Simplify and isolate: A case study on how idenTx streamlines preclinical research

For today’s post in our immune checkpoint series, we’ll discuss work published in Cell in 2018 by Sade-Feldman et al., and how they leveraged the economy of cost from AIM’s idenTx organ-on-a-chip assays to turn what would have been a six-variable animal study into a comparatively simple in vitro study. In their research, the group identified specific T cell markers and states associated with regression or progression of tumors in response to immune checkpoint therapy.

Classifying T cells in response to immune checkpoint blockade therapy

The authors focused their studies on CD8+ T cells since it’s known that the number of infiltrating CD8+ T cells in a tumor may influence the response to immune checkpoint therapy.

When analysing the CD8+ T cells from different patients’ tumors, the authors distinguished two main groups: one with high expression of genes linked to memory, activation, and cell survival, including the TCF7 gene; and the other group with increased expression of genes related to exhaustion. The first group was enriched in tumors from patients who responded to immune checkpoint blockade therapy, while the second group showed up in non-responder tumors. Further analysis divided each group into 3 different sub-clusters of CD8+ T cells. Looking at gene expression on these 6 groups, the authors realized that there were different states of these CD8+ T cells, and they could transition from one state to another over time. For example, after PD-1 therapy, the expression of TCF7 (one of the markers that defines the different clusters) is lost when these T cells transition to an effector phenotype.

Using AIM Biotech idenTx chips as a 3D in vitro model to define T cell states

Then, scientists wanted to confirm which T cell states are important for eradicating the tumors upon anti-PD-1 therapy. The authors took mouse tumor biopsies and separated cells by cell sorting. They classified cells by CD39 expression (known to be expressed in terminally exhausted T cells) and TIM3 (a marker of T cell dysfunction in cancer and chronic infections). They grew spheroids from mouse tumor samples into the idenTx chip and added either CD39-TIM3- (double negative, DN) cells, CD39+TIM3+ (double positive, DP) cells, or a mix of DN+DP cells. Then, they treated each set either with anti-PD-1, or the Immunoglobulin G antibody as a control. To test if T cell exhaustion impacted the tumor eradication in the presence of these different cell types, they counted the number of dead cells after five days of treatment. The authors found that CD39 negative and TIM3 negative T cell subpopulations are the most effective for killing cancer cells, and are the cells needed for an effective immune checkpoint blockade therapy.

Verifying ex vivo results obtained on the idenTx chip with an in vivo experiment

Using a melanoma model, scientists treated mice with POM-1 (a CD39 inhibitor) and anti-TIM3 while mice were subjected to anti-PD-1 therapy. The authors found that treated mice showed a reduced tumor size and an increased survival rate compared to non-treated mice, confirming in an in vivo model the results obtained in vitro with idenTx chips.

With the number of variables to isolate and control for, using mice from the start would have caused this study to swell in cost and logistical complexity, but it would have been infeasible on traditional lab assays. By using a simple and versatile 3D cell culture assay like idenTx from AIM Biotech to narrow down the variables first, the authors were able to reach their conclusions comparatively quickly before verifying the results in animals. Consider how such benefits may contribute to your research goals.

Gathering more predictive, human-relevant data is what AIM Biotech is all about. Want to discuss how idenTx can transform your drug discovery research? Use the chat bubble on the bottom right corner of this page, and we’ll reach out to you—or check out our Contact Us page. Also be sure to look at how our contract research services can help streamline your workflow.

*Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Sade-Feldman M, Et al. Cell. 2018 Nov 1;175(4):998-1013.e20. doi: 10.1016/j.cell.2018.10.038. Erratum in: Cell. 2019 Jan 10;176(1-2):404. PMID: 30388456; PMCID: PMC6641984.