A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

Triple-negative breast cancer (TNBC), the poorest-prognosis breast cancer subtype, lacks clinically approved biomarkers for patient risk stratification, treatment management, and immunotherapies. Prior literature has shown that interrogation of the tumor-immune microenvironment (TIME) may be a promising approach for the discovery of novel biomarkers that can fill these gaps. Recent developments in high-dimensional tissue imaging technology, such as multiplexed ion beam imaging (MIBI), provide spatial context to protein expression in the TIME, opening doors for in-depth characterization of cellular processes. We developed a computational pipeline for the robust examination of the TIME using MIBI. We discover that profiling the functional proteins involved in cell-to-cell interactions in the TIME predicts recurrence and overall survival in TNBC. The interactions between CD45RO and Beta Catenin and CD45RO and HLA-DR were the most relevant for patient stratification. We demonstrated the clinical relevance of the immunoregulatory proteins PD-1, PD-L1, IDO, and Lag3 by tying their interactions to recurrence and survival. Multivariate analysis revealed that our methods provide additional prognostic information compared to clinical variables. Our novel computational pipeline produces interpretable results, and is generalizable to other cancer types.

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Multiplexed imaging analysis of the tumor-immune microenvironment reveals predictors of outcome in triple-negative breast cancer

Communications Biology ◽

10.1038/s42003-021-02361-1 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Aalok Patwa ◽

Rikiya Yamashita ◽

Jin Long ◽

Tyler Risom ◽

Michael Angelo ◽

...

Keyword(s):

Breast Cancer ◽

Triple Negative Breast Cancer ◽

Triple Negative ◽

Ion Beam ◽

Breast Cancer Subtype ◽

Tissue Imaging ◽

Immune Microenvironment ◽

Prognostic Information ◽

Tumor Immune Microenvironment ◽

Prior Literature

AbstractTriple-negative breast cancer, the poorest-prognosis breast cancer subtype, lacks clinically approved biomarkers for patient risk stratification and treatment management. Prior literature has shown that interrogation of the tumor-immune microenvironment may be a promising approach to fill these gaps. Recently developed high-dimensional tissue imaging technology, such as multiplexed ion beam imaging, provide spatial context to protein expression in the microenvironment, allowing in-depth characterization of cellular processes. We demonstrate that profiling the functional proteins involved in cell-to-cell interactions in the microenvironment can predict recurrence and overall survival. We highlight the immunological relevance of the immunoregulatory proteins PD-1, PD-L1, IDO, and Lag3 by tying interactions involving them to recurrence and survival. Multivariate analysis reveals that our methods provide additional prognostic information compared to clinical variables. In this work, we present a computational pipeline for the examination of the tumor-immune microenvironment using multiplexed ion beam imaging that produces interpretable results, and is generalizable to other cancer types.

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Multiplexed Imaging Analysis of the Tumor-Immune Microenvironment Reveals Predictors of Outcome in Triple-Negative Breast Cancer

10.21203/rs.3.rs-132431/v1 ◽

2021 ◽

Author(s):

Aalok Patwa ◽

Rikiya Yamashita ◽

Jin Long ◽

Leeat Keren ◽

Michael R. Angelo ◽

...

Keyword(s):

Breast Cancer ◽

Triple Negative Breast Cancer ◽

Triple Negative ◽

Ion Beam ◽

Breast Cancer Subtype ◽

Beta Catenin ◽

Computational Pipeline ◽

Immune Microenvironment ◽

Prognostic Information ◽

Tumor Immune Microenvironment

Abstract Triple-negative breast cancer (TNBC), the poorest-prognosis breast cancer subtype, lacks clinically approved biomarkers for patient risk stratification, treatment management, and immunotherapies. Prior literature has shown that interrogation of the tumor-immune microenvironment (TIME) may be a promising approach for the discovery of novel biomarkers that can fill these gaps. Recent developments in high-dimensional tissue imaging technology, such as multiplexed ion beam imaging (MIBI), provide spatial context to protein expression in the TIME, opening doors for in-depth characterization of cellular processes. We developed a computational pipeline for the robust examination of the TIME using MIBI. We discover that profiling the functional proteins involved in cell-to-cell interactions in the TIME predicts recurrence and overall survival in TNBC. The interactions between CD45RO and Beta Catenin and CD45RO and HLA-DR were the most relevant for patient stratification. We demonstrated the clinical relevance of the immunoregulatory proteins PD-1, PD-L1, IDO, and Lag3 by tying their interactions to recurrence and survival. Multivariate analysis revealed that our methods provide additional prognostic information compared to clinical variables. Our novel computational pipeline produces interpretable results, and is generalizable to other cancer types.

