American Association for Cancer Research
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00085472can191305-sup-221233_4_supp_6036608_q4g66y.pdf (21.51 kB)

Supplementary Table S3 from Clonal ZEB1-Driven Mesenchymal Transition Promotes Targetable Oncologic Antiangiogenic Therapy Resistance

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posted on 2023-03-31, 03:25 authored by Ankush Chandra, Arman Jahangiri, William Chen, Alan T. Nguyen, Garima Yagnik, Matheus P. Pereira, Saket Jain, Joseph H. Garcia, Sumedh S. Shah, Harsh Wadhwa, Rushikesh S. Joshi, Jacob Weiss, Kayla J. Wolf, Jung-Ming G. Lin, Sören Müller, Jonathan W. Rick, Aaron A. Diaz, Luke A. Gilbert, Sanjay Kumar, Manish K. Aghi

Supplementary Table S3 has primer sequences used to validate GBM subtype genes

Funding

American Brain Tumor Association

McDonnell Foundation

American Cancer Society

University of California Cancer Research

NIH

Howard Hughes Medical Institute

UCSF School of Medicine

NSF

History

ARTICLE ABSTRACT

Glioblastoma (GBM) responses to bevacizumab are invariably transient with acquired resistance. We profiled paired patient specimens and bevacizumab-resistant xenograft models pre- and post-resistance toward the primary goal of identifying regulators whose targeting could prolong the therapeutic window, and the secondary goal of identifying biomarkers of therapeutic window closure. Bevacizumab-resistant patient specimens and xenografts exhibited decreased vessel density and increased hypoxia versus pre-resistance, suggesting that resistance occurs despite effective therapeutic devascularization. Microarray analysis revealed upregulated mesenchymal genes in resistant tumors correlating with bevacizumab treatment duration and causing three changes enabling resistant tumor growth in hypoxia. First, perivascular invasiveness along remaining blood vessels, which co-opts vessels in a VEGF-independent and neoangiogenesis-independent manner, was upregulated in novel biomimetic 3D bioengineered platforms modeling the bevacizumab-resistant microenvironment. Second, tumor-initiating stem cells housed in the perivascular niche close to remaining blood vessels were enriched. Third, metabolic reprogramming assessed through real-time bioenergetic measurement and metabolomics upregulated glycolysis and suppressed oxidative phosphorylation. Single-cell sequencing of bevacizumab-resistant patient GBMs confirmed upregulated mesenchymal genes, particularly glycoprotein YKL-40 and transcription factor ZEB1, in later clones, implicating these changes as treatment-induced. Serum YKL-40 was elevated in bevacizumab-resistant versus bevacizumab-naïve patients. CRISPR and pharmacologic targeting of ZEB1 with honokiol reversed the mesenchymal gene expression and associated stem cell, invasion, and metabolic changes defining resistance. Honokiol caused greater cell death in bevacizumab-resistant than bevacizumab-responsive tumor cells, with surviving cells losing mesenchymal morphology. Employing YKL-40 as a resistance biomarker and ZEB1 as a target to prevent resistance could fulfill the promise of antiangiogenic therapy. Bevacizumab resistance in GBM is associated with mesenchymal/glycolytic shifts involving YKL-40 and ZEB1. Targeting ZEB1 reduces bevacizumab-resistant GBM phenotypes.

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