1
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Ravi R, Noonan KA, Pham V, Bedi R, Zhavoronkov A, Ozerov IV, Makarev E, V Artemov A, Wysocki PT, Mehra R, Nimmagadda S, Marchionni L, Sidransky D, Borrello IM, Izumchenko E, Bedi A. Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy. Nat Commun 2018. [PMID: 29467463 DOI: 10.1038/s41467-017-02696-6.pmid:29467463;pmcid:pmc5821872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
A majority of cancers fail to respond to immunotherapy with antibodies targeting immune checkpoints, such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) or programmed death-1 (PD-1)/PD-1 ligand (PD-L1). Cancers frequently express transforming growth factor-β (TGFβ), which drives immune dysfunction in the tumor microenvironment by inducing regulatory T cells (Tregs) and inhibiting CD8+ and TH1 cells. To address this therapeutic challenge, we invent bifunctional antibody-ligand traps (Y-traps) comprising an antibody targeting CTLA-4 or PD-L1 fused to a TGFβ receptor II ectodomain sequence that simultaneously disables autocrine/paracrine TGFβ in the target cell microenvironment (a-CTLA4-TGFβRIIecd and a-PDL1-TGFβRIIecd). a-CTLA4-TGFβRIIecd is more effective in reducing tumor-infiltrating Tregs and inhibiting tumor progression compared with CTLA-4 antibody (Ipilimumab). Likewise, a-PDL1-TGFβRIIecd exhibits superior antitumor efficacy compared with PD-L1 antibodies (Atezolizumab or Avelumab). Our data demonstrate that Y-traps counteract TGFβ-mediated differentiation of Tregs and immune tolerance, thereby providing a potentially more effective immunotherapeutic strategy against cancers that are resistant to current immune checkpoint inhibitors.
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Affiliation(s)
- Rajani Ravi
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Kimberly A Noonan
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Vui Pham
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Rishi Bedi
- Department of Computer Science, Stanford University, Palo Alto, CA, 94305, USA
| | - Alex Zhavoronkov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD, 21218, USA
| | - Ivan V Ozerov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD, 21218, USA
| | - Eugene Makarev
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD, 21218, USA
| | - Artem V Artemov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD, 21218, USA
| | - Piotr T Wysocki
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Ranee Mehra
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Sridhar Nimmagadda
- Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD, 21287, USA
| | - Luigi Marchionni
- Center for Computational Genomics, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Ivan M Borrello
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Evgeny Izumchenko
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Atul Bedi
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
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2
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Ravi R, Noonan KA, Pham V, Bedi R, Zhavoronkov A, Ozerov IV, Makarev E, V Artemov A, Wysocki PT, Mehra R, Nimmagadda S, Marchionni L, Sidransky D, Borrello IM, Izumchenko E, Bedi A. Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy. Nat Commun 2018; 9:741. [PMID: 29467463 PMCID: PMC5821872 DOI: 10.1038/s41467-017-02696-6] [Citation(s) in RCA: 221] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/18/2017] [Indexed: 12/24/2022] Open
Abstract
A majority of cancers fail to respond to immunotherapy with antibodies targeting immune checkpoints, such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) or programmed death-1 (PD-1)/PD-1 ligand (PD-L1). Cancers frequently express transforming growth factor-β (TGFβ), which drives immune dysfunction in the tumor microenvironment by inducing regulatory T cells (Tregs) and inhibiting CD8+ and TH1 cells. To address this therapeutic challenge, we invent bifunctional antibody-ligand traps (Y-traps) comprising an antibody targeting CTLA-4 or PD-L1 fused to a TGFβ receptor II ectodomain sequence that simultaneously disables autocrine/paracrine TGFβ in the target cell microenvironment (a-CTLA4-TGFβRIIecd and a-PDL1-TGFβRIIecd). a-CTLA4-TGFβRIIecd is more effective in reducing tumor-infiltrating Tregs and inhibiting tumor progression compared with CTLA-4 antibody (Ipilimumab). Likewise, a-PDL1-TGFβRIIecd exhibits superior antitumor efficacy compared with PD-L1 antibodies (Atezolizumab or Avelumab). Our data demonstrate that Y-traps counteract TGFβ-mediated differentiation of Tregs and immune tolerance, thereby providing a potentially more effective immunotherapeutic strategy against cancers that are resistant to current immune checkpoint inhibitors.
