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Almubarak HF, Tan W, Hoffmann AD, Wei J, El-Shennawy L, Squires JR, Sun Y, Dashzeveg NK, Simonton B, Jia Y, Iyer R, Xu Y, Nicolaescu V, Elli D, Randall GC, Schipma MJ, Swaminathan S, Ison MG, Liu H, Fang D, Shen Y. Physics-driven structural docking and protein language models accelerate antibody screening and design for broad-spectrum antiviral therapy. bioRxiv 2024:2024.03.01.582176. [PMID: 38496411 PMCID: PMC10942297 DOI: 10.1101/2024.03.01.582176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Therapeutic antibodies have become one of the most influential therapeutics in modern medicine to fight against infectious pathogens, cancer, and many other diseases. However, experimental screening for highly efficacious targeting antibodies is labor-intensive and of high cost, which is exacerbated by evolving antigen targets under selective pressure such as fast-mutating viral variants. As a proof-of-concept, we developed a machine learning-assisted antibody generation pipeline that greatly accelerates the screening and re-design of immunoglobulins G (IgGs) against a broad spectrum of SARS-CoV-2 coronavirus variant strains. These viruses infect human host cells via the viral spike protein binding to the host cell receptor angiotensin-converting enzyme 2 (ACE2). Using over 1300 IgG sequences derived from convalescent patient B cells that bind with spike's receptor binding domain (RBD), we first established protein structural docking models in assessing the RBD-IgG-ACE2 interaction interfaces and predicting the virus-neutralizing activity of each IgG with a confidence score. Additionally, employing Gaussian process regression (also known as Kriging) in a latent space of an antibody language model, we predicted the landscape of IgGs' activity profiles against individual coronaviral variants of concern. With functional analyses and experimental validations, we efficiently prioritized IgG candidates for neutralizing a broad spectrum of viral variants (wildtype, Delta, and Omicron) to prevent the infection of host cells in vitro and hACE2 transgenic mice in vivo. Furthermore, the computational analyses enabled rational redesigns of selective IgG clones with single amino acid substitutions at the RBD-binding interface to improve the IgG blockade efficacy for one of the severe, therapy-resistant strains - Delta (B.1.617). Our work expedites applications of artificial intelligence in antibody screening and re-design even in low-data regimes combining protein language models and Kriging for antibody sequence analysis, activity prediction, and efficacy improvement, in synergy with physics-driven protein docking models for antibody-antigen interface structure analyses and functional optimization.
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Affiliation(s)
- Hannah Faisal Almubarak
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Driskill Graduate Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Wuwei Tan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843
| | - Andrew D. Hoffmann
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Juncheng Wei
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Lamiaa El-Shennawy
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Joshua R. Squires
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843
| | - Nurmaa K. Dashzeveg
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Brooke Simonton
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Yuzhi Jia
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Radhika Iyer
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Yanan Xu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Vlad Nicolaescu
- Howard T. Ricketts Laboratory and Department of Microbiology, the University of Chicago, Chicago, IL 60637
| | - Derek Elli
- Howard T. Ricketts Laboratory and Department of Microbiology, the University of Chicago, Chicago, IL 60637
| | - Glenn C. Randall
- Howard T. Ricketts Laboratory and Department of Microbiology, the University of Chicago, Chicago, IL 60637
| | - Matthew J. Schipma
- NUseq Core Facility, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Suchitra Swaminathan
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Division of Rheumatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | | | - Huiping Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Deyu Fang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 60611
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843
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2
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Dashzeveg NK, Jia Y, Zhang Y, Gerratana L, Patel P, Shajahan A, Dandar T, Ramos EK, Almubarak HF, Adorno-Cruz V, Taftaf R, Schuster EJ, Scholten D, Sokolowski MT, Reduzzi C, El-Shennawy L, Hoffmann AD, Manai M, Zhang Q, D'Amico P, Azadi P, Colley KJ, Platanias LC, Shah AN, Gradishar WJ, Cristofanilli M, Muller WA, Cobb BA, Liu H. Dynamic Glycoprotein Hyposialylation Promotes Chemotherapy Evasion and Metastatic Seeding of Quiescent Circulating Tumor Cell Clusters in Breast Cancer. Cancer Discov 2023; 13:2050-2071. [PMID: 37272843 PMCID: PMC10481132 DOI: 10.1158/2159-8290.cd-22-0644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 04/14/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
