A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer.

Breast cancer is a heterogeneous disease. Tumor cells and associated healthy cells form ecosystems that determine disease progression and response to therapy. To characterize features of breast cancer ecosystems and their associations with clinical data, we analyzed 144 human breast tumor and 50 non-tumor tissue samples using mass cytometry. The expression of 73 proteins in 26 million cells was evaluated using tumor and immune cell-centric antibody panels. Tumors displayed individuality in tumor cell composition, including phenotypic abnormalities and phenotype dominance. Relationship analyses between tumor and immune cells revealed characteristics of ecosystems related to immunosuppression and poor prognosis. High frequencies of PD-L1+ tumor-associated macrophages and exhausted T cells were found in high-grade ER+ and ER- tumors. This large-scale, single-cell atlas deepens our understanding of breast tumor ecosystems and suggests that ecosystem-based patient classification will facilitate identification of individuals for precision medicine approaches targeting the tumor and its immunoenvironment.

Foreign body reaction after CyPass® Micro-Stent implantation: a case series.

PURPOSE: To retrospectively assess the histopathological particularities of explanted CyPass® Micro-Stent of patients with significant loss of endothelial cell density. METHODS: This is a case series of fourteen eyes from eleven patients who underwent CyPass® Micro-Stent implantation due to mild to moderate glaucoma and who subsequently suffered from loss of endothelial cell density. Therefore, the explantation of the device was necessary. In addition to the retrospective evaluation of the intraocular pressure and the endothelial cell density at the time of implantation and explantation, every surgically removed implant was histologically examined and evaluated. RESULTS: Fourteen eyes of eleven patients were in total analysed. The patients-seven males and four females-had a mean age of 62.9 years. The average time between CyPass implantation and explantation was 3.7 years. Eight patients suffered from primary-open-angle glaucoma (POAG), while two patients had a pseudoexfoliation glaucoma (PXG) and one patient had low-pressure glaucoma. Ten of the patients were already pseudophakic before the CyPass implantation and four patients underwent previously glaucoma interventions. There was a significant reduction in the intraocular pressure from 18.57 ± 5.27 mmHg at the time of implantation to 14.78 ± 3.32 mmHg at the time of explantation (p = 0.037). The average endothelial cell density decreased from 1843.67 ± 421.81 to 932.92 ± 412.86/mm2 at the time of explantation (p < 0.01). The histological findings showed a fibrous obliteration of the CyPass accompanied by a chronic granulomatous inflammation with giant cell macrophages. Histologically, these findings were consistent with a foreign body granuloma. CONCLUSIONS: Implants made of polyimides such as the CyPass® Micro-Stent are considered to be biocompatible, but there is no guarantee not to be obliterated or encapsulated. This is the first case series that has detected a foreign body granuloma in multiple eyes after CyPass implantation. However, there is no connection with the type of glaucoma, the extent of previous operations or with the presence of a prolonged postoperative inflammatory reaction.

Cancer-associated fibroblast classification in single-cell and spatial proteomics data.

Cancer-associated fibroblasts (CAFs) are a diverse cell population within the tumour microenvironment, where they have critical effects on tumour evolution and patient prognosis. To define CAF phenotypes, we analyse a single-cell RNA sequencing (scRNA-seq) dataset of over 16,000 stromal cells from tumours of 14 breast cancer patients, based on which we define and functionally annotate nine CAF phenotypes and one class of pericytes. We validate this classification system in four additional cancer types and use highly multiplexed imaging mass cytometry on matched breast cancer samples to confirm our defined CAF phenotypes at the protein level and to analyse their spatial distribution within tumours. This general CAF classification scheme will allow comparison of CAF phenotypes across studies, facilitate analysis of their functional roles, and potentially guide development of new treatment strategies in the future.

A comprehensive single-cell map of T cell exhaustion-associated immune environments in human breast cancer.

Immune checkpoint therapy in breast cancer remains restricted to triple negative patients, and long-term clinical benefit is rare. The primary aim of immune checkpoint blockade is to prevent or reverse exhausted T cell states, but T cell exhaustion in breast tumors is not well understood. Here, we use single-cell transcriptomics combined with imaging mass cytometry to systematically study immune environments of human breast tumors that either do or do not contain exhausted T cells, with a focus on luminal subtypes. We find that the presence of a PD-1high exhaustion-like T cell phenotype is associated with an inflammatory immune environment with a characteristic cytotoxic profile, increased myeloid cell activation, evidence for elevated immunomodulatory, chemotactic, and cytokine signaling, and accumulation of natural killer T cells. Tumors harboring exhausted-like T cells show increased expression of MHC-I on tumor cells and of CXCL13 on T cells, as well as altered spatial organization with more immature rather than mature tertiary lymphoid structures. Our data reveal fundamental differences between immune environments with and without exhausted T cells within luminal breast cancer, and show that expression of PD-1 and CXCL13 on T cells, and MHC-I - but not PD-L1 - on tumor cells are strong distinguishing features between these environments.

Comparison of MammaPrint and TargetPrint results with clinical parameters in German patients with early stage breast cancer.

The 70-gene expression profile MammaPrint is a powerful prognostic indicator for disease outcome in breast cancer patients with improved prediction of recurrence risk compared to currently used guidelines. The microarray-based test TargetPrint further provides reliable, quantitative assessment of mRNA expression levels of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2). This study was performed as a validation of MammaPrint and TargetPrint in an unselected German breast cancer population and was designed to determine the degree of concordance with currently applied clinical parameters. One hundred and forty cases of breast cancer stage I and II were classified as being low or high risk for distant metastasis using MammaPrint. Results were compared to current clinical risk classifications and adjuvant treatment management. Immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH)/chromogenic in situ hybridization (CISH) assessments of ER, PR and HER2 were further compared with gene expression read-outs using TargetPrint. Thirty-two percent of patients (19/59) with a poor prognosis-signature identified via MammaPrint did not receive adjuvant systemic treatment apart from endocrine therapy and were potentially undertreated; whereas 42% (35/77) of patients with a good prognosis-signature received chemotherapy and were potentially overtreated. Comparison of microarray receptor results with IHC and FISH/CISH were concordant in 97% for ER; 86% for PR; and 94% for HER2. In this German study population, MammaPrint would have resulted in altered treatment advice for adjuvant systemic therapy in 40% of patients. Furthermore, TargetPrint presented high concordance for ER, PR and Her2 with IHC and FISH/CISH analysis.