High-Throughput Screening of Epigenetic Inhibitors in Meningiomas Identifies HDAC, G9a, and Jumonji-Domain Inhibition as Potential Therapies

Abstract

Background Epigenetics may predict treatment sensitivity and clinical course for patients with meningiomas more accurately than histopathology. Nonetheless, targeting epigenetic mechanisms is understudied for pharmacotherapeutic development for these tumors. The bio-molecular insights and potential therapeutic development of meningioma epigenetics led us to investigate epigenetic inhibition in meningiomas. Methods We screened a 43-tumor cohort using a 139-compound epigenetic inhibitor library to assess sensitivity of relevant meningioma subgroups to epigenetic inhibition. The cohort was composed of 5 cell lines and 38 tumors cultured directly from surgery; mean patient age was 56.6 years ± 13.9 standard deviation. Tumor categories: 38 primary tumors, 5 recurrent; 33 from females, 10 from males; 32 = grade 1; 10 = grade 2; 1 = grade 3. Results Consistent with our previous results, histone deacetylase inhibitors (HDACi) were the most efficacious class. Panobinostat significantly reduced cell viability in 36 of 43 tumors; 41 tumors had significant sensitivity to some HDACi. G9a inhibition and Jumonji-domain inhibition also significantly reduced cell viability across the cohort; tumors that lost sensitivity to panobinostat maintained sensitivity to either G9a or Jumonji-domain inhibition. Sensitivity to G9a and HDAC inhibition increased with tumor grade; tumor responses did not separate by gender. Few differences were found between recurrent and primary tumors, or between those with prior radiation versus those without. Conclusions Few efforts have investigated the efficacy of targeting epigenetic mechanisms to treat meningiomas, making the clinical utility of epigenetic inhibition largely unknown. Our results suggest that epigenetic inhibition is a targetable area for meningioma pharmacotherapy.

Keywords: G9a; HDAC; Jumonji domain; meningioma; screening.

Fig. 1

Full meningioma cohort sensitivity to epigenetic compound library. (a) Heat map of the full tumor cohort ( n  = 43) screened with the 139-compound epigenetic library shown on a scale from 0 to 100% cell viability. (b) Broadly effective compounds were determined as compounds that significantly ( p  < 0.05) reduce the average viability of the cohort to 80% or less and are displayed as a rank-ordered heat map by the most effective compound across the entire cohort. Each compound is displayed with a table showing the average cohort viability (Avg), standard deviation (SD), p -value ( p ), and number of samples the compound significantly reduced viability in (Num Sig). Compounds are colored by mechanism of action, including histone deacetylase (HDAC), Jumonji histone demethylase (Jumonji Domain), and G9a histone methyltransferase (G9a). (c) The top five most effective compounds for each tumor sample, determined as significantly reducing viability the most, are displayed as the filled tiles in the heat map. Compounds that are not in the top five are shown as white space.

Fig. 2

Meningioma cohort separated by sensitivity to panobinostat.(a) Tumor samples sensitive to panobinostat ( n  = 35) were determined as those in which panobinostat significantly ( p  < 0.05) reduced individual cell viability to 80% or less. (b) Meningioma samples that did not meet these criteria were considered as panobinostat nonsensitive ( n  = 8). Of the panobinostat nonsensitive group (b), there were two tumor samples that were only sensitive to other compounds (c) , displayed with the most effective compound for each tumor: OTX015 was the most effective compound for J4–1 and UNC0631 was the most effective compound for K9–7. Broadly effective compounds are colored by mechanism of action.

Fig. 3

Meningioma cohort compared by tumor grade. Heat maps displaying the broadly most effective compounds for grade 1 (a) , grade 2 (b) , and grade 3 (c) meningiomas. Broadly effective compounds for each tumor grade were determined as compounds that significantly ( p  < 0.05) reduce the average viability to 80% or less and are limited to the top 15 most effective compounds, when applicable. Heat maps are displayed with a table showing the average cohort viability (Avg), standard deviation (SD), p -value ( p ), and number of samples each compound significantly reduced viability in (Num Sig). Compounds are colored by mechanism of action.

Fig. 4

Meningioma cohort compared across primary and recurrent tumors. Heat maps displaying the broadly most effective compounds for primary (a) and recurrent (b) meningiomas in our cohort. Broadly effective compounds for primary and recurrent tumors were determined as compounds that significantly ( p  < 0.05) reduce the average viability to 80% or less and are limited to the top 15 most effective compounds, when applicable. Heat maps are displayed with a table showing the average cohort viability (Avg), standard deviation (SD), p -value ( p ), and number of samples each compound significantly reduced viability in (Num Sig). Compounds are colored by mechanism of action.

Fig. 5

Meningioma cohort compared by history of radiation. Heat maps displaying the broadly most effective compounds for meningiomas that have no history of radiation (a) and prior history of radiation (b) . Broadly effective compounds for no and prior radiation groups were determined as compounds that significantly ( p  < 0.05) reduce the average viability to 80% or less and are limited to the top 15 most effective compounds, when applicable. Heat maps are displayed with a table showing the average cohort viability (Avg), standard deviation (SD), p -value ( p ), and number of samples each compound significantly reduced viability in (Num Sig). Compounds are colored by mechanism of action.

Fig. 6

Meningioma cohort compared across patient gender. Heat maps displaying the broadly most effective compounds for meningiomas from male (a) and female (b) patients. Broadly effective compounds for tumors from male and female patients were determined as compounds that significantly ( p  < 0.05) reduce the average viability to 80% or less and are limited to the top 15 most effective compounds, when applicable. Heat maps are displayed with a table showing the average cohort viability (Avg), standard deviation (SD), p -value ( p ), and number of samples each compound significantly reduced viability in (Num Sig). Compounds are colored by mechanism of action.