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 6

GSCs preferentially display primary cilia.

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GSCs preferentially display primary cilia. (A) Immunofluorescence imagin...
(A) Immunofluorescence imaging of Ac-tubulin, IFT88, polyglutamylated-tubulin, and ARL13B in 3 patient-derived GSCs (GSC387, GSC23, GSC3028). Ac-tubulin or polyglutamylated-tubulin is shown in green, IFT88 or ARL13B in red, and DAPI in blue. (B) Quantification of primary cilia positive cells in GSC387, GSC23, and GSC3028. Data are presented as mean ± SD. At least 100 cells in each GSC line from 3 independent experiments were tested. (C) Immunofluorescence imaging of polyglutamylated-tubulin and ARL13B in patient-derived GSCs (GSC23 and GSC3028) following the double thymidine block. Polyglutamylated-tubulin is shown in green, ARL13B in red, and DAPI in blue. (D) Quantitative data are shown as mean ± SD. Statistical analysis was performed using 1-way ANOVA with Tukey’s correction for multiple comparisons. (E) Immunostaining of Ac-tubulin and IFT88 in 2 matched GSCs and DGCs (GSC387 and GSC23). Ac-tubulin is shown in green, IFT88 in red, and DAPI in blue. (F) Quantification of primary cilia positive cells in 2 matched GSCs and DGCs. 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 multiple comparisons. (G) Epifluorescent images showing ARL13B+ cilia (green, arrows) with GTUB+ basal bodies (red, arrowheads) from patient glioblastoma biopsies from a 34 year old man, 66 year old man, 68 year old woman, and 74 year old woman. Arrows with asterisks indicate cilia enlarged below and separated by individual and merged channels. Scale bars: 5 or 20 μm. **P < 0.01, ****P < 0.0001.