Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Randomized Controlled Trial
. 2024 Nov 19;5(11):101825.
doi: 10.1016/j.xcrm.2024.101825.

Molecular adaptation to neoadjuvant immunotherapy in triple-negative breast cancer

Carsten Denkert  1 , Andreas Schneeweiss  2 , Julia Rey  3 , Thomas Karn  4 , Akira Hattesohl  5 , Karsten E Weber  3 , Sivaramakrishna Rachakonda  3 , Michael Braun  6 , Jens Huober  7 , Paul Jank  5 , Hans-Peter Sinn  8 , Dirk-Michael Zahm  9 , Bärbel Felder  3 , Claus Hanusch  6 , Julia Teply-Szymanski  5 , Frederik Marmé  10 , Tanja Fehm  11 , Jörg Thomalla  12 , Bruno V Sinn  13 , Thorsten Stiewe  14 , Michal Marczyk  15 , Jens-Uwe Blohmer  16 , Marion van Mackelenbergh  17 , Christian Schem  18 , Peter Staib  19 , Theresa Link  20 , Volkmar Müller  21 , Elmar Stickeler  22 , Daniel G Stover  23 , Christine Solbach  24 , Otto Metzger-Filho  25 , Christian Jackisch  26 , Charles E Geyer Jr  27 , Peter A Fasching  28 , Lajos Pusztai  29 , Valentina Nekljudova  3 , Michael Untch  30 , Sibylle Loibl  31
Affiliations
Randomized Controlled Trial

Molecular adaptation to neoadjuvant immunotherapy in triple-negative breast cancer

Carsten Denkert et al. Cell Rep Med. .

Abstract

Therapy-induced molecular adaptation of triple-negative breast cancer is crucial for immunotherapy response and resistance. We analyze tumor biopsies from three different time points in the randomized neoadjuvant GeparNuevo trial (NCT02685059), evaluating the combination of durvalumab with chemotherapy, for longitudinal alterations of gene expression. Durvalumab induces an activation of immune and stromal gene expression as well as a reduction of proliferation-related gene expression. Immune genes are positive prognostic factors irrespective of treatment, while proliferation genes are positive prognostic factors only in the durvalumab arm. We identify stromal-related gene expression as a contributor to immunotherapy resistance and poor therapy response. The results provide evidence from clinical trial cohorts suggesting a role for stromal reorganization in therapy resistance to immunotherapy and in the generation of an immune-suppressive microenvironment, which might be relevant for future therapy approaches targeting the tumor stroma parallel to immunotherapy, such as combinations of immunotherapy with anti-angiogenic therapy.