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Affiliation(s)
- Rajani Ravi
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Kimberly A Noonan
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Vui Pham
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Rishi Bedi
- Department of Computer Science, Stanford University, Palo Alto, CA, 94305, USA
| | - Alex Zhavoronkov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD, 21218, USA
| | - Ivan V Ozerov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD, 21218, USA
| | - Eugene Makarev
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD, 21218, USA
| | - Artem V Artemov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD, 21218, USA
| | - Piotr T Wysocki
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Ranee Mehra
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Sridhar Nimmagadda
- Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD, 21287, USA
| | - Luigi Marchionni
- Center for Computational Genomics, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Ivan M Borrello
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Evgeny Izumchenko
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Atul Bedi
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
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3
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West MD, Labat I, Sternberg H, Larocca D, Nasonkin I, Chapman KB, Singh R, Makarev E, Aliper A, Kazennov A, Alekseenko A, Shuvalov N, Cheskidova E, Alekseev A, Artemov A, Putin E, Mamoshina P, Pryanichnikov N, Larocca J, Copeland K, Izumchenko E, Korzinkin M, Zhavoronkov A. Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression of COX7A1 in embryonic and cancer cells. Oncotarget 2017; 9:7796-7811. [PMID: 29487692 PMCID: PMC5814259 DOI: 10.18632/oncotarget.23748] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 09/18/2017] [Accepted: 12/20/2017] [Indexed: 12/19/2022] Open
Abstract
Here we present the application of deep neural network (DNN) ensembles trained on transcriptomic data to identify the novel markers associated with the mammalian embryonic-fetal transition (EFT). Molecular markers of this process could provide important insights into regulatory mechanisms of normal development, epimorphic tissue regeneration and cancer. Subsequent analysis of the most significant genes behind the DNNs classifier on an independent dataset of adult-derived and human embryonic stem cell (hESC)-derived progenitor cell lines led to the identification of COX7A1 gene as a potential EFT marker. COX7A1, encoding a cytochrome C oxidase subunit, was up-regulated in post-EFT murine and human cells including adult stem cells, but was not expressed in pre-EFT pluripotent embryonic stem cells or their in vitro-derived progeny. COX7A1 expression level was observed to be undetectable or low in multiple sarcoma and carcinoma cell lines as compared to normal controls. The knockout of the gene in mice led to a marked glycolytic shift reminiscent of the Warburg effect that occurs in cancer cells. The DNN approach facilitated the elucidation of a potentially new biomarker of cancer and pre-EFT cells, the embryo-onco phenotype, which may potentially be used as a target for controlling the embryonic-fetal transition.
