Quantitative functional profiling of ERCC2 mutations deciphers cisplatin sensitivity in bladder cancer
Judit Börcsök, Diyavarshini Gopaul, Daphne Devesa-Serrano, Clémence Mooser, Nicolas Jonsson, Matteo Cagiada, Dag R. Stormoen, Maya N. Ataya, Brendan J. Guercio, Hristos Z. Kaimakliotis, Gopa Iyer, Kresten Lindorff-Larsen, Lars Dyrskjøt, Kent W. Mouw, Zoltan Szallasi, Claus S. Sørensen
Judit Börcsök, Diyavarshini Gopaul, Daphne Devesa-Serrano, Clémence Mooser, Nicolas Jonsson, Matteo Cagiada, Dag R. Stormoen, Maya N. Ataya, Brendan J. Guercio, Hristos Z. Kaimakliotis, Gopa Iyer, Kresten Lindorff-Larsen, Lars Dyrskjøt, Kent W. Mouw, Zoltan Szallasi, Claus S. Sørensen
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Research Article Cell biology Genetics Oncology

Quantitative functional profiling of ERCC2 mutations deciphers cisplatin sensitivity in bladder cancer

Abstract

Tumor gene alterations can serve as predictive biomarkers for therapy response. The nucleotide excision repair (NER) helicase ERCC2 carries heterozygous missense mutations in approximately 10% of bladder tumors, and these may predict sensitivity to cisplatin treatment. To explore the clinical actionability of ERCC2 mutations, we assembled a multinational cohort of 2,012 individuals with bladder cancer and applied the highly quantitative CRISPR-Select assay to functionally profile recurrent ERCC2 mutations. We also developed a single-allele editing version of CRISPR-Select to assess heterozygous missense variants in their native context. From the cohort, 506 ERCC2 mutations were identified, with 93% being heterozygous missense variants. CRISPR-Select pinpointed deleterious, cisplatin-sensitizing mutations, particularly within the conserved helicase domains. Importantly, single-allele editing revealed that heterozygous helicase-domain mutations markedly increased cisplatin sensitivity. Integration with clinical data confirmed that these mutations were associated with improved response to platinum-based neoadjuvant chemotherapy. Comparison with computational algorithms showed substantial discrepancies, highlighting the importance of precision functional assays for interpreting mutation effects in clinically relevant contexts. Our results demonstrate that CRISPR-Select provides a robust platform to advance biomarker-driven therapy in bladder cancer and supports its potential integration into precision oncology workflows.

Authors

Judit Börcsök, Diyavarshini Gopaul, Daphne Devesa-Serrano, Clémence Mooser, Nicolas Jonsson, Matteo Cagiada, Dag R. Stormoen, Maya N. Ataya, Brendan J. Guercio, Hristos Z. Kaimakliotis, Gopa Iyer, Kresten Lindorff-Larsen, Lars Dyrskjøt, Kent W. Mouw, Zoltan Szallasi, Claus S. Sørensen

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Figure 5

Comparison of CRISPR-Select and computational predictions of ERCC2.

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Comparison of CRISPR-Select and computational predictions of ERCC2. (A) ...
(A) Computational prediction of functionally important sites in ERCC2 using the Cagiada model. The heatmap shows that 2/3 (66%) of ERCC2 variants in the helicase domains are predicted to have a functionally or structurally detrimental effect, i.e., stable-but-inactive (SBI) (45%) or total-loss (TL) (21%) variants. (B) The bar plot shows the ratio of variants in each class predicted by the Cagiada model within and outside of the helicase domains (HDs) of ERCC2. The ratio of variants within and outside of the HDs was compared by the Fisher’s exact test: P = 5 × 10–3. (C) Comparison of CRISPR-Select functional experimental results using MCF10A TP53-KO cells and computational predictions by multiple functional and variant prediction tools. Values in “D12” and “D12+Cis” columns are showing the mean values of 3 independent experiments conducted by CRISPR-Select.