose-response surface can also be used to extract synergy scores based on other reference models, which we illustrate for the Highest Single Agent model. The interaction is modelled in a flexible manner, using a Gaussian process formulation. Since the proposed approach is based on a statistical model, it allows the natural inclusion of replicates, handles missing data and uneven concentration grids, and provides uncertainty quantification around the results. The model is implemented in the open-source Stan programming language providing a computationally efficient sampler, a fast approximation of the posterior through variational inference, and features parallel processing for working with large drug combination screens.
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Affiliation(s)
- Leiv Rønneberg
- Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Norway
| | - Andrea Cremaschi
- Singapore Institute for Clinical Sciences (SICS), A*STAR, Singapore
| | - Robert Hanes
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, Oslo 0379, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, Oslo 0379, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway
| | - Manuela Zucknick
- Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Norway
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11
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Procaspase-Activating Compound-1 Synergizes with TRAIL to Induce Apoptosis in Established Granulosa Cell Tumor Cell Line (KGN) and Explanted Patient Granulosa Cell Tumor Cells In Vitro. Int J Mol Sci 2021; 22:ijms22094699. [PMID: 33946730 PMCID: PMC8124867 DOI: 10.3390/ijms22094699] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 12/19/2022] Open
Abstract
Granulosa cell tumors (GCT) constitute only ~5% of ovarian neoplasms yet have significant consequences, as up to 80% of women with recurrent GCT will die of the disease. This study investigated the effectiveness of procaspase-activating compound 1 (PAC-1), an activator of procaspase-3, in treating adult GCT (AGCT) in combination with selected apoptosis-inducing agents. Sensitivity of the AGCT cell line KGN to these drugs, alone or in combination with PAC-1, was tested using a viability assay. Our results show a wide range in cytotoxic activity among the agents tested. Synergy with PAC-1 was most pronounced, both empirically and by mathematical modelling, when combined with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). This combination showed rapid kinetics of apoptosis induction as determined by caspase-3 activity, and strongly synergistic killing of both KGN as well as patient samples of primary and recurrent AGCT. We have demonstrated that the novel combination of two pro-apoptotic agents, TRAIL and PAC-1, significantly amplified the induction of apoptosis in AGCT cells, warranting further investigation of this combination as a potential therapy for AGCT.
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12
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Ianevski A, Giri AK, Aittokallio T. SynergyFinder 2.0: visual analytics of multi-drug combination synergies. Nucleic Acids Res 2020; 48:W488-W493. [PMID: 32246720 PMCID: PMC7319457 DOI: 10.1093/nar/gkaa216] [Citation(s) in RCA: 469] [Impact Index Per Article: 117.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/15/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
SynergyFinder (https://synergyfinder.fimm.fi) is a stand-alone web-application for interactive analysis and visualization of drug combination screening data. Since its first release in 2017, SynergyFinder has become a widely used web-tool both for the discovery of novel synergistic drug combinations in pre-clinical model systems (e.g. cell lines or primary patient-derived cells), and for better understanding of mechanisms of combination treatment efficacy or resistance. Here, we describe the latest version of SynergyFinder (release 2.0), which has extensively been upgraded through the addition of novel features supporting especially higher-order combination data analytics and exploratory visualization of multi-drug synergy patterns, along with automated outlier detection procedure, extended curve-fitting functionality and statistical analysis of replicate measurements. A number of additional improvements were also implemented based on the user requests, including new visualization and export options, updated user interface, as well as enhanced stability and performance of the web-tool. With these improvements, SynergyFinder 2.0 is expected to greatly extend its potential applications in various areas of multi-drug combinatorial screening and precision medicine.
