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562 Combined spatial and transcriptomic analysis identifies immune microenvironment factors associated with checkpoint inhibition response in triple negative breast cancer
  1. Brooke Robertson1,
  2. Matthew Loya1,
  3. Wei Han2,
  4. Angelo Harris1,
  5. Clifton Drew1,
  6. Chung-Wein Lee1,
  7. Mohammed Qutaish1,
  8. Nora Pencheva3,
  9. Patrick Franken3,
  10. Louise Koopman3,
  11. Mark Fereshteh1 and
  12. Omar Jabado1
  1. 1Genmab, Princeton, NJ, USA
  2. 2Genmab, Plainsboro, NJ, USA
  3. 3Genmab, Utrecht, Netherlands
  • Journal for ImmunoTherapy of Cancer (JITC) preprint. The copyright holder for this preprint are the authors/funders, who have granted JITC permission to display the preprint. All rights reserved. No reuse allowed without permission.


Background Triple-negative breast cancer (TNBC) accounts for 10–20% of newly diagnosed breast cancers worldwide, is usually diagnosed in younger women, and has the worst prognosis among breast cancer subtypes.1 2 Due to limited treatment options, chemotherapy remains integral to the TNBC treatment regime, with the recent addition of chemotherapy plus PARP or anti-PD1 inhibitors. While these advancements provided a much-needed benefit to a subset of patients, a deeper understanding is necessary to determine which patients will benefit from current and future immunotherapies. To provide insight into alterations in patient response, we sought to characterize the molecular and immune microenvironment in baseline and post standard of care matched samples. We used a multimodal approach including immunohistochemistry (IHC), multiplex immunofluorescence (mIF), and single-slide FFPE tumor gene expression to characterize matched pre- and post-TNBC tumor samples.

Methods A cohort of 34 patients diagnosed with TNBC were commercially sourced. Matched tumor biopsies were collected following neoadjuvant chemotherapy and following progression on 2nd line pembrolizumab or nivolumab monotherapy. These matched samples were profiled using IHC (CD3, CD8, PDL1), mIF (CD20, CD163/CD68, CD11c and PanCK) and single-slide FFPE whole transcriptomic profiling. Response to anti-PD1 therapy was scored using RESIST 1.1 (best overall response [BOR], progressive disease [PD] or partial response [PR]) and progression free survival (PFS).

Results Differential gene expression analysis was performed to identify predictors of partial response to anti-PD1 therapy; higher expression of macrophage associated genes CD163 and FOLR2 were associated with PD patients. Prognostic genes, such as IGSF9,3 CERS6 4 and GRHL2,5 were identified in PR patients have been previously implicated in breast cancer. Cell-type signature analysis identified a significant enrichment of adipocytes and macrophages (M2 subtype) in PD patients. Moreover, regardless of patient response, adipocytes and endothelial cells were significantly enriched prior to anti-PD1 therapy. CD3 and CD8 counts were comparable before and after anti-PD1 treatment.

Conclusions Consistent with our findings, M2 macrophages, identified by CD163 expression, have been correlated with a worse prognosis in TNBC patients.6 Additionally, cancer-associated adipocytes7 and endothelial cells8 may be important in breast cancer progression and metastasis. In our cohort, the TNBC tumor microenvironment contained immunosuppressive factors, adipocytes [fatty acid metabolism], and endothelial cells [angiogenesis] that could be used to stratify patients that are more likely to benefit from immunotherapies. Furthermore, directly targeting these immunosuppressive factors prior to immunotherapy could help establish a more responsive tumor microenvironment.


  1. Bauer K, Brown M, Cress R, Parise C, Caggiano V. Descriptive analysis of estrogen receptor (ER)-negative, progesterone receptor (PR)-negative, and HER2-negative invasive breast cancer, the so-called triple-negative phenotype. Cancer. 2007; 109:1721−1728.

  2. Lehmann B, Bauer J, Chen X, Sanders M, Chakravarthy A, Shyr Y, and Pietenpol J. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest. 2011; 121: 2750−2767.

  3. Li Y, Deng Y, Zhao Y, Zhang W, Zhang S, Zhang L, Wang B, Xu Y, Chen S. Immunoglobulin superfamily 9 (IGSF9) is trans-activated by p53, inhibits breast cancer metastasis via FAK. Oncogene. 2022; 41: 4658−4672.

  4. Chen H, He B, Ke F. Ceramide Synthase 6 Mediates Triple-Negative Breast Cancer Response to Chemotherapy Through RhoA- and EGFR-Mediated Signaling Pathways. J Breast Cancer. 2022; 25: 500−512.

  5. Xiang X, Bin Deng Z, Zhuang X, Ju S, Mu J, Jiang H, Zhang L, Yan J, Miller D, Zhang H. Grhl2 Determines the Epithelial Phenotype of Breast Cancers and Promotes Tumor Progression. PLoS One. 2012; 7: e50781.

  6. Bao X, Shi R, Zhao T, Wang Y, Anastasov N, Rosemann M, Fang W. Integrated analysis of single-cell RNA-seq and bulk RNA-seq unravels tumour heterogeneity plus M2-like tumour-associated macrophage infiltration and aggressiveness in TNBC. Cancer Immunol Immunother. 2021; 70:189−202.

  7. Wu Q, Li B, Li Z, Li J, Sun S, Sun S. Cancer-associated adipocytes: key players in breast cancer progression. J Hematol Oncol. 2019; 12: 95.

  8. Ma Y,Li Y, Guo P, Zhao J, Qin Q, Wang J, , Liang Z, Wei D, Wang Z, Shen J, He S, Tang Q, Lu G, Shiand G, Meng Endothelial Cells Potentially Participate in the Metastasis of Triple-Negative Breast Cancer. J Immunol Res. 2022; 2022: 5412007.

Ethics Approval Subjects provided informed consent to Capital Biosciences (tissue vendor) for genetic and protein analysis.

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