Functional Immune Landscaping in Cancer Research and Beyond

Functional single cell proteomics technology helps accelerate the development of curative medicine

Jing Zhou, PhD

Jing Zhou is the Chief Scientific Officer at IsoPlexis. She is responsible for developing single-cell assays for precisely profiling the functional properties and heterogeneity of immune cells using IsoPlexis’ IsoCode proteomics platform, and for discovery of predictive biomarkers as correlates of patient outcome to immunotherapies. Since joining IsoPlexis in 2015, she has led multiple studies with various biopharma and trial center leaders. These novel findings have led to numerous presentations at prestigious scientific conferences including AACR, ASH, ASCO, SITC, FOCiS and high-impact publications in journals such as Cell, Nat Commun., Blood, Front Immunol., AJT, and JITC. Prior to IsoPlexis, she was an immunologist at the Yale School of Medicine with a good track record of 40+ scientific publications in leading journals. Jing earned her medical degree in clinical medicine from Bengbu Medical College, MS and PhD in immunology from Shanghai Jiao Tong University, and has been the principal investigator of NIH, AHA and Yale University grants.

Q: Can you describe how IsoPlexis’ single-cell functional immune landscaping technology works?

A: Here at IsoPlexis, our highly multiplexed functional proteomics platform generates high dimensional data across thousands of live single cells that reveals the functional heterogeneity among phenotypically similar cell subsets across multiple research areas and disease indications. The platform also provides cellular functional overview with unique identification of highly polyfunctional subsets that drive the response. 

Our technology analyzes 30+ secreted proteins across thousands of live single cells per chip. We can identify polyfunctional cell subsets, defined as single cells that co-secrete at least two proteins simultaneously. The functional single-cell proteomic data generated on our platform includes several lists of datasets such as polyfunctionality and polyfunctional strength index, and we also provide advanced functional visualizations that reveal complex cell clusters with polyfunctional profiles and distinct cytokine signatures. 

These highly polyfunctional cell subsets are associated with many outcomes, but they are masked when analyzed via surface phenotyping alone; our functional single cell proteomics technology helps researchers capture unique potency and durability matrices from single cells to monitor and predict the therapeutic outcomes of multiple human diseases and accelerate the development of curative medicine.

Q: How has this technology been used to identify blood-based biomarkers that predict progression-free survival in melanoma patients?

A: At the 2020 SITC conference, Nektar Therapeutics presented data from a Phase 2 clinical trial patient cohort with metastatic melanoma, highlighting a critical blood-based biomarker for melanoma patients identified by IsoPlexis’ functional single-cell proteomics analysis.

In this trial, we profiled blood CD4+ and CD8+ T cells from melanoma patients before and after a combination therapy of BMS’ Nivolumab (Nivo) and Nektar’s Bempegaldeskleukin (NKTR-214). We found that these blood-based biomarkers predicted progression-free survival in this melanoma patient cohort, providing a non-invasive tool to enable early stratification and deeper insight into the biological differences of responders and non-responders to immunotherapies. Therefore, this analysis could facilitate the development of personalized therapeutics for cancer patients.

Q: Has this technology played a role in uncovering biomarkers of immune-related adverse events related to immune therapies?

A: Studies have shown that CAR-T therapy can lead to the development of immune-related adverse events such as cytokine release syndrome (CRS) and neurotoxicity. IsoPlexis’ technology uniquely characterizes the function and relationship between the single-cell pre-infusion CAR-T product and clinical outcomes including clinical response, CRS, and neurotoxicity. We published these findings in Blood in 2018 and in this study, the pre-infusion CD19 CAR-T product from non-Hodgkin lymphoma patients was profiled with our 32-plex proteomics panel in response to CD19 antigens. 

Our findings demonstrate that the single-cell polyfunctional metric can be a powerful tool in predicting and monitoring immune-related adverse events in CAR-T immunotherapy. The pre-infusion CAR-T product analysis produced useful insights for potentially manufacturing CAR-T products with better attributes, which could improve CAR-T efficacy and prevent adverse immune responses.

Q: How has this technology played a role in areas outside of cancer, such as COVID-19?

A: Besides cancer, IsoPlexis’ technology has been used in autoimmune disease such as multiple sclerosis, lupus, inflammatory bowel disease (IBD), neurodegenerative diseases such as Alzheimer’s and dementia, organ transplantation such as heart transplantation in pediatric patients, antibody and T cell-mediated allograft rejection, and of course, infectious diseases such as malaria and COVID-19. 

We have published COVID-19 work in several high impact journals such as Cell, Immunity, and BMC Neurology. For example, I want to emphasize our recent publication in Cell to highlight our impact in COVID-19 work. In this publication, our single-cell secreted proteomics identified immune biomarkers of COVID-19 severity and revealed markedly upregulated polyfunctional cells with a variety of inflammatory cytokine secretions in both CD4+ and CD8+ T cells as well as monocytes from COVID-19 patients compared to healthy subjects. Our data shows that biomarkers established from our technology enable the stratification of patients based on the prediction of disease progression to administer critical early-stage treatments tailored to individual patients’ immune profiles. 

Our single-cell biomarker detection may also provide critical information for vaccine and therapeutic development, as it helps researchers uncover therapeutic targets such as the polyfunctional inflammatory monocytes we identified on our platform in the Cell study.

Q: Are there any other biomarker studies that you would like to highlight?

A: I’d like to highlight our recent publication in the organ transplantation field in the American Journal of Transplantation. In this study, for the first time, we identified polyfunctional subsets in alloreactive effector memory T cells triggered by allogeneic endothelial cells, especially induced by panel-reactive antibody-activated endothelial cells. These polyfunctional subsets may be key drivers of alloimmune rejection and will not be detected by conventional technologies. In this collaboration with Yale University, we found that the panel-reactive antibody-treated human endothelial cells can significantly increase the CD4+ and CD8+ effector memory T cell polyfunctionality, which may contribute to a high risk of allograft rejection. Our data also demonstrates the impact of IL-1 receptor antagonist and anti-IL-15 blocking in reducing alloreactive effector memory T cell polyfunctionality, suggesting potential treatments for allograft rejection.

This study demonstrates how our functional single-cell proteomics uniquely enables the detection of true protein secretion patterns from live single cells, identifies highly polyfunctional subsets with unique cytokine signatures, and provides deeper insight into cellular functionality and kinetics that can be correlated with in vivo biology. It also shows that our single-cell analysis has high impact in organ transplantation. Hopefully, our data will provide useful insight into the development of more effective therapeutic strategies.