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Zhao G, Newbury P, Ishi Y, Chekalin E, Zeng B, Glicksberg BS, Wen A, Paithankar S, Sasaki T, Suri A, Nazarian J, Pacold ME, Brat DJ, Nicolaides T, Chen B, Hashizume R. Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma. Acta Neuropathol Commun 2022; 10:150. [PMID: 36274161 PMCID: PMC9590174 DOI: 10.1186/s40478-022-01463-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/13/2022] [Indexed: 11/25/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is an aggressive incurable brainstem tumor that targets young children. Complete resection is not possible, and chemotherapy and radiotherapy are currently only palliative. This study aimed to identify potential therapeutic agents using a computational pipeline to perform an in silico screen for novel drugs. We then tested the identified drugs against a panel of patient-derived DIPG cell lines. Using a systematic computational approach with publicly available databases of gene signature in DIPG patients and cancer cell lines treated with a library of clinically available drugs, we identified drug hits with the ability to reverse a DIPG gene signature to one that matches normal tissue background. The biological and molecular effects of drug treatment was analyzed by cell viability assay and RNA sequence. In vivo DIPG mouse model survival studies were also conducted. As a result, two of three identified drugs showed potency against the DIPG cell lines Triptolide and mycophenolate mofetil (MMF) demonstrated significant inhibition of cell viability in DIPG cell lines. Guanosine rescued reduced cell viability induced by MMF. In vivo, MMF treatment significantly inhibited tumor growth in subcutaneous xenograft mice models. In conclusion, we identified clinically available drugs with the ability to reverse DIPG gene signatures and anti-DIPG activity in vitro and in vivo. This novel approach can repurpose drugs and significantly decrease the cost and time normally required in drug discovery.
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Affiliation(s)
- Guisheng Zhao
- grid.137628.90000 0004 1936 8753Department of Pediatrics, New York University Langone Health, 160 East 32nd St., New York, NY 10016 USA
| | - Patrick Newbury
- grid.17088.360000 0001 2150 1785Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI 49503 USA
| | - Yukitomo Ishi
- grid.16753.360000 0001 2299 3507Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior St., Simpson Querrey 4-514, Chicago, IL 60611 USA ,grid.413808.60000 0004 0388 2248Division of Hematology, Oncology, Neuro-Oncology & Stem Cell Transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Box 205, Chicago, IL 60611 USA
| | - Eugene Chekalin
- grid.17088.360000 0001 2150 1785Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI 49503 USA
| | - Billy Zeng
- grid.17088.360000 0001 2150 1785Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI 49503 USA
| | - Benjamin S. Glicksberg
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029 USA ,grid.416167.30000 0004 0442 1996Icahn School of Medicine at Mount Sinai, Hasso Plattner Institute for Digital Health at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029 USA
| | - Anita Wen
- grid.17088.360000 0001 2150 1785Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI 49503 USA
| | - Shreya Paithankar
- grid.17088.360000 0001 2150 1785Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI 49503 USA
| | - Takahiro Sasaki
- grid.16753.360000 0001 2299 3507Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, 303 East Superior St., Chicago, IL 60611 USA ,grid.412857.d0000 0004 1763 1087Department of Neurological Surgery, Wakayama Medical University, 811-1 Kimiidera, Wakayama, Japan
| | - Amreena Suri
- grid.16753.360000 0001 2299 3507Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior St., Simpson Querrey 4-514, Chicago, IL 60611 USA ,grid.413808.60000 0004 0388 2248Division of Hematology, Oncology, Neuro-Oncology & Stem Cell Transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Box 205, Chicago, IL 60611 USA
| | - Javad Nazarian
- grid.239560.b0000 0004 0482 1586Children’s National Medical Center, 111 Michigan Avenue NW, Washington, DC 20010 USA ,grid.412341.10000 0001 0726 4330University Children’s Hospital Zurich, Steinwiesstrasse 75, 8032 Zurich, Switzerland
| | - Michael E. Pacold
- grid.137628.90000 0004 1936 8753Department of Radiation Oncology, New York University Langone Health, 550 First Avenue, New York, NY 10016 USA
| | - Daniel J. Brat
- grid.16753.360000 0001 2299 3507Department of Pathology, Robert H. Lurie Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611 USA
| | - Theodore Nicolaides
- grid.137628.90000 0004 1936 8753Department of Pediatrics, New York University Langone Health, 160 East 32nd St., New York, NY 10016 USA
| | - Bin Chen
- Department of Pediatrics and Human Development, Michigan State University, Secchia Center, Room 732, 15 Michigan St. NE, Grand Rapids, MI, 49503, USA. .,Department of Pharmacology and Toxicology, Michigan State University, 1355 Bogue St, East Lansing, MI, 48824, USA. .,Department of Computer Science and Engineering, Michigan State University, 428 S. Shaw Lane, East Lansing, MI, 48824, USA.
| | - Rintaro Hashizume
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior St., Simpson Querrey 4-514, Chicago, IL, 60611, USA. .,Division of Hematology, Oncology, Neuro-Oncology & Stem Cell Transplantation, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 East Chicago Avenue, Box 205, Chicago, IL, 60611, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 East Superior St., Chicago, IL, 60611, USA.