Most circulating tumor cells (CTC) are detected as single cells, whereas a small proportion of CTCs in multicellular clusters with stemness properties possess 20- to 100-times higher metastatic propensity than the single cells. Here we report that CTC dynamics in both singles and clusters in response to therapies predict overall survival for breast cancer. Chemotherapy-evasive CTC clusters are relatively quiescent with a specific loss of ST6GAL1-catalyzed α2,6-sialylation in glycoproteins. Dynamic hyposialylation in CTCs or deficiency of ST6GAL1 promotes cluster formation for metastatic seeding and enables cellular quiescence to evade paclitaxel treatment in breast cancer. Glycoproteomic analysis reveals newly identified protein substrates of ST6GAL1, such as adhesion or stemness markers PODXL, ICAM1, ECE1, ALCAM1, CD97, and CD44, contributing to CTC clustering (aggregation) and metastatic seeding. As a proof of concept, neutralizing antibodies against one newly identified contributor, PODXL, inhibit CTC cluster formation and lung metastasis associated with paclitaxel treatment for triple-negative breast cancer. SIGNIFICANCE This study discovers that dynamic loss of terminal sialylation in glycoproteins of CTC clusters contributes to the fate of cellular dormancy, advantageous evasion to chemotherapy, and enhanced metastatic seeding. It identifies PODXL as a glycoprotein substrate of ST6GAL1 and a candidate target to counter chemoevasion-associated metastasis of quiescent tumor cells. This article is featured in Selected Articles from This Issue, p. 1949.
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Affiliation(s)
- Nurmaa K. Dashzeveg
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yuzhi Jia
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Youbin Zhang
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lorenzo Gerratana
- Department of Medicinal Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Priyam Patel
- Quantitative Data Science Core, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Asif Shajahan
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Tsogbadrakh Dandar
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Erika K. Ramos
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Hannah F. Almubarak
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Valery Adorno-Cruz
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rokana Taftaf
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Emma J. Schuster
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - David Scholten
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Michael T. Sokolowski
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Carolina Reduzzi
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Division of Hematology-Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Lamiaa El-Shennawy
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Andrew D. Hoffmann
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Maroua Manai
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Qiang Zhang
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Paolo D'Amico
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Karen J. Colley
- Department of Biochemistry and Molecular Genetics, University of Illinois Chicago, Chicago, Illinois
| | - Leonidas C. Platanias
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ami N. Shah
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - William J. Gradishar
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Massimo Cristofanilli
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Division of Hematology-Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - William A. Muller
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Brian A. Cobb
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Huiping Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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3
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Hoffmann AD, Weinberg SE, Swaminathan S, Chaudhuri S, Almubarak HF, Schipma MJ, Mao C, Wang X, El-Shennawy L, Dashzeveg NK, Wei J, Mehl PJ, Shihadah LJ, Wai CM, Ostiguin C, Jia Y, D'Amico P, Wang NR, Luo Y, Demonbreun AR, Ison MG, Liu H, Fang D. Unique molecular signatures sustained in circulating monocytes and regulatory T cells in convalescent COVID-19 patients. Clin Immunol 2023; 252:109634. [PMID: 37150240 PMCID: PMC10162478 DOI: 10.1016/j.clim.2023.109634] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/09/2023]
Abstract
Over two years into the COVID-19 pandemic, the human immune response to SARS-CoV-2 during the active disease phase has been extensively studied. However, the long-term impact after recovery, which is critical to advance our understanding SARS-CoV-2 and COVID-19-associated long-term complications, remains largely unknown. Herein, we characterized single-cell profiles of circulating immune cells in the peripheral blood of 100 patients, including convalescent COVID-19 and sero-negative controls. Flow cytometry analyses revealed reduced frequencies of both short-lived monocytes and long-lived regulatory T (Treg) cells within the patients who have recovered from severe COVID-19. sc-RNA seq analysis identifies seven heterogeneous clusters of monocytes and nine Treg clusters featuring distinct molecular signatures in association with COVID-19 severity. Asymptomatic patients contain the most abundant clusters of monocytes and Tregs expressing high CD74 or IFN-responsive genes. In contrast, the patients recovered from a severe disease have shown two dominant inflammatory monocyte clusters featuring S100 family genes: one monocyte cluster of S100A8 & A9 coupled with high HLA-I and another cluster of S100A4 & A6 with high HLA-II genes, a specific non-classical monocyte cluster with distinct IFITM family genes, as well as a unique TGF-β high Treg Cluster. The outpatients and seronegative controls share most of the monocyte and Treg clusters patterns with high expression of HLA genes. Surprisingly, while presumably short-lived monocytes appear to have sustained alterations over 4 months, the decreased frequencies of long-lived Tregs (high HLA-DRA and S100A6) in the outpatients restore over the tested convalescent time (≥ 4 months). Collectively, our study identifies sustained and dynamically altered monocytes and Treg clusters with distinct molecular signatures after recovery, associated with COVID-19 severity.
