Benchmark of screening markers for KEAP1/NFE2L2 mutations and joint analysis with the K1N2-score

Christoph Arolt^#¹, Andreas H Scheel^#¹, Margaret Dugan², Robert Wild², Vanessa Richartz¹, Barbara Holz¹, Johannes Brägelmann^{1

3

4

5}, Svenja Wagener-Ryczek¹, Sabine Merkelbach-Bruse^{1

6}, Juergen Wolf^{6

7}, Reinhard Buettner^{1

6}, Luigi Catanzariti², Matthias Scheffler^#^{8

9}, Axel M Hillmer^#^{10

11}

Affiliations

¹ Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
² Dracen Pharmaceuticals Inc., San Diego, CA, USA.
³ Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
⁴ Department of Translational Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
⁵ Mildred Scheel School of Oncology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
⁶ Lung Cancer Group Cologne, Center for Integrated Oncology Cologne/Bonn, University Hospital Cologne, Cologne, Germany.
⁷ Department I for Internal Medicine, Center for Integrated Oncology Cologne/Bonn, University Hospital Cologne, Cologne, Germany.
⁸ Lung Cancer Group Cologne, Center for Integrated Oncology Cologne/Bonn, University Hospital Cologne, Cologne, Germany. matthias.scheffler@uk-koeln.de.
⁹ Department I for Internal Medicine, Center for Integrated Oncology Cologne/Bonn, University Hospital Cologne, Cologne, Germany. matthias.scheffler@uk-koeln.de.
¹⁰ Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany. ahillmer@uni-koeln.de.
¹¹ Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. ahillmer@uni-koeln.de.

^# Contributed equally.

PMID: 39528799
PMCID: PMC11554772
DOI: 10.1038/s41698-024-00744-1

Benchmark of screening markers for KEAP1/NFE2L2 mutations and joint analysis with the K1N2-score

Christoph Arolt et al. NPJ Precis Oncol. 2024.

. 2024 Nov 11;8(1):259.

doi: 10.1038/s41698-024-00744-1.

Authors

Affiliations

¹ Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
² Dracen Pharmaceuticals Inc., San Diego, CA, USA.
³ Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
⁴ Department of Translational Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
⁵ Mildred Scheel School of Oncology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
⁶ Lung Cancer Group Cologne, Center for Integrated Oncology Cologne/Bonn, University Hospital Cologne, Cologne, Germany.
⁷ Department I for Internal Medicine, Center for Integrated Oncology Cologne/Bonn, University Hospital Cologne, Cologne, Germany.
⁸ Lung Cancer Group Cologne, Center for Integrated Oncology Cologne/Bonn, University Hospital Cologne, Cologne, Germany. matthias.scheffler@uk-koeln.de.
⁹ Department I for Internal Medicine, Center for Integrated Oncology Cologne/Bonn, University Hospital Cologne, Cologne, Germany. matthias.scheffler@uk-koeln.de.
¹⁰ Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany. ahillmer@uni-koeln.de.
¹¹ Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. ahillmer@uni-koeln.de.

^# Contributed equally.

PMID: 39528799
PMCID: PMC11554772
DOI: 10.1038/s41698-024-00744-1

Abstract

Our recently published K1N2-score robustly predicts KEAP1/NFE2L2-mutations and pathway activation status, while its accessibility might be limited. We tested if the RNA expression data of six pathway-related genes and NQO1-IHC might be a reliable alternative using 348 KEAP1/NFE2L2 mutation-enriched NSCLC. While TXNRD1 RNA testing was the best-performing single-gene test, the combination of single-gene screening and validation with the K1N2-score achieved the highest performance when predicting mutation status or pathway activation.