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Affiliation(s)
| | - Ivan Labat
- AgeX Therapeutics, Inc., Alameda, CA, USA
| | | | | | | | | | | | - Eugene Makarev
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA
| | - Alex Aliper
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA
| | - Andrey Kazennov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey Alekseenko
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA.,Innopolis University, Innoplis, Russia
| | - Nikolai Shuvalov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Evgenia Cheskidova
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Aleksandr Alekseev
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Artem Artemov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA
| | - Evgeny Putin
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA.,Computer Technologies Lab, ITMO University, St. Petersburg, Russia
| | - Polina Mamoshina
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA
| | - Nikita Pryanichnikov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA
| | | | | | - Evgeny Izumchenko
- Johns Hopkins University, School of Medicine, Department of Otolaryngology-Head and Neck Cancer Research, Baltimore, MD, USA
| | - Mikhail Korzinkin
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA
| | - Alex Zhavoronkov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, USA.,The Biogerontology Research Foundation, Trevissome Park, Truro, UK
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4
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Makarev E, Schubert AD, Kanherkar RR, London N, Teka M, Ozerov I, Lezhnina K, Bedi A, Ravi R, Mehra R, Hoque MO, Sloma I, Gaykalova DA, Csoka AB, Sidransky D, Zhavoronkov A, Izumchenko E. In silico analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia. Cell Death Discov 2017; 3:17022. [PMID: 28580171 PMCID: PMC5439156 DOI: 10.1038/cddiscovery.2017.22] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 01/30/2017] [Revised: 02/23/2017] [Accepted: 03/13/2017] [Indexed: 12/16/2022] Open
Abstract
A subset of patients with oral squamous cell carcinoma (OSCC), the most common subtype of head and neck squamous cell carcinoma (HNSCC), harbor dysplastic lesions (often visually identified as leukoplakia) prior to cancer diagnosis. Although evidence suggest that leukoplakia represents an initial step in the progression to cancer, signaling networks driving this progression are poorly understood. Here, we applied in silico Pathway Activation Network Decomposition Analysis (iPANDA), a new bioinformatics software suite for qualitative analysis of intracellular signaling pathway activation using transcriptomic data, to assess a network of molecular signaling in OSCC and pre-neoplastic oral lesions. In tumor samples, our analysis detected major conserved mitogenic and survival signaling pathways strongly associated with HNSCC, suggesting that some of the pathways identified by our algorithm, but not yet validated as HNSCC related, may be attractive targets for future research. While pathways activation landscape in the majority of leukoplakias was different from that seen in OSCC, a subset of pre-neoplastic lesions has demonstrated some degree of similarity to the signaling profile seen in tumors, including dysregulation of the cancer-driving pathways related to survival and apoptosis. These results suggest that dysregulation of these signaling networks may be the driving force behind the early stages of OSCC tumorigenesis. While future studies with larger leukoplakia data sets are warranted to further estimate the values of this approach for capturing signaling features that characterize relevant lesions that actually progress to cancers, our platform proposes a promising new approach for detecting cancer-promoting pathways and tailoring the right therapy to prevent tumorigenesis.
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Affiliation(s)
- Eugene Makarev
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD 21218, USA
| | - Adrian D Schubert
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | | | - Nyall London
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Mahder Teka
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD 21218, USA
| | - Ivan Ozerov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD 21218, USA
| | - Ksenia Lezhnina
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD 21218, USA
| | - Atul Bedi
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Rajani Ravi
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Rannee Mehra
- Department of Oncology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Mohammad O Hoque
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Ido Sloma
- R&D, Champions Oncology, Baltimore, MD, USA
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Antonei B Csoka
- Department of Anatomy, Howard University, Washington, DC, USA
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Alex Zhavoronkov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, B301, 1101 33rd Street, Baltimore, MD 21218, USA.,D. Rogachev Federal Research and Clinical Center for Pediatric Hematology, Oncology, and Immunology, Samory Mashela 1, Moscow 117997, Russia.,The Biogerontology Research Foundation, 2354 Chynoweth House, Trevissome Park, Truro TR4 8UN, UK
| | - Evgeny Izumchenko
- Department of Otolaryngology-Head and Neck Cancer Research, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
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5