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Affiliation(s)
- Andrew D Hoffmann
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sam E Weinberg
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Suchitra Swaminathan
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Division of Rheumatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shuvam Chaudhuri
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hannah Faisal Almubarak
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Matthew J Schipma
- NUseq Core Facility, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Chengsheng Mao
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Xinkun Wang
- NUseq Core Facility, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lamiaa El-Shennawy
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nurmaa K Dashzeveg
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Juncheng Wei
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Paul J Mehl
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Laura J Shihadah
- NUseq Core Facility, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ching Man Wai
- NUseq Core Facility, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Carolina Ostiguin
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yuzhi Jia
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Paolo D'Amico
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Neale R Wang
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yuan Luo
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alexis R Demonbreun
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Michael G Ison
- Division of Infectious Disease, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Division of Organ Transplantation, Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Respiratory Diseases Branch, Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA.
| | - Huiping Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
| | - Deyu Fang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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4
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Ramos EK, Tsai CF, Jia Y, Cao Y, Manu M, Taftaf R, Hoffmann AD, El-Shennawy L, Gritsenko MA, Adorno-Cruz V, Schuster EJ, Scholten D, Patel D, Liu X, Patel P, Wray B, Zhang Y, Zhang S, Moore RJ, Mathews JV, Schipma MJ, Liu T, Tokars VL, Cristofanilli M, Shi T, Shen Y, Dashzeveg NK, Liu H. Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity. eLife 2022; 11:e82669. [PMID: 36193887 PMCID: PMC9581534 DOI: 10.7554/elife.82669] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022] Open
Abstract
Tumor-initiating cells with reprogramming plasticity or stem-progenitor cell properties (stemness) are thought to be essential for cancer development and metastatic regeneration in many cancers; however, elucidation of the underlying molecular network and pathways remains demanding. Combining machine learning and experimental investigation, here we report CD81, a tetraspanin transmembrane protein known to be enriched in extracellular vesicles (EVs), as a newly identified driver of breast cancer stemness and metastasis. Using protein structure modeling and interface prediction-guided mutagenesis, we demonstrate that membrane CD81 interacts with CD44 through their extracellular regions in promoting tumor cell cluster formation and lung metastasis of triple negative breast cancer (TNBC) in human and mouse models. In-depth global and phosphoproteomic analyses of tumor cells deficient with CD81 or CD44 unveils endocytosis-related pathway alterations, leading to further identification of a quality-keeping role of CD44 and CD81 in EV secretion as well as in EV-associated stemness-promoting function. CD81 is coexpressed along with CD44 in human circulating tumor cells (CTCs) and enriched in clustered CTCs that promote cancer stemness and metastasis, supporting the clinical significance of CD81 in association with patient outcomes. Our study highlights machine learning as a powerful tool in facilitating the molecular understanding of new molecular targets in regulating stemness and metastasis of TNBC.
