MASS CYTOMETRY PUBLICATIONS

TRENDING NOW

Welcome to the December issue of Trending Now, a quarterly anthology of recent impactful publications by researchers using CyTOF® technology to help expand our understanding of human health and disease.

December 2019

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WHAT’S NEW IN

MASS CYTOMETRYAdvances in single-cell technology have had a huge impact on translational and clinical research.

Mass cytometry in clinical trials

Given the incredible heterogeneity inherent in the human immune system, robust high-parameter immune profiling methods suitable for use in clinical trials are imperative to effectively evaluate immune behavior in an unbiased manner at the single-cell level. Mass cytometry has emerged as a valuable platform that enables broad profiling of immune cells, simultaneously quantifying more molecular features in one assay without the degree of signal overlap and background issues common in alternative cytometric methods. The technology’s high-dimensional capabilities provide robust data that can elucidate cellular processes and thus enable the development of new therapies as well as the potential stratification of patients into defined treatment groups based on their predicted response to therapy.

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Mass cytometry is employed more and more in clinical research, supporting more than 60 clinical trials globally. Its value stems from the ability to standardize instrument performance from site to site and to perform detailed cell characterization in a single-tube assay, minimizing use of biological sample material and yielding an unbiased view of the complete immune landscape. Furthermore, the use of barcoding to improve sample throughput and staining consistency (Palladium Barcoding Application Note FLDM-00012) as well as the added flexibility to stain, freeze and ship samples are attractive benefits for clinical research. Here is a look at published results from several of these trials.

Clinical trials citing CyTOF technologySource: clinicaltrials.gov

n Cumulative total n New trials

*Through September 2019

Trials by research area

n Immuno-oncology

n Infection and vaccine

n Oncology

n Surgery

n Autoimmunity

n Other

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Successes with immune monitoring

Immune monitoring provides insights into immune response by enabling discovery and identification of phenotypic changes and potential predictive signatures in immune cells over the course of a treatment. Recently published clinical trial results involve the use of immune monitoring to predict response to therapy and also to test a potential therapy itself. A collaboration out of Genentech investigated whether immune monitoring can be used to predict response to non-small cell lung cancer therapy (Fehlings et al.). Using a 29-marker CyTOF® panel together with cellular barcoding to screen peripheral blood before and after treatment, the group identified and characterized 20 different neoantigen-specific CD8+ T cell populations that had distinct phenotypes in responding patients. These findings demonstrate that not only can these rare cell subtypes be identified in patient samples at frequencies ranging from 0.01% to 0.65% of total CD8+ T cells but also that monitoring a specific subset of cells can potentially be used to predict therapeutic efficacy.

Taking a similar approach, a multi-institution collaboration* used immune monitoring by mass cytometry as a predictive measure of human lifespan while exploring epigenetic aging (Fahy et al.). Based on evidence that thymic involution affects critical immune cell populations as a person ages, the team tested whether recombinant human growth hormone treatment could help thymic regeneration and thus prevent or reverse signs of immunosenescence. Upon evaluation of PBMC samples using a 36- marker CyTOF panel, researchers observed immunological changes that preserved the thymus, improved risk factors for many age-related diseases and correlated with a younger epigenetic age.

*Stanford University; University of British Columbia, University of California, Los Angeles; Intervene Immune

Fehlings et al. Journal for ImmunoTherapy of Cancer. Total number of unique neoantigen-specific T cells (hits) detected from 782 candidate neoantigens (left) and frequencies of neoantigen-specific T cells detected within the responders and non-responders groups pre- and post-treatment (right). Abbreviations: ND, not detected; PR, responders; PD, non-responders.

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Inducing immune modulation

Clinical trials focusing on multiple myeloma aimed to test whether a combination therapy can induce tumor sensitization and immune modulation. Researchers at Dana-Farber Cancer Institute examined therapeutic targeting of the bone marrow microenvironment and its interaction with tumor cells, leading to sensitization of tumor cells to apoptosis (Ghobrial et al.). CyTOF analysis included sample barcoding and helped demonstrate significant mobilization of plasma cells, CD34+ stem cells and T cells in response to a combination therapy.

Evaluating therapies and vaccine primers

Clinical trials using mass cytometry have also explored the potential of combination therapies that involve vaccine primers, aiming to improve the efficacy of immunotherapy and overcome obstacles limiting a successful antitumor response. A pilot trial from the University of California, Los Angeles, sought to enhance transgenic adoptive cell therapy used to treat sarcomas and melanomas by including a dendritic cell vaccination that stimulates T cell expansion (Nowicki et al.). Immune monitoring of treated transgenic cells using a 33-marker mass cytometry panel demonstrated a shift from long-term memory phenotypes to more short-lived effector phenotypes over time in a comparison between two cohorts.