Keywords: PD-L1; gene expression; immunotherapy; neoadjuvant; pathway analysis; triple-negative breast cancer.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests C.D. reports grants from European Commission H2020, grants from German Cancer Aid Translational Oncology, grants from German Breast Group, and grants from BMBF to the institution during the conduct of the study; personal fees from Novartis, personal fees from Roche, personal fees from MSD Oncology, personal fees from Daiichi Sankyo, personal fees from AstraZeneca and Molecular Health, grants from Myriad, personal fees from Merck, and other funding from Sividon Diagnostics outside the submitted work; in addition, C.D. has a patent VMScope digital pathology software with royalties paid, a patent WO2020109570A1—cancer immunotherapy pending, and a patent WO2015114146A1 and WO2010076322A1—therapy response issued. J.R. declares to be a GBG Forschungs GmbH employee. GBG Forschungs GmbH received funding for research grants from AbbVie, Amgen, AstraZeneca, BMS, Daiichi Sankyo, Gilead, Molecular Health, Novartis, Pfizer, and Roche (paid to the institution). Funding was also received (non-financial/medical writing) from Daiichi Sankyo, Gilead, Novartis, Pfizer, Roche, and Seagen (paid to the institution). GBG Forschungs GmbH has royalties in VM Scope and patents pending: EP14153692.0, EP21152186.9, and EP15702464.7. T.K. reports a patent WO2020109570A1 pending. S.R. declares to be a GBG Forschungs GmbH employee. GBG Forschungs GmbH received funding for research grants from AbbVie, Amgen, AstraZeneca, BMS, Daiichi Sankyo, Gilead, Molecular Health, Novartis, Pfizer, and Roche (paid to the institution). J.H. reports research funding from Lilly; honoraria from Lilly, Novartis, Roche, Pfizer, AstraZeneca, Seagen, Gilead, and Daiichi; consulting and advisory relationships with Lilly, Novartis, Roche, Pfizer, AstraZeneca, Gilead, and Daiichi; travel expenses from Roche, Novartis, Daiichi, and Gilead. P.J. reports research funding and travel expenses from Gilead Sciences GmbH. C.H. reports an advisory role and speakers bureau role for AstraZeneca, Roche, Novartis, and Aristo Pharma. B.V.S. is an employee of BioNTech SE and reports a patent WO2020109570A1 pending. J.-U.B. reports consultation fees, honoraria, and reimbursement for attending symposia from AstraZeneca, Amgen, Daiichi Sankyo, Eisai, Gilead, Lilly, MSD, Novartis, Pfizer, Roche, and Seagen. M.v.M. reports personal fees, honoraria, or travel grants from Amgen, AstraZeneca, Daiichi Sankyo, Genomic Health, GSK, Lilly, Molecular Health, MSD, Mylan, Novartis, Pfizer, Pierre Fabre, Roche, and Seagen. C. Schem reports speaker activities for Roche, Pfizer, Novartis, Celgen, Novartis, Exact Sciences, MSD, AstraZeneca, Lilly, and Seagen, as well as advisory boards for Roche, Astra Zeneca, Pfizer, Novartis, MSD, Amgen, Exact Sciences, Stemline, Lilly, and Novartis. T.L. reports personal fees from Amgen, Roche, Teva, Clovis, Tesaro, MSD, Novartis, Pfizer, Lilly, GSK, Gilead, AstraZeneca, Daiichi Sankyo, Stemline, and Seagen outside of the submitted work. T.L. participates in advisory boards from Amgen, MSD, Tesaro, Roche, Pfizer, Lilly, Myriad, Esai, GSK, Gilead, Daiichi Sankyo, Roche, and AstraZeneca outside of the submitted work and T.L. received travel support from Pfizer, PharmaMar, MSD, Celgene, Roche, AstraZeneca, Gilead, Daiichi Sankyo, Stemline, and Clovis outside of the submitted work. P.S. reports grants, personal fees, and non-financial support from AbbVie, Amgen, AstraZeneca, Bristol Myers Squibb Company, MSD, Incyte, Janssen-Cilag, Novartis, Takeda, Pfizer, and