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Affiliation(s)
- Erika K Ramos
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
- Driskill Graduate Program in Life Science, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National LaboratoryWashingtonUnited States
| | - Yuzhi Jia
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
| | - Yue Cao
- Department of Electrical and Computer Engineering, TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M UniversityCollege StationUnited States
| | - Megan Manu
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
| | - Rokana Taftaf
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
- Driskill Graduate Program in Life Science, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Andrew D Hoffmann
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
| | | | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National LaboratoryWashingtonUnited States
| | | | - Emma J Schuster
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
- Driskill Graduate Program in Life Science, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - David Scholten
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
- Driskill Graduate Program in Life Science, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Dhwani Patel
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
| | - Xia Liu
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
- Department of Toxicology and Cancer Biology, University of KentuckyLexingtonUnited States
| | - Priyam Patel
- Quantitative Data Science Core, Center for Genetic Medicine, Northwestern University Feinberg School of MedicineChicagoUnited States
| | - Brian Wray
- Quantitative Data Science Core, Center for Genetic Medicine, Northwestern University Feinberg School of MedicineChicagoUnited States
| | - Youbin Zhang
- Department of Medicine, Hematology/Oncology Division, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Shanshan Zhang
- Pathology Core Facility, Northwestern UniversityChicagoUnited States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National LaboratoryWashingtonUnited States
| | - Jeremy V Mathews
- Pathology Core Facility, Northwestern UniversityChicagoUnited States
| | - Matthew J Schipma
- Quantitative Data Science Core, Center for Genetic Medicine, Northwestern University Feinberg School of MedicineChicagoUnited States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National LaboratoryWashingtonUnited States
| | - Valerie L Tokars
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
| | - Massimo Cristofanilli
- Department of Medicine, Hematology/Oncology Division, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National LaboratoryWashingtonUnited States
| | - Yang Shen
- Department of Electrical and Computer Engineering, TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M UniversityCollege StationUnited States
| | | | - Huiping Liu
- Department of Pharmacology, Northwestern UniversityChicagoUnited States
- Department of Medicine, Hematology/Oncology Division, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
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5
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Hoffmann AD, Weinberg SE, Swaminathan S, Chaudhuri S, Mubarak HF, Schipma MJ, Mao C, Wang X, El-Shennawy L, Dashzeveg NK, Wei J, Mehl PJ, Shihadah LJ, Wai CM, Ostiguin C, Jia Y, D'Amico P, Wang NR, Luo Y, Demonbreun AR, Ison MG, Liu H, Fang D. Unique molecular signatures sustained in circulating monocytes and regulatory T cells in Convalescent COVID-19 patients. bioRxiv 2022:2022.03.26.485922. [PMID: 35378753 PMCID: PMC8978941 DOI: 10.1101/2022.03.26.485922] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Over two years into the COVID-19 pandemic, the human immune response to SARS-CoV-2 during the active disease phase has been extensively studied. However, the long-term impact after recovery, which is critical to advance our understanding SARS-CoV-2 and COVID-19-associated long-term complications, remains largely unknown. Herein, we characterized multi-omic single-cell profiles of circulating immune cells in the peripheral blood of 100 patients, including covenlesent COVID-19 and sero-negative controls. The reduced frequencies of both short-lived monocytes and long-lived regulatory T (Treg) cells are significantly associated with the patients recovered from severe COVID-19. Consistently, sc-RNA seq analysis reveals seven heterogeneous clusters of monocytes (M0-M6) and ten Treg clusters (T0-T9) featuring distinct molecular signatures and associated with COVID-19 severity. Asymptomatic patients contain the most abundant clusters of monocyte and Treg expressing high CD74 or IFN-responsive genes. In contrast, the patients recovered from a severe disease have shown two dominant inflammatory monocyte clusters with S100 family genes: S100A8 & A9 with high HLA-I whereas S100A4 & A6 with high HLA-II genes, a specific non-classical monocyte cluster with distinct IFITM family genes, and a unique TGF-β high Treg Cluster. The outpatients and seronegative controls share most of the monocyte and Treg clusters patterns with high expression of HLA genes. Surprisingly, while presumably short-ived monocytes appear to have sustained alterations over 4 months, the decreased frequencies of long-lived Tregs (high HLA-DRA and S100A6) in the outpatients restore over the tested convalescent time (>= 4 months). Collectively, our study identifies sustained and dynamically altered monocytes and Treg clusters with distinct molecular signatures after recovery, associated with COVID-19 severity.
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6
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Taftaf R, Liu X, Singh S, Jia Y, Dashzeveg NK, Hoffmann AD, El-Shennawy L, Ramos EK, Adorno-Cruz V, Schuster EJ, Scholten D, Patel D, Zhang Y, Davis AA, Reduzzi C, Cao Y, D'Amico P, Shen Y, Cristofanilli M, Muller WA, Varadan V, Liu H. ICAM1 initiates CTC cluster formation and trans-endothelial migration in lung metastasis of breast cancer. Nat Commun 2021; 12:4867. [PMID: 34381029 PMCID: PMC8358026 DOI: 10.1038/s41467-021-25189-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor cell (CTC) clusters mediate metastasis at a higher efficiency and are associated with lower overall survival in breast cancer compared to single cells. Combining single-cell RNA sequencing and protein analyses, here we report the profiles of primary tumor cells and lung metastases of triple-negative breast cancer (TNBC). ICAM1 expression increases by 200-fold in the lung metastases of three TNBC patient-derived xenografts (PDXs). Depletion of ICAM1 abrogates lung colonization of TNBC cells by inhibiting homotypic tumor cell-tumor cell cluster formation. Machine learning-based algorithms and mutagenesis analyses identify ICAM1 regions responsible for homophilic ICAM1-ICAM1 interactions, thereby directing homotypic tumor cell clustering, as well as heterotypic tumor-endothelial adhesion for trans-endothelial migration. Moreover, ICAM1 promotes metastasis by activating cellular pathways related to cell cycle and stemness. Finally, blocking ICAM1 interactions significantly inhibits CTC cluster formation, tumor cell transendothelial migration, and lung metastasis. Therefore, ICAM1 can serve as a novel therapeutic target for metastasis initiation of TNBC. Circulating tumor cell (CTC) clusters are more efficient at mediating metastasis as compared to single cells and are associated with poor prognosis in breast cancer. Here, the authors show that ICAM1 is enriched in CTC clusters and its loss suppresses cell-cell interaction and CTC cluster formation, and propose ICAM1 as a therapeutic target for treating breast cancer metastasis.
