An ex vivo tumor fragment platform to dissect response to PD-1 blockade in cancer

Voabil, Paula; Bruijn, Marjolein de; Roelofsen, Lisanne M.; Hendriks, Sanne H.; Brokamp, Simone; Braber, Marlous van den; Broeks, Annegien; Sanders, Joyce; Herzig, Petra; Zippelius, Alfred; Blank, Christian U.; Hartemink, Koen J.; Monkhorst, Kim; Haanen, John B.A.G.; Schumacher, Ton N.; Thommen, Daniela S.

doi:10.1038/s41591-021-01398-3

Cited by 201 publications

(222 citation statements)

References 51 publications

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“…Several emerging testing strategies that have been applied in other areas of cancer are a model for potential use in the identification of HRD. For example, the feasibility of an ex vivo tumor fragment platform to predict response to PD-1 blockade was recently established [151]. In this approach, tumor fragments are embedded in an artificial matrix and cryopreserved prior to characterization using multi-omics techniques, or are perturbed and analyzed to assess response to treatment [151].…”

Section: Current Limitations and Next-generation Strategies In Testing For Hrdmentioning

confidence: 99%

“…For example, the feasibility of an ex vivo tumor fragment platform to predict response to PD-1 blockade was recently established [151]. In this approach, tumor fragments are embedded in an artificial matrix and cryopreserved prior to characterization using multi-omics techniques, or are perturbed and analyzed to assess response to treatment [151]. Ex vivo tumor assessment for HRD could incorporate orthogonal testing, including functional assessment, interrogation of TME immune status and NGS.…”

Section: Current Limitations and Next-generation Strategies In Testing For Hrdmentioning

confidence: 99%

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Determinants of Homologous Recombination Deficiency in Pancreatic Cancer

Wattenberg

Reiss

2021

Cancers

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Pancreatic cancer is a treatment-resistant malignancy associated with high mortality. However, defective homologous recombination (HR), a DNA repair mechanism required for high-fidelity repair of double-strand DNA breaks, is a therapeutic vulnerability. Consistent with this, a subset of patients with pancreatic cancer show unique tumor responsiveness to HR-dependent DNA damage triggered by certain treatments (platinum chemotherapy and PARP inhibitors). While pathogenic mutations in HR genes are a major driver of this sensitivity, another layer of diverse tumor intrinsic and extrinsic factors regulate the HR deficiency (HRD) phenotype. Defining the mechanisms that drive HRD may guide the development of novel strategies and therapeutics to induce treatment sensitivity in non-HRD tumors. Here, we discuss the complexity underlying HRD in pancreatic cancer and highlight implications for identifying and treating this distinct subset of patients.

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Section: Current Limitations and Next-generation Strategies In Testing For Hrdmentioning

confidence: 99%

Section: Current Limitations and Next-generation Strategies In Testing For Hrdmentioning

confidence: 99%

Determinants of Homologous Recombination Deficiency in Pancreatic Cancer

Wattenberg

Reiss

2021

Cancers

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“…PDTF cultures were performed as described previously. 9 In brief, cryopreserved PDTFs were thawed slowly, washed extensively with tumour medium […”

Section: Pdtf Culturesmentioning

confidence: 99%

Integrated functional and spatial profiling of tumour immune responses induced by immunotherapy: the iPROFILER platform

Koelzer

Herzig

Zlobec

et al. 2021

Immuno-Oncology and Technology

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Background: Cancer immunotherapy elicits functional activation and changes in immune cell distribution in cancer. Tumour heterogeneity is a reason for treatment failure but is difficult to capture in experimental settings. This proof-of-principle study describes the integrated functional and digital spatial profiling platform iPROFILER to capture in-situ immune activation patterns with high precision. Materials and methods: iPROFILER combines an algorithm-based image analysis approach for spatial profiling with functional analyses of patient-derived tumour fragments (PDTFs). This study utilized a folate receptor 1 (FOLR1)xCD3 bispecific antibody in dual-affinity re-targeting (DART) format as a tool for inducing T-cell responses in patient tumour samples, and an in-depth investigation of the immune perturbations induced in the tumour microenvironment was performed. Results: Ex-vivo DART stimulation induces upregulation of multiple activation markers in CD4þ and CD8þ T-cell populations and secretion of pro-inflammatory cytokines in FOLR1-positive tumour specimens. This response was reduced or absent in tissue samples that did not express FOLR1. Immunological responses were driven by a strong induction of interferon gamma (IFNg) and IFNg-induced chemokines suggestive of activation of cytotoxic or Th1-like T cells. Ex-vivo DART treatment led to a numerical increase in effector T cells and an upregulation of immune activation markers in the tumour microenvironment as captured by digital image analysis. Analysis of immune activation in tumour and stromal regions further supported the potential of the platform to measure local differences in cell-type-specific activation patterns. Conclusions: iPROFILER effectively combines functional and spatial readouts to investigate immune responses ex vivo in human tumour samples.