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Affiliation(s)
- Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, FI-00290 Helsinki, Finland
- Helsinki Institute for Information Technology (HIIT), Department of Computer Science, Aalto University, FI-02150 Espoo, Finland
| | - Anil K Giri
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, FI-00290 Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, FI-00290 Helsinki, Finland
- Helsinki Institute for Information Technology (HIIT), Department of Computer Science, Aalto University, FI-02150 Espoo, Finland
- Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, N-0310 Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway
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13
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Identifying Therapies to Combat Epithelial Mesenchymal Plasticity-Associated Chemoresistance to Conventional Breast Cancer Therapies Using An shRNA Library Screen. Cancers (Basel) 2020; 12:cancers12051123. [PMID: 32365878 PMCID: PMC7281530 DOI: 10.3390/cancers12051123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Breast cancer (BC) is a heterogeneous disease for which the commonly used chemotherapeutic agents primarily include the anthracyclines (doxorubicin, epirubicin), microtubule inhibitors (paclitaxel, docetaxel, eribulin), and alkylating agents (cyclophosphamide). While these drugs can be highly effective, metastatic tumours are frequently refractory to treatment or become resistant upon tumour relapse. METHODS We undertook a cell polarity/epithelial mesenchymal plasticity (EMP)-enriched short hairpin RNA (shRNA) screen in MDA-MB-468 breast cancer cells to identify factors underpinning heterogeneous responses to three chemotherapeutic agents used clinically in breast cancer: Doxorubicin, docetaxel, and eribulin. shRNA-transduced cells were treated for 6 weeks with the EC10 of each drug, and shRNA representation assessed by deep sequencing. We first identified candidate genes with depleted shRNA, implying that their silencing could promote a response. Using the Broad Institute's Connectivity Map (CMap), we identified partner inhibitors targeting the identified gene families that may induce cell death in combination with doxorubicin, and tested them with all three drug treatments. RESULTS In total, 259 shRNAs were depleted with doxorubicin treatment (at p < 0.01), 66 with docetaxel, and 25 with eribulin. Twenty-four depleted hairpins overlapped between doxorubicin and docetaxel, and shRNAs for TGFB2, RUNX1, CCDC80, and HYOU1 were depleted across all the three drug treatments. Inhibitors of MDM/TP53, TGFBR, and FGFR were identified by CMap as the top pharmaceutical perturbagens and we validated the combinatorial benefits of the TGFBR inhibitor (SB525334) and MDM inhibitor (RITA) with doxorubicin treatment, and also observed synergy between the inhibitor SB525334 and eribulin in MDA-MB-468 cells. CONCLUSIONS Taken together, a cell polarity/EMP-enriched shRNA library screen identified relevant gene products that could be targeted alongside current chemotherapeutic agents for the treatment of invasive BC.
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Meyer CT, Wooten DJ, Lopez CF, Quaranta V. Charting the Fragmented Landscape of Drug Synergy. Trends Pharmacol Sci 2020; 41:266-280. [PMID: 32113653 PMCID: PMC7986484 DOI: 10.1016/j.tips.2020.01.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/16/2020] [Accepted: 01/29/2020] [Indexed: 12/16/2022]
Abstract
Even as the clinical impact of drug combinations continues to accelerate, no consensus on how to quantify drug synergy has emerged. Rather, surveying the landscape of drug synergy reveals the persistence of historical fissures regarding the appropriate domains of conflicting synergy models - fissures impacting all aspects of combination therapy discovery and deployment. Herein we chronicle the impact of these divisions on: (i) the design, interpretation, and reproducibility of high-throughput combination screens; (ii) the performance of algorithms to predict synergistic mixtures; and (iii) the search for higher-order synergistic interactions. Further progress in each of these subfields hinges on reaching a consensus regarding the long-standing rifts in the field.
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Affiliation(s)
- Christian T Meyer
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA
| | - David J Wooten
- Department of Physics, Pennsylvania State University, University Park, PA, USA
| | - Carlos F Lopez
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Vito Quaranta
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
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Sun Y, Hou L, Qin L, Liu Y, Li J, Qian Q. RCorp: a resource for chemical disease semantic extraction in Chinese. BMC Med Inform Decis Mak 2019; 19:234. [PMID: 31801523 PMCID: PMC6894109 DOI: 10.1186/s12911-019-0936-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Background To robustly identify synergistic combinations of drugs, high-throughput screenings are desirable. It will be of great help to automatically identify the relations in the published papers with machine learning based tools. To support the chemical disease semantic relation extraction especially for chronic diseases, a chronic disease specific corpus for combination therapy discovery in Chinese (RCorp) is manually annotated. Methods In this study, we extracted abstracts from a Chinese medical literature server and followed the annotation framework of the BioCreative CDR corpus, with the guidelines modified to make the combination therapy related relations available. An annotation tool was incorporated to the standard annotation process. Results The resulting RCorp consists of 339 Chinese biomedical articles with 2367 annotated chemicals, 2113 diseases, 237 symptoms, 164 chemical-induce-disease relations, 163 chemical-induce-symptom relations, and 805 chemical-treat-disease relations. Each annotation includes both the mention text spans and normalized concept identifiers. The corpus gets an inter-annotator agreement score of 0.883 for chemical entities, 0.791 for disease entities which are measured by F score. And the F score for chemical-treat-disease relations gets 0.788 after unifying the entity mentions. Conclusions We extracted and manually annotated a chronic disease specific corpus for combination therapy discovery in Chinese. The result analysis of the corpus proves its quality for the combination therapy related knowledge discovery task. Our annotated corpus would be a useful resource for the modelling of entity recognition and relation extraction tools. In the future, an evaluation based on the corpus will be held.
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Affiliation(s)
- Yueping Sun
- Institute of Medical Information, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100020, China
| | - Li Hou
- Institute of Medical Information, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100020, China.
| | - Lu Qin
- Institute of Medical Information, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100020, China
| | - Yan Liu
- Institute of Medical Information, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100020, China
| | - Jiao Li
- Institute of Medical Information, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100020, China
| | - Qing Qian
- Institute of Medical Information, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100020, China
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