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Affiliation(s)
- Rokana Taftaf
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xia Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Salendra Singh
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Yuzhi Jia
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nurmaa K Dashzeveg
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Andrew D Hoffmann
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lamiaa El-Shennawy
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Erika K Ramos
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Valery Adorno-Cruz
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Emma J Schuster
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David Scholten
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Dhwani Patel
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Youbin Zhang
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Andrew A Davis
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Carolina Reduzzi
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yue Cao
- Department of Electrical and Computer Engineering, TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA
| | - Paolo D'Amico
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - William A Muller
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Vinay Varadan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Huiping Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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7
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Adorno-Cruz V, Hoffmann AD, Liu X, Dashzeveg NK, Taftaf R, Wray B, Keri RA, Liu H. ITGA2 promotes expression of ACLY and CCND1 in enhancing breast cancer stemness and metastasis. Genes Dis 2021; 8:493-508. [PMID: 34179312 PMCID: PMC8209312 DOI: 10.1016/j.gendis.2020.01.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/22/2020] [Accepted: 01/26/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer metastasis is largely incurable and accounts for 90% of breast cancer deaths, especially for the aggressive basal-like or triple negative breast cancer (TNBC). Combining patient database analyses and functional studies, we examined the association of integrin family members with clinical outcomes as well as their connection with previously identified microRNA regulators of metastasis, such as miR-206 that inhibits stemness and metastasis of TNBC. Here we report that the integrin receptor CD49b-encoding ITGA2, a direct target of miR-206, promotes breast cancer stemness and metastasis. ITGA2 knockdown suppressed self-renewal related mammosphere formation and pluripotency marker expression, inhibited cell cycling, compromised migration and invasion, and therefore decreased lung metastasis of breast cancer. ITGA2 overexpression reversed miR-206-caused cell cycle arrest in G1. RNA sequencing analyses revealed that ITGA2 knockdown inhibits genes related to cell cycle regulation and lipid metabolism, including CCND1 and ACLY as representative targets, respectively. Knockdown of CCND1 or ACLY inhibits mammosphere formation of breast cancer cells. Overexpression of CCND1 rescues the phenotype of ITGA2 knockdown-induced cell cycle arrest. ACLY-encoded ATP citrate lyase is essential to maintain cellular acetyl-CoA levels. CCND1 knockdown further mimics ITGA2 knockdown in abolishing lung colonization of breast cancer cells. We identified that the low levels of miR-206 as well as high expression levels of ITGA2, ACLY and CCND1 are associated with an unfavorable relapse-free survival of the patients with estrogen receptor-negative or high grade breast cancer, especially basal-like or TNBC, possibly serving as potential biomarkers of cancer stemness and therapeutic targets of breast cancer metastasis.
