Abstract 489: Unveiling markers of response to ATR inhibitor and TMZ combinations in rare tumor PDXs
Authors: Yingdong Zhao, Mariam M. Konate, Ming-Chung Li, Peter I. Wu, Li Chen, Lindsay Dutko, Alyssa Chapman, Nikitha Nair, Melinda G. Hollingshead, Shahanawaz Jiwani, Biswajit Das, Julia Krushkal, Andrea R. Voth, Larry V. Rubinstein, Howard Stotler, Shannon Uzelac, Justine Mills, Tiffanie Chase-Miner, Suzanne D. Borgel, Cindy R. Timme, Lijun Chen, Yingwei Hu, Hui Zhang, Alice P. Chen, Chris A. Karlovich, P Mickey Williams, Yvonne A. Evrard, Lisa M. McShane, James H. Doroshow
Journal: Cancer Research (2025)

Rare tumors are unique cancers that often present distinct biological behaviors and treatment responses. Researchers face significant challenges in the study of those tumors due to limited patient samples, lack of comprehensive genomic data, and difficulties in establishing appropriate preclinical models for effective drug testing. The identification of effective drug combinations for cancer treatment remains a major challenge, largely due to tumor heterogeneity and variable therapeutic responses. ATR is a key kinase involved in the DNA damage response. The combination of ATR inhibitors with temozolomide (TMZ) [ATRi+TMZ] enhances the cytotoxic effects of TMZ by targeting DNA damage response pathways, particularly in cancer cells with impaired DNA repair mechanisms, offering a promising therapeutic strategy for tumors resistant to conventional treatments. This study utilized gene expression profiling of 38 rare tumor patient-derived xenograft (PDX) models available in the NCI Patient-Derived Models Repository (PDMR) (https://pdmr.cancer.gov) to identify potential biomarkers that predict responses to TMZ combined with either of two ATR inhibitors, i.e., AZD6738 (Ceralasertib) and BAY1895344 (Elimusertib). We conducted comprehensive analyses including gene expression correlation with response, network interaction and gene set enrichment analysis. Our study revealed that lower MGMT expression (i.e., MGMTlow, normalized count &amp;lt;50) in PDX models was associated with sensitivity to ATRi+TMZ combination therapy as expected; 3/4 and 4/4 MGMTlow models were sensitive to AZD6738+TMZ and BAY1895344+TMZ combination, respectively. However, MGMThigh status did not necessarily denote resistance; a portion of MGMThigh models were also sensitive to the ATRi+TMZ combinations. In MGMThigh PDXs, network analysis and GSEA revealed that ATRi+TMZ sensitive models had significant (p&amp;lt;0.001) enrichment of highly expressed DNA replication genes such as MCM2 compared to resistant models. Moreover, elevated MCM2 expression was associated with sensitivity to ATRi+TMZ: 8/8 and 7/9 MGMThigh/MCM2high models were sensitive to AZD6738+TMZ and BAY1895344+TMZ, respectively. Correspondingly, 14/18 and 24/24 MGMThigh/MCM2low PDX models were resistant to AZD6738+TMZ and BAY1895344+TMZ, respectively. We used mass spectrometry-based proteomics data from a subset of rare tumor models in our RNAseq-based dataset to validate the MGMT/MCM2 expression association with ATRi+TMZ response, confirming a similar trend. Our findings revealed distinct expression signatures associated with favorable responses to two ATR inhibitors when individually combined with TMZ, highlighting candidate markers that could guide treatment decisions. Additional validation in a larger study would establish the potential utility of these candidate genes for patient selection in clinical trials. Citation Format: Yingdong Zhao, Mariam M. Konate, Ming-Chung Li, Peter I. Wu, Li Chen, Lindsay Dutko, Alyssa Chapman, Nikitha Nair, Melinda G. Hollingshead, Shahanawaz Jiwani, Biswajit Das, Julia Krushkal, Andrea R. Voth, Larry V. Rubinstein, Howard Stotler, Shannon Uzelac, Justine Mills, Tiffanie Chase-Miner, Suzanne D. Borgel, Cindy R. Timme, Lijun Chen, Yingwei Hu, Hui Zhang, Alice P. Chen, Chris A. Karlovich, P Mickey Williams, Yvonne A. Evrard, Lisa M. McShane, James H. Doroshow. Unveiling markers of response to ATR inhibitor and TMZ combinations in rare tumor PDXs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 489.