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Hippo/YAP signaling choreographs the tumor immune microenvironment to promote triple negative breast cancer progression via TAZ/IL-34 axis

Cancer Letters ◽

10.1016/j.canlet.2021.12.016 ◽

2021 ◽

Author(s):

Zheng Wang ◽

Fan Wang ◽

Xin-Yuan Ding ◽

Tian-En Li ◽

Hao-Yu Wang ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Progression ◽

Triple Negative Breast Cancer ◽

Triple Negative ◽

Breast Cancer Progression ◽

Immune Microenvironment ◽

Tumor Immune Microenvironment

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Characterization of the tumor immune microenvironment of triple-negative breast cancer (TNBC) patients who self-identify as African American (AA) or non-African American (NonAA).

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.564 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 564-564

Author(s):

Kim Blenman ◽

Michal Marczyk ◽

Tao Qing ◽

Tess O'Meara ◽

Vesal Yaghoobi ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

African American ◽

Triple Negative Breast Cancer ◽

Somatic Mutations ◽

Triple Negative ◽

Immune Microenvironment ◽

Gene Level ◽

Tumor Immune Microenvironment ◽

Pathway Level

564 Background: What tumor biological differences, if any, contribute to the higher incidence and worse prognosis of triple negative breast cancer (TNBC) in African American (AA) compared to NonAA patients are unknown. We hypothesized that differences in the tumor immune microenvironment may contribute to the outcome disparities. The purpose of this study was to characterize and compare the immune microenvironment of TNBC between patients self-identified as NonAA or AA. Methods: Formalin fixed paraffin embedded surgically resected cancer and paired normal tissues collected before any systemic therapy and the corresponding clinical data were collected for NonAA (n = 56) and AA (n = 54) stage I-III TNBC treated at Yale Cancer Center between 2000-2017. The two cohorts were matched for clinical stage, age of diagnosis, and year of diagnosis. We performed somatic and germline whole exome sequencing (WES), bulk RNA sequencing, and immunohistochemistry to assess PD-L1 expression (SP142). Stromal tumor infiltrating lymphocytes (sTILs) were assessed on H&E slides. Mutation load, mutation frequencies, and gene expression differences were compared at gene and pathway level. Immune cell composition was estimated through gene expression deconvolution analyses (TIDE). Results: Tumor mutational burden was similar between the two cohorts. At gene level, few genes had significantly different somatic mutation frequencies, or differential mRNA expression between AA and NonAA samples. Pathway level alterations showed inflammation, immunity (adaptive; innate), antigen presentation, and allograft rejection pathways were more affected by somatic mutations in AA samples. The affected genes differed from cancer to cancer and were not recurrent and therefore were missed at gene level analysis. Gene set enrichment and co-expression analysis also showed higher immune related pathway expression in AA samples. Unsupervised co-expression cluster analysis confirmed coordinated overexpression of genes involved in immunity, inflammation, and cytokine/chemokine signaling in AA patients. Two immunotherapy response predictive signatures, immune inflamed and the IFNG as well as sTILs score and PD-L1 positivity were also higher in AA samples. These findings raise the possibility that immune checkpoint inhibitors might be particularly effective in AA patients. In NonAA samples, the EMT transition, angiogenesis, adipogenesis, myogenesis, fatty acid metabolism, TGFβ signaling, UV-response, and hypoxia pathways were overexpressed. TIDE analysis suggested higher levels of TAM M2, overall TIDE score, and the Immune Exclusion score in NonAA samples. Conclusions: TNBC in AA patients more frequently harbor somatic mutations in genes involved with immune functions and overexpress immune and inflammatory genes compared to NonAA patients.

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Adipogenesis in triple-negative breast cancer is associated with unfavorable tumor immune microenvironment and with worse survival

Scientific Reports ◽

10.1038/s41598-021-91897-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Masanori Oshi ◽

Yoshihisa Tokumaru ◽

Fernando A. Angarita ◽

Lan Lee ◽

Li Yan ◽

...