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Ozawa H, Ranaweera RS, Izumchenko E, Makarev E, Zhavoronkov A, Fertig EJ, Howard JD, Markovic A, Bedi A, Ravi R, Perez J, Le QT, Kong CS, Jordan RC, Wang H, Kang H, Quon H, Sidransky D, Chung CH. SMAD4 Loss Is Associated with Cetuximab Resistance and Induction of MAPK/JNK Activation in Head and Neck Cancer Cells. Clin Cancer Res 2017; 23:5162-5175. [PMID: 28522603 DOI: 10.1158/1078-0432.ccr-16-1686] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [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: 07/03/2016] [Revised: 12/01/2016] [Accepted: 05/15/2017] [Indexed: 01/01/2023]
Abstract
Purpose: We previously demonstrated an association between decreased SMAD4 expression and cetuximab resistance in head and neck squamous cell carcinoma (HNSCC). The purpose of this study was to further elucidate the clinical relevance of SMAD4 loss in HNSCC.Experimental Design: SMAD4 expression was assessed by IHC in 130 newly diagnosed and 43 patients with recurrent HNSCC. Correlative statistical analysis with clinicopathologic data was also performed. OncoFinder, a bioinformatics tool, was used to analyze molecular signaling in TCGA tumors with low or high SMAD4 mRNA levels. The role of SMAD4 was investigated by shRNA knockdown and gene reconstitution of HPV-negative HNSCC cell lines in vitro and in vivoResults: Our analysis revealed that SMAD4 loss was associated with an aggressive, HPV-negative, cetuximab-resistant phenotype. We found a signature of prosurvival and antiapoptotic pathways that were commonly dysregulated in SMAD4-low cases derived from TCGA-HNSCC dataset and an independent oral cavity squamous cell carcinoma (OSCC) cohort obtained from GEO. We show that SMAD4 depletion in an HNSCC cell line induces cetuximab resistance and results in worse survival in an orthotopic mouse model in vivo We implicate JNK and MAPK activation as mediators of cetuximab resistance and provide the foundation for the concomitant EGFR and JNK/MAPK inhibition as a potential strategy for overcoming cetuximab resistance in HNSCCs with SMAD4 loss.Conclusions: Our study demonstrates that loss of SMAD4 expression is a signature characterizing the cetuximab-resistant phenotype and suggests that SMAD4 expression may be a determinant of sensitivity/resistance to EGFR/MAPK or EGFR/JNK inhibition in HPV-negative HNSCC tumors. Clin Cancer Res; 23(17); 5162-75. ©2017 AACR.
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Affiliation(s)
- Hiroyuki Ozawa
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Ruchira S Ranaweera
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Evgeny Izumchenko
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Eugene Makarev
- Insilico Medicine, Inc, ETC, Johns Hopkins University, Baltimore, Maryland
| | - Alex Zhavoronkov
- Insilico Medicine, Inc, ETC, Johns Hopkins University, Baltimore, Maryland
| | - Elana J Fertig
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
- Department of Health Science Informatics, Johns Hopkins University, Baltimore, Maryland
| | - Jason D Howard
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Ana Markovic
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Atul Bedi
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rajani Ravi
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jimena Perez
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Quynh-Thu Le
- Department of Pathology, Stanford University School of Medicine Stanford, California
| | - Christina S Kong
- Department of Pathology, Stanford University School of Medicine Stanford, California
| | - Richard C Jordan
- Departments of Orofacial Sciences and Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Hao Wang
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Hyunseok Kang
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Harry Quon
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, Maryland
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christine H Chung
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland.
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, Florida
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6
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Zhavoronkov A, Izumchenko E, Kanherkar RR, Teka M, Cantor C, Manaye K, Sidransky D, West MD, Makarev E, Csoka AB. Pro-fibrotic pathway activation in trabecular meshwork and lamina cribrosa is the main driving force of glaucoma. Cell Cycle 2017; 15:1643-52. [PMID: 27229292 PMCID: PMC4934076 DOI: 10.1080/15384101.2016.1170261] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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] [Indexed: 12/21/2022] Open
Abstract
While primary open-angle glaucoma (POAG) is a leading cause of blindness worldwide, it still does not have a clear mechanism that can explain all clinical cases of the disease. Elevated IOP is associated with increased accumulation of extracellular matrix (ECM) proteins in the trabecular meshwork (TM) that prevents normal outflow of aqueous humor (AH) and has damaging effects on the fine mesh-like lamina cribrosa (LC) through which the optic nerve fibers pass. Applying a pathway analysis algorithm, we discovered that an elevated level of TGFβ observed in glaucoma-affected tissues could lead to pro-fibrotic pathway activation in TM and in LC. In turn, activated pro-fibrotic pathways lead to ECM remodeling in TM and LC, making TM less efficient in AH drainage and making LC more susceptible to damage from elevated IOP via ECM transformation in LC. We propose pathway targets for potential therapeutic interventions to delay or avoid fibrosis initiation in TM and LC tissues.
