Background Malignant pleural mesothelioma (PM) is an aggressive cancer with limited treatment options. Although immune checkpoint blockade (ICB) with nivolumab plus ipilimumab improves overall survival and has become standard-of-care, responses are variable and there are no predictive biomarkers for treatment outcome among PM patients with epithelioid histology.

Methods We developed an eight-gene T-cell and six-gene B-cell transcriptomic signature. To quantify T- and B-cell infiltration, a geometric-mean T- and B-cell expression score was calculated for each patient. Immune profiles were generated in three ICB-naïve PM cohorts (n = 448), and Kaplan-Meier analysis was used to evaluate prognostic value of the signatures. Predictive value was tested in five independent ICB-treated cohorts (n = 104).

Results In ICB-naïve patients, high B-cell infiltration was associated with longer overall survival (hazard ratio (HR): 0.50, 95% confidence interval (CI): 0.31-0.82), whereas T-cell infiltration had no prognostic value. Among patients treated with 2nd line treatment with nivolumab plus ipilimumab, high T-cell infiltration predicted better objective response and improved overall survival (HR: 0.06, 95% CI: 0.01-0.36). This effect was absent in patients treated with 2nd line nivolumab alone or any other anti-PD1/PDL1 drug combined with non-immunotherapeutics. B-cell infiltration showed no predictive value in any ICB-treated group.

Conclusions The eight-gene T-cell signature is a specific predictor of outcome after 2nd line treatment with nivolumab plus ipilimumab, while B-cell infiltration is prognostic in ICB-naïve disease.

Jasper van Genugten, Daniel Faulkner, Jens C. Hahne, and Maria Disselhorst declare no competing interests. Lodewyk Wessels received project funding from Bristol-Myers-Squibb. Dean Fennell reports grants from Aldeyra, Astex Therapeutics, Bayer, BMS and Boehringer Ingelheim, Owkin; non-financial support from BerGenBio, Clovis, Eli Lilly, MSD, Roche, and Tesaro GSK; personal fees from Aldeyra, Cambridge Clinical Laboratories, Ikena, Opna Bio, Owkin, RS Oncology, Roche, MSD. Paul Baas has received research grants, travel support and is consultant for BMS and MSD for his institution

This study did not receive any external funding.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Amsterdam, 05/09/2024 Dear Jasper van Genugten Your application, entitled: Evaluating an in silico pipeline to investigate T- and B-cell infiltration in malignant pleural mesothelioma., for the use of human material and or data is registered under number IRBd24-234. Your application has been reviewed and approved by the NKI-AVL Institutional Review Board (IRB). The NKI IRB is a board for tailor-made reviewing of non-WMO research with human material and data. The purpose of the IRB is to assure that appropriate steps are taken to protect the rights and welfare of humans participating as subjects in a research study and to safeguard ethical conduct of research concerning, amongst others, the Dutch norm for information securityNEN7510 and the GDPR. The decision is based on all the documents registered on 05/09/2024 in IRBART (IRBd24-234) which can be viewed on this page. This application reviewed by the IRB does not meet the WMO criteria and can be considered as a non-WMO statement. For the record, this approval letter only applies to the study as far as it is carried out in the NKI-AVL. If the study will also be carried out in other centers, you are advised to check percenter whether there is a local testing procedure there. Sincerely Dr. A. Broeks Committee Secretary IRB On behalf of Institutional Review Board (IRB) The Netherlands Cancer Institute, Amsterdam

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Most of the datasets analyzed in this study (Zhang et al., and the INITIATE, NivoMes, MiST3, MiST4, and MiST5 clinical trial datasets) are not publicly available due to patient privacy and data sharing restrictions. The authors do not have permission to redistribute these datasets. Processed data from the study by Hmeljak et al. (2018) were retrieved from Firebrowse (http://firebrowse.org/). Additional processed data and analysis scripts are available from the authors upon reasonable request.