Characterization, immune cell phenotyping and differential gene expression analysis of brain metastases and primary breast cancer samples

Sep 23, 2026

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Tumor heterogeneity in breast cancer is well established, yet metastatic brain lesions remain comparatively understudied. Rising incidence of brain metastases in metastatic breast cancer and poor outcomes drive the need to clarify molecular drivers of formation, progression, and immune evasion. An integrated analysis of matched brain metastases and primary tumors used immunohistochemistry, in-situ hybridization, tumor-infiltrating lymphocyte quantification, and bulk RNA sequencing across ten paired patients.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages9

Reading Time23 min

AccessFree to download

Introduction

Integrated analysis of paired samples

Methods and biomarkers assessed

Immune profiling and microenvironment shifts

Study implications and limitations

[www. nature.com/scientificreports](www. nature.com/scientificreports) OPEN Characterization, immune cell phenotyping and differential gene expression analysis of brain metastases and primary breast cancer samples Franz Josef Gassner1,2,3, Gabriel Rinnerthaler2,4,5,6, Vanessa Castagnaviz1,5, Alejandra Gonzalez-Martinez1,2,3,10, Thomas Parigger1,2,3, Stephan Drothler1,2,3, Richard Greil2,3,5,6, Roland Geisberger1,2,3, Theo F. J. Kraus7, Alexander Romagna8,9, Christoph Schwartz8,11, Barbara Ladisich8, Karl Sotlar7, Cornelia Hauser-Kronberger7, BeateAlinger-Scharinger7, Markus Steiner1,2,3, Nadja Zaborsky1,2,3 & Simon Peter Gampenrieder1,2,5􀀍 Tumor heterogeneity in breast cancer is well recognized, but research has largely focused on primary tumors, while metastatic lesions, particularly brain metastases (BM), remain understudied. With the rising incidence of BM in metastatic breast cancer (MBC) and their poor prognosis, a deeper understanding of the molecular mechanisms driving BM formation, progression, and immune evasion is crucial for developing better therapeutic strategies. We performed an integrated analysis of BM and matched primary breast tumors using immunohistochemistry, in-situ hybridization, tumor-infiltrating lymphocyte (TIL) quantification, and bulk RNA sequencing. Tumor receptor status, gene expression profiles, immune cell composition, and pathway alterations were analyzed in ten patients with paired samples. Changes in receptor status were observed between primary tumors and BM, including alterations in estrogen receptor and HER2 expression. RNA sequencing revealed differentially expressed genes and pathways, with an apparent downregulation of immune-related genes in BM. Immune profiling suggested a shift in the tumor microenvironment, with BM showing lower B-and CD8 +T-cell infiltration and a relative increase in M2 macrophages and follicular helper T-cells. While these findings are descriptive and limited by sample size, they point towards a potentially more immunosuppressive milieu in BM that may contribute to immune evasion and reduced responsiveness to checkpoint inhibitor therapy. Our study highlights molecular and immunological differences between primary breast tumors and BM. The altered immune landscape in BM, characterized by diminished TIL infiltration and an increase in immunosuppressive cells, warrants further investigation in larger, more homogeneous cohorts. Keywords Tumor microenvironment, Immune escape, Immunotherapy, Breast cancer heterogeneity, Brain metastasis immunoprofiling 1Cancer Research Laboratory of the Department of Internal Medicine III, University Hospital Salzburg, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, Salzburg 5020, Austria. 2Cancer Cluster Salzburg, Salzburg, Austria. 3Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Salzburg, Austria. 4Division of Oncology, Department for Internal Medicine, Medical University Graz, Graz, Austria. 5Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, University Hospital Salzburg, Paracelsus Medical University Salzburg, Salzburg, Austria. 6Austrian Group for Medical Tumor Therapy (AGMT) GmbH, Salzburg, Austria. 7Pathologic Institute of the University Hospital Salzburg, Paracelsus Medical University Salzburg, Salzburg, Austria. 8Department of Neurosurgery, University Hospital Salzburg, Paracelsus Medical University Salzburg, Salzburg, Austria. 9Department of Neurosurgery, München Klinik Bogenhausen, Munich, Germany. 10Department of Biosciences, Paris-Lodron-University Salzburg, Salzburg, Austria. 11 Department of Neurosurgery, University Hospital Innsbruck, Medical University Innsbruck, Innsbruck, Austria. 􀀍 email: [s.gampenrieder@salk.at](s.gampenrieder@salk.at) [www. nature.com/scientificreports/](www. nature.com/scientificreports/) Metastatic breast cancer

FAQs

What was the main goal of this study on brain metastases?

To identify molecular and immunological differences between brain metastases and matched primary breast tumors, focusing on immune evasion mechanisms and gene expression changes that could inform better therapies.

Which experimental approaches were used to compare brain metastases with primary breast tumors?

The study performed immunohistochemistry, in-situ hybridization, tumor-infiltrating lymphocyte quantification, and bulk RNA sequencing on ten paired patient samples.

What immune microenvironment changes were observed in brain metastases?

Brain metastases showed lower B-cell and CD8+ T-cell infiltration and a relative increase in M2 macrophages and follicular helper T-cells, suggesting a more immunosuppressive milieu.

Sep 23, 2026

Upload by Jacob