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Affiliation(s)
- Alex Zhavoronkov
- a Insilico Medicine, Inc., ETC, Johns Hopkins University , Baltimore , MD , USA.,b The Biogerontology Research Foundation , London , UK
| | - Evgeny Izumchenko
- e Johns Hopkins University , Department of Otolaryngology-Head and Neck Surgery
| | - Riya R Kanherkar
- c Vision Genomics, LLC , Washington, DC , USA.,d Epigenetics Laboratory, Howard University , Washington, DC , USA
| | - Mahder Teka
- c Vision Genomics, LLC , Washington, DC , USA
| | - Charles Cantor
- f Boston University , Boston , MA , USA.,g Retrotope, Inc ; Los Altos Hills , CA , USA
| | - Kebreten Manaye
- d Epigenetics Laboratory, Howard University , Washington, DC , USA
| | | | | | - Eugene Makarev
- a Insilico Medicine, Inc., ETC, Johns Hopkins University , Baltimore , MD , USA
| | - Antonei Benjamin Csoka
- c Vision Genomics, LLC , Washington, DC , USA.,d Epigenetics Laboratory, Howard University , Washington, DC , USA
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7
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Makarev E, Fortney K, Litovchenko M, Braunewell KH, Zhavoronkov A, Atala A. Quantifying signaling pathway activation to monitor the quality of induced pluripotent stem cells. Oncotarget 2016; 6:23204-12. [PMID: 26327604 PMCID: PMC4695112 DOI: 10.18632/oncotarget.4673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 04/27/2015] [Accepted: 08/10/2015] [Indexed: 11/25/2022] Open
Abstract
Many attempts have been made to evaluate the safety and potency of human induced pluripotent stem cells (iPSCs) for clinical applications using transcriptome data, but results so far have been ambiguous or even contradictory. Here, we characterized stem cells at the pathway level, rather than at the gene level as has been the focus of previous work. We meta-analyzed publically-available gene expression data sets and evaluated signaling and metabolic pathway activation profiles for 20 human embryonic stem cell (ESC) lines, 12 human iPSC lines, five embryonic body lines, and six fibroblast cell lines. We demonstrated the close resemblance of iPSCs with ESCs at the pathway level, and provided examples of how pathway activity can be applied to identify iPSC line abnormalities or to predict in vitro differentiation potential. Our results indicate that pathway activation profiling is a promising strategy for evaluating the safety and potency of iPSC lines in translational medicine applications.
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Affiliation(s)
- Eugene Makarev
- Atlas Regeneration, Inc, Winston-Salem, NC, USA.,Insilico Medicine, Inc, ETC, Johns Hopkins University, Baltimore, MD, USA
| | - Kristen Fortney
- Atlas Regeneration, Inc, Winston-Salem, NC, USA.,Department of Developmental Biology, Stanford University Medical Center, Stanford, CA, USA
| | - Maria Litovchenko
- Department of Computational Genomics, Ludwig Maximilian University of Munich, Germany
| | - Karl H Braunewell
- Department of Neurophysiology, Medical Faculty, Ruhr University Bochum, Germany
| | - Alex Zhavoronkov
- Insilico Medicine, Inc, ETC, Johns Hopkins University, Baltimore, MD, USA.,The Biogerontology Research Foundation, London, UK
| | - Anthony Atala
- Atlas Regeneration, Inc, Winston-Salem, NC, USA.,Department of Urology, Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
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8
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Abstract
Fibrosis, a progressive accumulation of extracellular matrix components, encompasses a wide spectrum of distinct organs, and accounts for an increasing burden of morbidity and mortality worldwide. Despite the tremendous clinical impact, the mechanisms governing the fibrotic process are not yet understood, and to date, no clinically reliable therapies for fibrosis have been discovered. Here we applied Regeneration Intelligence, a new bioinformatics software suite for qualitative analysis of intracellular signaling pathway activation using transcriptomic data, to assess a network of molecular signaling in lung and liver fibrosis. In both tissues, our analysis detected major conserved signaling pathways strongly associated with fibrosis, suggesting that some of the pathways identified by our algorithm but not yet wet-lab validated as fibrogenesis related, may be attractive targets for future research. While the majority of significantly disrupted pathways were specific to histologically distinct organs, several pathways have been concurrently activated or downregulated among the hepatic and pulmonary fibrosis samples, providing new evidence of evolutionary conserved pathways that may be relevant as possible therapeutic targets. While future confirmatory studies are warranted to validate these observations, our platform proposes a promising new approach for detecting fibrosis-promoting pathways and tailoring the right therapy to prevent fibrogenesis.
