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Druggable genome CRISPRi screen in hydrogels reveals regulators of cortactin-driven actin remodeling promoting glioblastoma invasion
Mufeng Hu, Anna Weldy, Isabella M. Lovalvo, Erin A. Akins, Saket Jain, Alexander Chang, Ankita Sati, Meeki Lad, Austin Lui, Akhil Rajidi, Ameya Kothekar, Erika A. Ding, Juan A. Oses Prieto, Pablo Estevez, Alma L. Burlingame, Sanjay Kumar, Manish K. Aghi
Mufeng Hu, Anna Weldy, Isabella M. Lovalvo, Erin A. Akins, Saket Jain, Alexander Chang, Ankita Sati, Meeki Lad, Austin Lui, Akhil Rajidi, Ameya Kothekar, Erika A. Ding, Juan A. Oses Prieto, Pablo Estevez, Alma L. Burlingame, Sanjay Kumar, Manish K. Aghi
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Research Article Cell biology Oncology

Druggable genome CRISPRi screen in hydrogels reveals regulators of cortactin-driven actin remodeling promoting glioblastoma invasion

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Abstract

To identify therapeutic targets limiting glioblastoma invasion, we applied druggable genome CRISPRi screens and multiomic analysis to patient-derived glioblastoma cells in micro-dissectible biomimetic 3D hydrogels that permitted separation and analysis of core versus invasive fractions. Of 2,550 genes screened, 12 encoded druggable targets whose suppression limited invasion, of which AURKB (encoding aurora kinase B) and ACP1 (encoding low molecular weight protein tyrosine phosphatase, LMW-PTP) were validated in neurosphere assays and in vivo. Proximity labeling identified cortactin as a link between LMW-PTP and aurora B, and we observed that cortactin underwent serine phosphorylation by aurora B and tyrosine dephosphorylation by LMW-PTP. Targeting ACP1 or AURKB via CRISPRi or inhibitors in culture and in vivo shifted the cortactin phosphorylation balance in glioblastoma, reducing levels of cortactin and the actin-related protein 2/3 (Arp2/3) complex that mediates cortactin-induced actin stabilization, thereby reducing actin-cortactin-Arp2/3 colocalization and subsequent actin polymerization. AURKB or ACP1 targeting shifted actin from cytoplasm to the nucleus, reducing mesenchymal gene expression. Biophysical analysis implicated AURKB in glioblastoma cell adhesion and stiffness needed for initial migration and ACP1 in mechanical stress resistance required for later migration. These findings revealed a targetable axis balancing kinase and phosphatase activities to regulate actin polymerization during glioblastoma invasion.

Authors

Mufeng Hu, Anna Weldy, Isabella M. Lovalvo, Erin A. Akins, Saket Jain, Alexander Chang, Ankita Sati, Meeki Lad, Austin Lui, Akhil Rajidi, Ameya Kothekar, Erika A. Ding, Juan A. Oses Prieto, Pablo Estevez, Alma L. Burlingame, Sanjay Kumar, Manish K. Aghi

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Figure 6

AURKB and ACP1 exert distinct effects on different aspects of GBM invasion.

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AURKB and ACP1 exert distinct effects on different aspects of GBM invas...
(A) GBM43/sgAURKB cells exhibited reduced fibronectin adhesion versus GBM43/sgGAL4 (P = 0.0001), while GBM43/sgACP1 cells had unchanged fibronectin adhesion (P = 0.9) (n = 3/group). (B) Atomic force microscopy revealed decreased single-cell stiffness in GBM43/sgAURKB cells versus GBM43/sgGAL4 cells (P = 0.0006), no changes in GBM43/sgACP1 or GBM43/sgCTTN cells (n = 50–75 individual cells/condition). Original magnification, ×10; scale bar: 100 μm. (C) Live/dead cell staining revealed that inhibiting LMW-PTP (ACP1) with LMW-PTP inhibitor I decreased cell viability/increased cell death in GBM43 cells attempting to invade during neurosphere assays (P = 0.04), with no changes with aurora B inhibitor AZD1152-HQPA (n = 4 spheres/condition). Original magnification, ×10; scale bar: 100 μm. (D) Light microscopy revealed that, in U87 GBM cells, inhibition with LMW-PTP inhibitor I altered (P = 0.008) leader/follower dynamics identified in 3D hydrogel assays; no changes noted with aurora B inhibitor AZD1152-HQPA (P = 0.7) based on counting leader cell number across 3 biological replicates. Original magnification, ×10; scale bar for day 0 and leftmost day 7 images:1 mm; scale bar for rightmost day 7 images: 50 μm; inset scale bar: 20 μm. (E) ACP1 expression increased from core cellular tumor to infiltrating tumor to leading edge (P = 4.4 × 10–6 cellular tumor versus leading edge), while AURKB expression decreased from core cellular tumor to infiltrating tumor to leading edge (P = 4.4 × 10–13 cellular tumor versus leading edge; P = 4.9 × 10–9 infiltrating tumor versus leading edge), assessed using the Ivy Glioblastoma Atlas Project, which transcriptomically profiled site-directed biopsies in newly diagnosed GBMs from 10 patients. ns, not significant; *P < 0.05; **P < 0.01; ***P < 0.001. One-way ANOVA with Tukey’s pairwise post hoc comparisons. Scatter dot plots show mean (horizontal bar) with standard deviation (vertical bar). For box and whisker plots, horizontal line in the box is the median; box extends from 25th to 75th percentile and whiskers from minimum to maximum value.

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