Keyword(s):

Breast Cancer ◽

Triple Negative Breast Cancer ◽

Cancer Biology ◽

Triple Negative ◽

Chemotherapy Response ◽

Related Gene ◽

Immune Microenvironment ◽

Gene Set ◽

Gene Sets ◽

Tumor Immune Microenvironment

AbstractCancer-associated adipocytes are known to cause inflammation; however, the role of adipogenesis, the formation of adipocytes, in breast cancer is unclear. We hypothesized that intra-tumoral adipogenesis reflects a different cancer biology than abundance of intra-tumoral adipocytes. The Molecular Signatures Database Hallmark adipogenesis gene set of gene set variant analysis was used to quantify adipogenesis. Total of 5,098 breast cancer patients in multiple cohorts (training; GSE96058 (n = 3273), validation; TCGA (n = 1069), treatment response; GSE25066 (n = 508) and GSE20194 (n = 248)) were analyzed. Adipogenesis did not correlate with abundance of adipocytes. Adipogenesis was significantly lower in triple negative breast cancer (TNBC). Elevated adipogenesis was significantly associated with worse survival in TNBC, but not in the other subtypes. High adipogenesis TNBC was significantly associated with low homologous recombination deficiency, but not with mutation load. High adipogenesis TNBC enriched metabolism-related gene sets, but neither of cell proliferation- nor inflammation-related gene sets, which were enriched to adipocytes. High adipogenesis TNBC was infiltrated with low CD8+ T cells and high M2 macrophages. Although adipogenesis was not associated with neoadjuvant chemotherapy response, high adipogenesis TNBC was significantly associated with low expression of PD-L1 and PD-L2 genes, and immune checkpoint molecules index. In conclusion, adipogenesis in TNBC was associated with cancer metabolism and unfavorable tumor immune microenvironment, which is different from abundance of adipocytes.

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Prognostic Significance and Tumor Immune Microenvironment Heterogenicity of m5C RNA Methylation Regulators in Triple-Negative Breast Cancer

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.657547 ◽

2021 ◽

Vol 9 ◽

Author(s):

Zhidong Huang ◽

Junfan Pan ◽

Helin Wang ◽

Xianqiang Du ◽

Yusheng Xu ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Triple Negative Breast Cancer ◽

Prognostic Value ◽

Triple Negative ◽

Gene Set Enrichment Analysis ◽

Immune Microenvironment ◽

Data Set ◽

Rna Methylation ◽

Tumor Immune Microenvironment

PurposeThe m5C RNA methylation regulators are closely related to tumor proliferation, occurrence, and metastasis. This study aimed to investigate the gene expression, clinicopathological characteristics, and prognostic value of m5C regulators in triple-negative breast cancer (TNBC) and their correlation with the tumor immune microenvironment (TIM).MethodsThe TNBC data, Luminal BC data and HER2 positive BC data set were obtained from The Cancer Genome Atlas and Gene Expression Omnibus, and 11 m5C RNA methylation regulators were analyzed. Univariate Cox regression and the least absolute shrinkage and selection operator regression models were used to develop a prognostic risk signature. The UALCAN and cBioportal databases were used to analyze the gene characteristics and gene alteration frequency of prognosis-related m5C RNA methylation regulators. Gene set enrichment analysis was used to analyze cellular pathways enriched by prognostic factors. The Tumor Immune Single Cell Hub (TISCH) and Timer online databases were used to explore the relationship between prognosis-related genes and the TIM.ResultsMost of the 11 m5C RNA methylation regulators were differentially expressed in TNBC and normal samples. The prognostic risk signature showed good reliability and an independent prognostic value. Prognosis-related gene mutations were mainly amplified. Concurrently, the NOP2/Sun domain family member 2 (NSUN2) upregulation was closely related to spliceosome, RNA degradation, cell cycle signaling pathways, and RNA polymerase. Meanwhile, NSUN6 downregulation was related to extracellular matrix receptor interaction, metabolism, and cell adhesion. Analysis of the TISCH and Timer databases showed that prognosis-related genes affected the TIM, and the subtypes of immune-infiltrating cells differed between NSUN2 and NSUN6.ConclusionRegulatory factors of m5C RNA methylation can predict the clinical prognostic risk of TNBC patients and affect tumor development and the TIM. Thus, they have the potential to be a novel prognostic marker of TNBC, providing clues for understanding the RNA epigenetic modification of TNBC.

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