Researchers at the Icahn School of Medicine at Mount Sinai strengthened PD-1 blockade therapy effectiveness by cross-priming T cells with an in situ vaccine (ISV) (Hammerich et al.). The combination initiated anti-tumor CD8+ T cell response and systemic cancer remission in patients with advanced-stage indolent non-Hodgkin’s lymphoma. CyTOF analysis demonstrated that cross-priming dendritic cells with an ISV is complementary and enhances antitumor T cell responses and PD1-blockade efficacy.

Compared with flow cytometry, CyTOF greatly increases the number of parameters that can be measured simultaneously per cell by eliminating cell-dependent background signals and the need for mathematical correction of spectral overlap caused by fluorescence.

—Adams et al.

A publication in Cytometry Part A employed high-dimensional mass cytometry to perform in-depth analysis of therapeutic effects on the composition of immune cell subsets in relapsed/refractory multiple myeloma patients and to take advantage of complete analysis from a single patient sample (Adams et al.). CyTOF technology was chosen to more robustly analyze patient samples in a single assay and to avoid relying on multiple flow cytometry acquisitions. The analysis identified immune cell phenotype modifications that correlate with positive treatment response.

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10,000 Immunomes Project

While we have a growing understanding of the critical role the immune system plays across most areas in biology, our knowledge is hindered by the inability to fully investigate immunological mechanisms using conventional assays. As demonstrated in these publications, mass cytometry is enabling us to overcome this barrier to comprehensively and reproducibly characterize immune populations across sample types.

In support of advancing immune-based research, the 10,000 Immunomes Project created at the University of California, San Francisco, collects and annotates data from 10 data types, including mass cytometry, flow cytometry, multiplex ELISA, gene expression array and clinical lab tests, on samples taken from over 10,000 healthy subjects.

The extensive mass cytometry data alone covers 24 immune cell populations from PBMC samples of more than 500 subjects. This diversity of data enables identification of specific immune cell subsets that vary between healthy subject groups separated by age and sex (Zalocusky et al.). The collective resource provides researchers with an extensive baseline reference of the diversity in healthy human immunology and can be used in future studies to make insightful comparisons between healthy and diseased states.

Zalocusky et al. Cell Reports. Resource development and selected applications for the 10,000 Immunomes Project.

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Sources

Adams, H.C. III et al. “High-parameter mass cytometry evaluation of relapsed/refractory multiple myeloma patients treated with daratumumab demonstrates immune modulation as a novel mechanism of action.” Cytometry Part A 95 (2019): 279–289.

Fahy, G.M. et al. “Reversal of epigenetic aging and immunosenescent trends in humans.” Aging Cell 18 (2019): e13028.

Fehlings, M. et al. “Late-differentiated effector neoantigen-specific CD8+ T cells are enriched in peripheral blood of non-small cell lung carcinoma patients responding to atezolizumab treatment.” Journal for ImmunoTherapy of Cancer 7 (2019): 249.

Palladium Barcoding Application Note FLDM-00012. The Benefits of Palladium Barcoding on Data Quality and Workflow. Fluidigm (2019)

These publications and more are available on the Fluidigm website.

A full list of clinical trials using CyTOF technology can be viewed at clinicaltrials.gov.

Ghobrial, I.M. et al. “Phase I/II trial of the CXCR4 inhibitor plerixafor in combination with bortezomib as a chemosensitization strategy in relapsed/refractory multiple myeloma.” American Journal of Hematology 94 (2019): 1,244–1,253.

Hammerich, L. et al. “Systemic clinical tumor regressions and potentiation of PD1 blockade with in situ vaccination.” Nature

Medicine 25 (2019): 814–824.

Nowicki, T.S. et al. “A pilot trial of the combination of transgenic NY-ESO-1-reactive adoptive transfer therapy with dendritic cell vaccination with or without ipilimumab.” Clinical Cancer

Research 25 (2019): 2,096–2,108.

Zalocusky, K.A. et al. “The 10,000 Immunomes Project: Building a Resource for Human Immunology.” Cell Reports 25 (2018): 513-522.

For Research Use Only. Not for use in diagnostic procedures.

Information in this publication is subject to change without notice. Patent and license information: fluidigm.com/legalnotices. Trademarks: Fluidigm, the Fluidigm logo, and CyTOF are trademarks and/or registered trademarks of Fluidigm Corporation in the United States and/or other countries. All other trademarks are the sole property of their respective owners. ©2019 Fluidigm Corporation. All rights reserved. 12/2019

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