Superenhancer activation of KLHDC8A drives glioma ciliation and hedgehog signaling
Derrick Lee, Ryan C. Gimple, Xujia Wu, Briana C. Prager, Zhixin Qiu, Qiulian Wu, Vikas Daggubati, Aruljothi Mariappan, Jay Gopalakrishnan, Matthew R. Sarkisian, David R. Raleigh, Jeremy N. Rich
Derrick Lee, Ryan C. Gimple, Xujia Wu, Briana C. Prager, Zhixin Qiu, Qiulian Wu, Vikas Daggubati, Aruljothi Mariappan, Jay Gopalakrishnan, Matthew R. Sarkisian, David R. Raleigh, Jeremy N. Rich
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Research Article Oncology

Superenhancer activation of KLHDC8A drives glioma ciliation and hedgehog signaling

Abstract

Glioblastoma ranks among the most aggressive and lethal of all human cancers. Self-renewing, highly tumorigenic glioblastoma stem cells (GSCs) contribute to therapeutic resistance and maintain cellular heterogeneity. Here, we interrogated superenhancer landscapes of primary glioblastoma specimens and patient-derived GSCs, revealing a kelch domain–containing gene, specifically Kelch domain containing 8A (KLHDC8A) with a previously unknown function as an epigenetically driven oncogene. Targeting KLHDC8A decreased GSC proliferation and self-renewal, induced apoptosis, and impaired in vivo tumor growth. Transcription factor control circuitry analyses revealed that the master transcriptional regulator SOX2 stimulated KLHDC8A expression. Mechanistically, KLHDC8A bound chaperonin-containing TCP1 (CCT) to promote the assembly of primary cilia to activate hedgehog signaling. KLHDC8A expression correlated with Aurora B/C Kinase inhibitor activity, which induced primary cilia and hedgehog signaling. Combinatorial targeting of Aurora B/C kinase and hedgehog displayed augmented benefit against GSC proliferation. Collectively, superenhancer-based discovery revealed KLHDC8A as what we believe to be a novel molecular target of cancer stem cells that promotes ciliogenesis to activate the hedgehog pathway, offering insights into therapeutic vulnerabilities for glioblastoma treatment.

Authors

Derrick Lee, Ryan C. Gimple, Xujia Wu, Briana C. Prager, Zhixin Qiu, Qiulian Wu, Vikas Daggubati, Aruljothi Mariappan, Jay Gopalakrishnan, Matthew R. Sarkisian, David R. Raleigh, Jeremy N. Rich

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Figure 8

In vivo dependency and novel therapeutic strategies for targeting KLHDC8A in glioblastoma.

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In vivo dependency and novel therapeutic strategies for targeting KLHDC8...
(A) Plot showing ranked therapeutic compounds based on correlation of KLHDC8A mRNA expression with drug sensitivity (AUC) in brain cancer cell lines in CTRP data set. (B) Dose-response curves of 2 paired GSCs and DGCs to Aurora B/C kinase inhibitor, GSK1070916. (C) Immunofluorescence imaging of primary cilia in GSC3028 and GSC23 following treatment of GSK1070916. Polyglutamylated-tubulin was labeled as green, ARL13B as red, and DAPI as blue. (D) Quantification of cells possessing primary cilia GSC3028 and GSC23. At least 100 cells in each GSC line from 3 independent experiments were tested. Quantitative data are shown as mean ± SD. Statistical analysis was performed using 1-way ANOVA with Tukey’s correction for multiple comparisons. (E) Immunoblot showing the protein expression of phospho-Aurora kinase B, Aurora kinase B, and GLI1 following treatment of GSK1070916. (F) Synergy plots of Sonidegib and GSK1070916 in GSC387 and GSC23 analyzed by R package Synergyfinder. (G) Kaplan-Meier curve showing survival of NSG immunocompromised mice following implantation with GSC23 or GSC3028 following knockdown of KLHDC8A. n = 5 per group. Statistical analysis was performed using Mantel-Cox log-rank test. (H) The knockdown efficiency of KLHDC8A measured by qPCR in GSC3028 and GSC23. n = 4. Quantitative data from 4 independent experiments are shown as mean ± SD. Statistical analysis was performed using 1-way ANOVA with Tukey’s multiple comparisons. *P < 0.05, **P < 0.01, ***P < 0.001. Scale bars: 5 or 20 μm.