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Affiliation(s)
- Valery Adorno-Cruz
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 11318, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrew D. Hoffmann
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Xia Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- University of Kentucky, College of Medicine, Lexington, KY 40536, USA
| | - Nurmaa K. Dashzeveg
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rokana Taftaf
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Brian Wray
- Bioinformatic Core, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ruth A. Keri
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 11318, USA
- Department of Genetics and Genome Sciences, The Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, OH 11318, USA
| | - Huiping Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Medicine, The Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Pathology and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 11318, USA
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8
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Liu X, Adorno-Cruz V, Chang YF, Jia Y, Kawaguchi M, Dashzeveg NK, Taftaf R, Ramos EK, Schuster EJ, El-Shennawy L, Patel D, Zhang Y, Cristofanilli M, Liu H. EGFR inhibition blocks cancer stem cell clustering and lung metastasis of triple negative breast cancer. Theranostics 2021; 11:6632-6643. [PMID: 33995681 PMCID: PMC8120216 DOI: 10.7150/thno.57706] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/21/2021] [Indexed: 02/07/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive and metastatic breast cancer subtypes lacking targeted therapy. Our recent work demonstrated that circulating tumor cell (CTC) clusters and polyclonal metastasis of TNBC are driven by aggregation of CD44+ cancer stem cells (CSC) and associated with an unfavorable prognosis, such as low overall survival. However, there is no existing therapeutic that can specifically block CTC or CSC cluster formation. Methods: Using patient-derived xenograft (PDX) models, we established an ex vivo tumor cell clustering assay for a pilot screening of blockade antibodies. After identifying EGFR as a target candidate, we modulated the gene expression and inhibited its kinase activity to determine its functional importance in tumor cell clustering and therapeutic inhibition of lung metastasis. We also examined the molecular regulation network of EGFR and a potential connection to CSC marker CD44 and microRNAs, which regulate CTC clustering. Results: We report here that EGFR inhibition successfully blocks circulating CSC (cCSC) clustering and lung metastasis of TNBC. EGFR enhances CD44-mediated tumor cell aggregation and CD44 stabilizes EGFR. Importantly, blocking EGFR by a novel anti-EGFR monoclonal antibody (clone LA1) effectively blocked cell aggregation in vitro and reduced lung metastasis in vivo. Furthermore, our data demonstrated that the tumor suppressor microRNA-30c serves as another negative regulator of cCSC clustering and lung metastasis by targeting CD44 as well as its downstream effector EGFR. Conclusion: Our studies identify a novel anti-EGFR therapeutic strategy to inhibit cCSC aggregation and therefore abolish cCSC cluster-mediated metastasis of TNBC.
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9
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Dashzeveg NK, Taftaf R, Ramos EK, Torre-Healy L, Chumakova A, Silver DJ, Alban TJ, Sinyuk M, Thiagarajan PS, Jarrar AM, Turaga SM, Saygin C, Mulkearns-Hubert E, Hitomi M, Rich JN, Gerson SL, Lathia JD, Liu H. New Advances and Challenges of Targeting Cancer Stem Cells. Cancer Res 2017; 77:5222-5227. [PMID: 28928129 DOI: 10.1158/0008-5472.can-17-0054] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/25/2017] [Accepted: 07/18/2017] [Indexed: 02/04/2023]
Abstract
The second International Cancer Stem Cell Conference in Cleveland, Ohio, on September 20-23, 2016, convened 330 attendees from academic, industrial, and clinical organizations. It featured a debate on the concepts and challenges of the cancer stem cells (CSC) as well as CSC-centered scientific sessions on clinical trials, genetics and epigenetics, tumor microenvironment, immune suppression, metastasis, therapeutic resistance, and emerging novel concepts. The conference hosted 35 renowned speakers, 100 posters, 20 short talks, and a preconference workshop. The reported advances of CSC research and therapies fostered new collaborations across national and international borders, and inspired the next generation's young scientists. Cancer Res; 77(19); 5222-7. ©2017 AACR.
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Affiliation(s)
- Nurmaa K Dashzeveg
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Rokana Taftaf
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Erika K Ramos
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Luke Torre-Healy
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Anastasia Chumakova
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Daniel J Silver
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Tyler J Alban
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Maksim Sinyuk
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Praveena S Thiagarajan
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Awad M Jarrar
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Soumya M Turaga
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Caner Saygin
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Erin Mulkearns-Hubert
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Masahiro Hitomi
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Jeremy N Rich
- Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio.,The Case Comprehensive Cancer Center, Cleveland, Ohio.,The National Center for Regenerative Medicine, Cleveland, Ohio
| | - Stanton L Gerson
- The Case Comprehensive Cancer Center, Cleveland, Ohio.,The National Center for Regenerative Medicine, Cleveland, Ohio.,The University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Justin D Lathia
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio.,The Case Comprehensive Cancer Center, Cleveland, Ohio.,The National Center for Regenerative Medicine, Cleveland, Ohio
| | - Huiping Liu
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois. .,The Case Comprehensive Cancer Center, Cleveland, Ohio.,The National Center for Regenerative Medicine, Cleveland, Ohio.,Department of Medicine (Hematology and Oncology Division) and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Deparmtent of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
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