Roche. V.M. received speaker honoraria from AstraZeneca, Daiichi Sankyo, Eisai, GSK, Pfizer, MSD, Medac, Novartis, Roche, Seagen, Onkowissen, high5 Oncology, Medscape, Gilead, and Pierre Fabre; consultancy honoraria from Roche, Pierre Fabre, Amgen, ClinSol, Novartis, MSD, Daiichi Sankyo, Eisai, Lilly, Sanofi, Seagen, Gilead, and Stemline; institutional research support from Novartis, Roche, Seagen, and Genentech; and travel grants from Roche, Pfizer, Daiichi Sankyo, and Gilead. L.P. has received consulting fees and honoraria for advisory board participation from Pfizer, AstraZeneca, Merck, Novartis, Bristol Myers Squibb, GlaxoSmithKline, Genentech/Roche, Personalis, Daiichi, Natera, and Exact Sciences and institutional research funding from Seagen, GlaxoSmithKline, AstraZeneca, Merck, Pfizer, and Bristol Myers Squibb. C.E.G. reports the following competing interests: Exact Sciences, Advisory Board, personal; AbbVie, Steering Committee member, institutional, co-chair of SC for BrighTNess; Daiichi Sankyo, member SC, institutional, co-chair of SC for DESTINY-Breast05; Genentech/Roche, SC member, institutional, co-chair of SC for lidERA; Genentech/Roche, coordinating PI, institutional, NSABP B-59/GeparDouze; and Genentech/Roche, SC member, institutional, co-chair of SC for KATHERINE. C.J. reports honoraria from AstraZeneca, Amgen, Daiichi Sankyo, Lilly, Roche, Pfizer, MSD Oncology, Pierre Fabre, Sanofi-Aventis, Seagen, Gilead, and Novartis and has a consulting or advisory role for Amgen, Lilly, Roche, Pfizer, Pierre Fabre, Novartis, MSD Oncology, Agendia, Seagen, Gilead, Lilly, Stemline, and Medac. V.N. declares to be a GBG Forschungs GmbH employee. GBG Forschungs GmbH received funding for research grants from AbbVie, AstraZeneca, BMS, Daiichi Sankyo, Gilead, Novartis, Pfizer, and Roche (paid to the institution). GBG Forschungs GmbH received other funding from Daiichi Sankyo, Gilead, Novartis, Pfizer, Roche, and Seagen (paid to the institution). GBG Forschungs GmbH has the following royalties/patents: EP14153692.0, EP21152186.9, EP15702464.7, EP19808852.8, and VM Scope GmbH. M.U. reports honoraria from AstraZeneca, Amgen, Daiichi Sankyo, Lilly, Roche, Pfizer, MSD Oncology, Pierre Fabre, Sanofi-Aventis, Myriad, Seagen, Gilead, and Novartis; has a consulting or advisory role for Amgen, Lilly, Roche, Pfizer, Pierre Fabre, Novartis, MSD Oncology, Agendia, Seagen, Gilead, Lily, Stemline, Genzyme, and Medac; and all honoraria and fees are paid to the employer/institution. S.L. reports grants and other funding from AbbVie; other funding from Amgen; grants and other funding from AstraZeneca; other funding from BMS; grants and other funding from Celgene; grants, non-financial support, and other funding from Daiichi Sankyo; other funding from EirGenix; other funding from Eisai Europe Ltd; other funding from GSK; grants, non-financial support, and other funding from Immunomedics/Gilead; other funding from Lilly; other funding from Merck; grants from Molecular Health; grants, non-financial support, and other funding from Novartis; grants, non-financial support, and other funding from Pfizer; other funding from Pierre Fabre; other funding from Relay Therapeutics; grants, non-financial support, and other funding from Roche; other funding from Sanofi; non-financial support and other funding from Seagen; and other funding from Olema Pharmaceuticals, outside the submitted work. In addition, S.L. has a patent EP14153692.0 pending, a patent EP21152186.9 pending, a patent EP15702464.7 issued, a patent EP19808852.8 pending, and a patent Digital Ki67 Evaluator with royalties paid.