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Xing J, Shankar R, Ko M, Zhang K, Zhang S, Drelich A, Paithankar S, Chekalin E, Chua MS, Rajasekaran S, Kent Tseng CT, Zheng M, Kim S, Chen B. Deciphering COVID-19 host transcriptomic complexity and variations for therapeutic discovery against new variants. iScience 2022; 25:105068. [PMID: 36093376 PMCID: PMC9439871 DOI: 10.1016/j.isci.2022.105068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/18/2022] [Revised: 07/11/2022] [Accepted: 08/30/2022] [Indexed: 12/04/2022] Open
Abstract
The molecular manifestations of host cells responding to SARS-CoV-2 and its evolving variants of infection are vastly different across the studied models and conditions, imposing challenges for host-based antiviral drug discovery. Based on the postulation that antiviral drugs tend to reverse the global host gene expression induced by viral infection, we retrospectively evaluated hundreds of signatures derived from 1,700 published host transcriptomic profiles of SARS/MERS/SARS-CoV-2 infection using an iterative data-driven approach. A few of these signatures could be reversed by known anti-SARS-CoV-2 inhibitors, suggesting the potential of extrapolating the biology for new variant research. We discovered IMD-0354 as a promising candidate to reverse the signatures globally with nanomolar IC50 against SARS-CoV-2 and its five variants. IMD-0354 stimulated type I interferon antiviral response, inhibited viral entry, and down-regulated hijacked proteins. This study demonstrates that the conserved coronavirus signatures and the transcriptomic reversal approach that leverages polypharmacological effects could guide new variant therapeutic discovery.
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Affiliation(s)
- Jing Xing
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Rama Shankar
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Meehyun Ko
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, 13488, Korea
| | - Keke Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Sulin Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Aleksandra Drelich
- Departments of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Shreya Paithankar
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Eugene Chekalin
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Mei-Sze Chua
- Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
- Helen DeVos Children’s Hospital, Grand Rapids, MI 49503, USA
| | - Chien-Te Kent Tseng
- Departments of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Center of Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, 13488, Korea
| | - Bin Chen
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
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Chekalin E, Paithankar S, Chen B. Abstract 1198: Discovering novel bispecific antibody targets through the mining of large-scale bulk and single cell RNA-seq databases. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Bispecific antibodies (bsAbs) that bind two distinct surface proteins in cancer cells are emerging as an appealing therapeutic strategy in cancer immunotherapy. Among thousands of surface proteins, experimentally identifying the best target pairs that are expressed only in cancer cells, but not in normal cells, is costly and time-consuming. The open bulk RNASeq and single-cell (sc)RNASeq offers a great resource to identify novel bispecific targets. Bulk RNASeq has been widely explored to identify therapeutic targets and biomarkers, resulting in voluminous data for various cancers and normal tissues, but the mixture of cell types in bulk RNASeq could not characterize the precise expression of targets in cancer cells, resulting in considerable false positives. scRNASeq provides a high resolution of target expression in individual cells, however, the challenges in solving the dropout issue and cell type classification hinder the direct use of scRNASeq in bsAbs target identification. Utilizing the OCTAD database consisting of over 20,000 bulk RNASeq samples, we proposed an approach that identifies target pairs that separate tumors from healthy the most, taking into account cluster heterogeneity, the distance between tumors and healthy as well as the angle between potential markers. Among the top pairs in Hepatocellular Carcinoma (HCC), CD33~PLVAP, for example, was a false positive because CD33 is myeloid and lymphoid cell lineage-specific. We thus assembled a scRNAseq database of healthy vital organs containing 39361 cells to aid selection. By comparing their expression with the expression of 18000 malignant cells predicted from 72000 cells of eight HCC samples, we identified target pairs that mostly express on the surface of the malignant HCC cells and had low or zero expression in vital organs. The most promising marker pair was GPC3~MUC13, presenting on the surface of over 30% of malignant HCC cells, with very low expression in vital organs. We further developed an R package to navigate the bsAbs target selection from open bulk RNASeq and scRNASeq.
Citation Format: Eugene Chekalin, Shreya Paithankar, Bin Chen. Discovering novel bispecific antibody targets through the mining of large-scale bulk and single cell RNA-seq databases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1198.
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Affiliation(s)
| | | | - Bin Chen
- 1Michigan State University, Grand Rapids, MI
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