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Conflict of interest statement

Competing interests M.D. is an employee of and holds stock options at Dracen Pharmaceuticals Inc. R.W. is an employee of, receives consulting fees from, and holds stocks and stock options at Dracen Pharmaceuticals Inc. S.W.-R. has received speaker honoraria from AstraZeneca and Invitae; and received support for attending meetings and travel from AstraZeneca and Novartis. S.M.-B. has received speaker honoraria from Amgen, AstraZeneca, Bayer, Bristol-Myers Squibb, GlaxoSmithKline, Janssen Merck, Merck Sharp & Dohme, Molecular Health, Novartis, Pfizer, QuIP, and DLS; and participates on advisory boards for AstraZeneca, Qiagen, and Roche. J.W. received research funds from Dracen Pharmaceuticals Inc., received research support (to institution) from Bristol-Myers Squibb, Janssen Pharmaceuticals, Novartis, Pfizer, and Biontech; and received consulting fees from Amgen, AstraZeneca, Bayer, Blueprint, Bristol-Myers Squibb, Boehringer Ingelheim, Chugai Europe, Daiichi-Sankyo, Ignyta, Jannsen, Eli Lilly, Loxo, Merck, Mirati, Merck Sharp & Dohme, Novartis, Pfizer, Roche, Seattle Genetics, Taked, and Turning Point. R.B. is funded by the German Cancer Aid in the program “Excellence Center for Oncology-CIO ABCD, Center for Molecular Medicine; has received consulting fees from AbbVie, Amgen, AstraZeneca, Bayer, Bristol-Myers Squibb, Boehringer Ingelheim, Illumina, Janssen, Eli Lilly, Merck-Serono, Merck Sharp & Dohme, Novartis, Qiagen, Pfizer, Roche, Sanofi, Targos MP Inc.; received lecture and presentation honoraries from AbbVie, Amgen, AstraZeneca, Bayer, Bristol-Myers Squibb, Boehringer Ingelheim, Illumina, Janssen, Eli Lilly, Merck-Serono, Merck Sharp & Dohme, Novartis, Qiagen, Pfizer, Roche, and Targos MP Inc.; is a member of the board of trustees of the German Cancer Aid; chairs the board of trustees for the Vladimir Totovic Foundation of the German Division Internation Academy of Pathology; and is co-owner of Timer Therapeutics (Germany) and Gnothis Inc. (Sweden). L.C. is a paid consultant of Dracen Pharmaceuticals. M.S. received research funds from Dracen Pharmaceutical Inc.; has received grants or holds contracts with Amgen, AstraZeneca, Boehringer Ingelheim, Janssen, Novartis, Pfizer, Roche, Sanofi-Aventis, Siemens Healthineers, Takeda, and Bristol-Myers Squibb; received support for attending meetings or travel from Janssen and Pfizer; and has a leadership or fiduciary role at the European Society for Medical Oncology and European Organization for Research and Treatment of Cancer. A.M.H. received research funds (to institution) from Dracen Pharmaceuticals Inc. The remaining authors declare no conflict of interest.

Figures

**Fig. 1. NQO1 protein expression in LUAD and LUSC (IHC).**
Exemplary NQO1 IHC images with absent (0), mild (1+), moderate (2+), and strong (3+) staining intensities, 400× magnification, 100 μm scalebar (A). NQO1 H-score in *KEAP1*mut, *NFE2L2*mut, and wildtype of LUAD (B) and LUSC (C), pooled analysis of the Cologne_use and the Cologne_validation cohorts. AUC curve of *KEAP1/NFE2L2* mutation prediction using NQO1 IHC in the Cologne validation dataset of LUAD (D) and LUSC (E).

**Fig. 2. Benchmark of screening markers for *KEAP1/NFE2L2* mutations and KEAP1/NFE2L2 pathway activation.**
Testing algorithm of the combinatorial approaches using the Cologne validation dataset (A). Youden’s J values of single and combinatorial tests predicting the *KEAP1/NFE2L2* mutation status for LUAD, LUSC, and the overall validation cohort (B). Detailed results of the best-performing combinatorial tests with the K1N2 score as reference; screening and validation refer to (A) indicating high sensitivity and low specificity at the screening step and high sensitivity and specificity after K1N2-score validation test of the positive screening cases (C). Youden’s J values for single-gene tests when predicting KEAP1/NFE2L2 pathway activation status as defined by the K1N2 score in LUAD, LUSC, and the overall validation cohort (D).

See this image and copyright information in PMC

References

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Benchmark of screening markers for KEAP1/NFE2L2 mutations and joint analysis with the K1N2-score

Affiliations

Benchmark of screening markers for KEAP1/NFE2L2 mutations and joint analysis with the K1N2-score

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Grants and funding

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Full Text Sources

Miscellaneous