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Affiliation(s)
- Eugene Makarev
- a Atlas Regeneration, Inc. , Winston-Salem , NC , USA.,b Insilico Medicine, Inc., ETC, Johns Hopkins University , Baltimore , MD , USA
| | - Evgeny Izumchenko
- c Department of Otolaryngology-Head & Neck Surgery , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Fumiaki Aihara
- d Advanced Academic Programs, Johns Hopkins University , Baltimore , MD , USA
| | - Piotr T Wysocki
- c Department of Otolaryngology-Head & Neck Surgery , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Qingsong Zhu
- b Insilico Medicine, Inc., ETC, Johns Hopkins University , Baltimore , MD , USA
| | - Anton Buzdin
- e The Biogerontology Research Foundation , London , UK
| | - David Sidransky
- c Department of Otolaryngology-Head & Neck Surgery , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Alex Zhavoronkov
- b Insilico Medicine, Inc., ETC, Johns Hopkins University , Baltimore , MD , USA.,f Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine , Winston-Salem , NC , USA
| | - Anthony Atala
- a Atlas Regeneration, Inc. , Winston-Salem , NC , USA.,g Pathway Pharmaceuticals, Ltd , Hong Kong , Hong Kong
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Makarev E, Isayev O, Atala A. Atlas Regeneration, Inc. Regen Med 2016; 11:141-3. [PMID: 26925598 DOI: 10.2217/rme.15.87] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Atlas Regeneration is dedicated to the development of novel data-driven solutions for regenerative medicine, adapting proven technologies, and analysis strategies to take a multiomics-wide view of stem cell quality and cell fate design. Our core offering is a global comprehensive map of stem cell differentiation, Universal Signalome Atlas for Regenerative Medicine, reflecting the pathway activation states across all characterized stem cells and their differentiated products. Key applications of Universal Signalome Atlas for Regenerative Medicine will include quality assurance for engineered cell products, and directed regeneration pharmacology, where we will screen and identify compounds that can efficiently convert pluripotent cells into desired subtypes. Another marketable piece of IP is development of specialized signaling pathway analysis systems Regeneration Intelligence which supposed to target the unmet needs of determination and prediction of stem cell signaling pathway activation to govern cell differentiation in specific directions.
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Affiliation(s)
- Eugene Makarev
- Atlas Regeneration Company, Inc., 111 N. Chestnut St., Ste 102, Winston Salem, NC 27101, USA
| | - Olexandr Isayev
- Atlas Regeneration Company, Inc., 111 N. Chestnut St., Ste 102, Winston Salem, NC 27101, USA
| | - Anthony Atala
- Atlas Regeneration Company, Inc., 111 N. Chestnut St., Ste 102, Winston Salem, NC 27101, USA.,Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
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Affiliation(s)
- P A Tsonis
- Laboratory of Molecular Biology, Department of Biology and Center for Tissue Regeneration and Engineering, University of Dayton, 300 College Park, Dayton, Ohio, 45469-2320, USA.
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