Figures

None
Graphical abstract
Figure 1
Figure 1
Clinical trial design and samples for biomarker analysis (A) Overview of the neoadjuvant phase 2 double-blind randomized placebo-controlled GeparNuevo trial (NCT02685059). (B) Longitudinal gene expression analysis for the evaluation of durvalumab and chemotherapy-related changes. Sequential formalin-fixed paraffin-embedded (FFPE) samples for longitudinal analysis: before the start of therapy (A-samples), after the window phase (B-samples), and after 12 weeks of chemotherapy +/− durvalumab (C-samples). (C) Description of three gene expression cohorts for independent validation: MEDI-4736 trial (NCT02489448), BrighTNess trial (NCT02032277), SCAN-B (NCT02306096). iDFS, invasive disease-free survival; DDFS, distant disease-free survival; OS, overall survival; durva, durvalumab; plac, placebo; TNBC, triple-negative breast cancer; TILs, tumor-infiltrating lymphocytes; pCR, pathological complete response; GSEA, gene set enrichment analysis.
Figure 2
Figure 2
Gene set enrichment for the clinical endpoints pCR and DDFS (A) 2D GSEA plot of the complete G9 biomarker cohort (both arms combined, pretherapeutic biopsies) using HTG-defined (HTG) and hallmark gene sets (HM). The normalized enrichment score (NES) for pCR (x axis, blue) and DDFS (y axis, orange) is shown. (B) 2D GSEA plot for the durvalumab arm and the two clinical endpoints pCR and DDFS. (C) 2D GSEA plot for the placebo arm and the two clinical endpoints pCR and DDFS.
Figure 3
Figure 3
Relevance of individual genes for survival and therapy response in the two therapy arms (A) Overview on the number of significant genes (p < 0.05) for increased or reduced pCR rate in the durvalumab arm as well as the placebo arm (Venn diagram). (B) Overview on the number of significant genes (p < 0.05) for improved or reduced DDFS in the durvalumab arm as well as the placebo arm (Venn diagram). (C–G) Overlap between significant genes for DDFS and pCR in the two trial arms, Venn diagram (D) as well as odds ratio (OR) for pCR and HR for DDFS for selected genes that are significant in more than one subgroup. Error bar: 95% CI.
Figure 4
Figure 4
Contribution of the combined immune, proliferation, and stromal gene set groups to prediction of pCR (A and B) Venn diagrams (A) as well as OR for pCR for selected genes from the three groups (B). (C and D) Contribution of combined immune, proliferation, and stromal gene set groups (GSGs) to DDFS Venn diagrams (C) as well as HR for DDFS for selected genes from the three groups (D). Error bar: 95% CI.
Figure 5
Figure 5
Evaluation of molecular alterations in longitudinal TNBC samples, comparing pretherapeutic core biopsies (A-samples) with core biopsies after the window phase (B-samples) (A and B) Volcano plots for the evaluation of differentially expressed genes in the window phase in the durvalumab (A) and the placebo arm (B). (C) Comparison of gene set enrichment in both therapy arms in the window phase of the trial. The normalized enrichment score (NES) for placebo (blue) and durvalumab (orange) is shown. (D and E) GSEA results for selected gene sets in the window phase with (D) or without (E) durvalumab. CTX, chemotherapy; FDR, false discovery rate.
Figure 6
Figure 6
Longitudinal gene expression changes and predictive and prognostic genes in GeparNuevo—Summary of main results for individual genes from the gene groups (A and B) Significant genes for pCR (OR, x axis) and DDFS (1/HR, y axis) for the durvalumab (A) and the placebo (B) arm of the GeparNuevo trial. Genes were selected based on significance (p < 0.01) for at least one endpoint (pCR and DDFS) in at least one of the study arms. Color coding: combined immune, proliferation, stromal gene groups; for genes that were linked to more than one group, immune and proliferation were the preferred groups. (C) Volcano plot highlighting longitudinal alterations induced by durvalumab during the window phase for selected genes relevant for immune activation, proliferation, and stromal remodeling. (D and E) Overview of gene expression data from all pretherapeutic biopsies, separated by trial arm (left, durvalumab arm, right: placebo arm). Genes were selected based on a significance (p < 0.01) for at least one endpoint (pCR or DDFS) in at least one trial arm or in the complete cohort. Genes were sorted into the combined immune, proliferation, and stromal gene group (as indicated in the STAR Methods section). In addition, the gene groups DNA repair and stem cell were included. Genes that were assigned into more than one gene group were duplicated for this figure. The heatmap in (D) is sorted based on the combined immune gene set; the heatmap in (E) is sorted based on the combined proliferation gene set.
Figure 7
Figure 7
Validation in three independent cohorts MEDI4736 (neoadjuvant durvalumab therapy), BrighTNess (neoadjuvant non-durvalumab therapy), and SCAN-B (survival data with non-immune therapy). (A and B) Stromal, proliferation, and immune genes for pCR in the two treatment arms of the GeparNuevo dataset (A) and the combined MEDI4736 and BrighTNess dataset (B). Similar distribution of the three main gene groups (stromal, immune, and proliferation) if the MEDI4736 (C) or BrighTNess (D) were combined with the SCAN-B cohort to cover the survival endpoint. In the GeparNuevo durvalumab arm as well as the MEDI4736 cohort, the combination of stromal and immune gene signatures (E, F) as well as proliferation and immune signatures (G, H) defined patient groups with similar pCR rates in both cohorts.
See this image and copyright information in PMC

References

    1. Carey L.A., Dees E.C., Sawyer L., Gatti L., Moore D.T., Collichio F., Ollila D.W., Sartor C.I., Graham M.L., Perou C.M. The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes. Clin. Cancer Res. 2007;13:2329–2334. - PubMed
    1. Liedtke C., Mazouni C., Hess K.R., André F., Tordai A., Mejia J.A., Symmans W.F., Gonzalez-Angulo A.M., Hennessy B., Green M., et al. Response to neoadjuvant therapy and long-term survival in patients with triple-negative breast cancer. J. Clin. Oncol. 2008;26:1275–1281. - PubMed
    1. Carey L., Winer E., Viale G., Cameron D., Gianni L. Triple-negative breast cancer: disease entity or title of convenience? Nat. Rev. Clin. Oncol. 2010;7:683–692. - PubMed
    1. Bianchini G., Balko J.M., Mayer I.A., Sanders M.E., Gianni L. Triple-negative breast cancer: challenges and opportunities of a heterogeneous disease. Nat. Rev. Clin. Oncol. 2016;13:674–690. - PMC - PubMed
    1. Bianchini G., De Angelis C., Licata L., Gianni L. Treatment landscape of triple- negative breast cancer - expanded options, evolving needs. Nat. Rev. Clin. Oncol. 2022;19:91–113. - PubMed

Publication types

MeSH terms

LinkOut - more resources