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“…Next, our data support the use of combination therapies with PD-1 pathway blockade to enhance rescue of exhausted, tumor-specific CD8 + T cells by targeting additional inhibitory molecules expressed on brain metastasis-infiltrating terminally-differentiated CD8 + T cells, such as CTLA-4 and LAG3 62,63 . These terminally-exhausted CD8 + T cells within the TME may re-gain effector function with PD-1 blockade and/or combination therapies that lead to enhanced tumor cell killing 31 . Finally, targeting the unique signaling niches in which brain metastasis-infiltrating CD8 + T cells reside provides an additional opportunity to harness the immune system to improve disease control in the brain.…”

Section: Discussionmentioning

confidence: 99%

“…ICB also acts on effector CD8 + T cells at the site of antigen to improve their effector function by increasing their expression of molecules such as granzymes and perforins. 23,24,30,31 Given its requirement for the proliferative burst in response to PD-1 pathway blockade, the progenitor population of exhausted CD8 + T cells has received significant attention in tumor immunology studies, many of which have quantified tumor-infiltrating TCF-1 + cells 26,[32][33][34] . However, the antigen specificity of tumor-infiltrating TCF-1 + CD8 + T cells is rarely determined.…”

Section: Introductionmentioning

confidence: 99%

The CD8⁺ T cell landscape of human brain metastases

Sudmeier

Hoang

Nduom

et al. 2021

Preprint

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Despite improved outcomes with checkpoint blockade immunotherapy, patients with brain metastases have the worst prognosis among patients with metastatic cancer. Immune checkpoint blockade agents target inhibitory receptors, such as PD-1, on exhausted CD8+ T cells to restore their anti-cancer function. Many patients, however, either do not respond or progress after an initial response to immune checkpoint blockade, and distant intracranial failure is common despite excellent options for local treatment of brain metastasis. To develop more effective therapeutic strategies for the treatment of brain metastases, an understanding of the phenotype of brain metastasis-infiltrating CD8+ T cells is essential. Here we performed a detailed characterization of the CD8+ T cells contained in brain metastases. Brain metastases were densely infiltrated by CD8+ T cells; blood contamination of tumor samples was rare. Compared to patient-matched circulating cells, brain metastasis-infiltrating CD8+ T cells had a distinct phenotype characterized by more frequent expression of PD-1, with subpopulations defined by expression of additional co-inhibitory molecules and the residence marker CD69. Single cell RNA-sequencing identified four phenotypic subpopulations within brain metastasis-infiltrating PD-1+ CD8+ T cells. Two of these populations — a terminally-differentiated and a dividing population — were characterized by high expression of co-inhibitory molecules and lacked expression of progenitor markers such as TCF-1. There was significant T cell receptor (TCR) overlap between the terminally-differentiated and dividing populations, suggesting that the dividing cells give rise to the terminally-differentiated cells. There was minimal TCR overlap between these two populations and other brain metastasis-infiltrating PD-1+ CD8+ T cells. T cell clones from brain metastasis-infiltrating CD8+ T cells were rare in circulation, particularly clones from the terminally-differentiated and dividing populations. We systematically identified bystander CD8+ T cells specific for microbial antigens; these cells infiltrated brain metastases and expressed genes shared with exhausted progenitor CD8+ T cells, such as TCF7 and IL7R. We performed spatial transcriptomics on brain metastases and used a novel method to obtain TCR sequences from spatial transcriptomics data. These data revealed distinct niches within the TME defined by their gene expression patterns and cytokine profiles. Terminally-differentiated CD8+ T cells preferentially occupied niches within the tumor parenchyma. Together, our results show that antigen-specificity restricts the spatial localization, phenotypic states, and differentiation pathways available to CD8+ T cells within the brain metastasis TME.

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An ex vivo tumor fragment platform to dissect response to PD-1 blockade in cancer

Cited by 201 publications

References 51 publications

Determinants of Homologous Recombination Deficiency in Pancreatic Cancer

Determinants of Homologous Recombination Deficiency in Pancreatic Cancer

Integrated functional and spatial profiling of tumour immune responses induced by immunotherapy: the iPROFILER platform

The CD8⁺ T cell landscape of human brain metastases

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An ex vivo tumor fragment platform to dissect response to PD-1 blockade in cancer

Cited by 201 publications

References 51 publications

Determinants of Homologous Recombination Deficiency in Pancreatic Cancer

Determinants of Homologous Recombination Deficiency in Pancreatic Cancer

Integrated functional and spatial profiling of tumour immune responses induced by immunotherapy: the iPROFILER platform

The CD8+ T cell landscape of human brain metastases

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Product

Resources

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The CD8⁺ T cell landscape of human brain metastases