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New approaches to CAR-T therapy

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Nirupama Deshpande on January 18, 2022

What is CAR-T cell therapy?

In the fight against cancer, immunotherapies that enlist and strengthen the power of a patient’s immune system to attack tumor cells have revolutionized treatment paradigms. One such approach called Adoptive Cell Transfer (ACT), which collects and uses a patient’s own immune cells, is in the spotlight. There are several types of ACT – TILs (tumor-infiltrating lymphocytes), TCRs (engineered T cell receptor cells), and CARs (chimeric antigen receptor cells). But the ACT that has progressed most rapidly is Chimeric Antigen Receptor-modified T (CAR-T) cell therapy in which the first step involves harvesting T cells from a patient.

These T cells are then genetically modified to express a tumor-specific binding receptor that is normally not present on the T cell and recognizes a tumor cell antigen. This results in a chimeric molecule, namely a T cell with the specificity of an antibody. These modified T cells are then expanded and infused back into the patient for tumor cell eradication.

Spatial transcriptomics and the biology of CAR-T cells

CAR-T cell therapy has been highly effective in the treatment of hematological malignancies, namely certain subtypes of B cell leukemia or lymphoma; however, in the fight against cancer, there is always good news and bad news. Despite the remarkable success of CAR-T cell therapies, relapses can occur.

While long-term follow-up data show that about one-third of patients achieve prolonged complete remission and are potentially cured, most patients either do not respond to CAR-T cell therapy or relapse after CAR-T cell therapy. These results are driving intense research into identifying mechanisms of resistance to therapy. Furthermore, to date, CAR-T cell therapy has only been used to treat hematological malignancies. Given the efficacy of this therapy, another indication that has emerged is for use with solid tumors.

Due to the intricacies of solid tumors and their locations in the human body, CAR-T cell therapy faces a lot of obstacles. One of the approaches towards understanding the functionality of CAR-T cells is the field of spatial transcriptomics. Towards this aim, NanoString’s  GeoMx® Digital Spatial Profiling (DSP) platform enables the spatial detection of highly multiplexed protein and RNA expression from a particular geographic region of interest within a sample. GeoMx DSP combined with NanoString’s nCounter® analysis system allows researchers to map out the expression of hundreds of genes (at the RNA or protein level) at single-cell resolution with high efficiency.

Recently, the launch of the Human Whole Transcriptome Atlas takes advantage of NGS readout to spatially profile 18,000+ transcripts.

Next, let’s take a look at the ongoing research happening in two labs that study the mechanism of resistance and expansion of CAR-T cell therapy in solid tumors using spatial transcriptomics.

Understanding mechanism of resistance to CAR-T cell therapy

Dr. Marco Ruella and his team at the University of Pennsylvania wanted to identify factors that contribute to resistance to CAR-T cell therapy. They set out to capture the molecular signature and characteristics of T cells using the nCounter platform. The lab used the CAR-T Characterization Panel customized for CAR19 (a type of CAR-T cells with a transgene insert) products.

The team analyzed samples from 46 patients with lymphoma treated with CAR19. Differential gene expression was analyzed and compared to patient outcomes. A distinct difference in the expression of various pathways was observed between patients who responded and did not respond to the therapy. Further, based on expression analysis, two distinct groups were observed within the non-responders, indicating that all relapse cases did not relapse for the same reason.

They also identified a difference in certain key factors between responders and non-responders. Dr. Ruella’s team also looked at biopsies from lymphoma patients treated with chemotherapy as well as CAR-T cell therapy. In each biopsy, they identified a region of interest to study gene expression spatially using the GeoMx Digital spatial profiler for a panel of human genes that includes content for immune cell type, immune activation status, drug targets, and pan-tumor modules. They observed certain differences in pathway-based expression between responders and non-responders. Investigations are still underway to understand how these expression pathways contribute to patient outcomes.

Dr. Ruella used a  CAR-T Characterization Panel customized for CAR19
Dr. Marco Ruella
Dr. Golden used GeoMx DSP to finely dissect gene expression across small regions of tumor tissue.
Dr. Ryan Golden

Expanding CAR-T Cell therapy to solid tumors

The fundamental prerequisite for CART-T cells to function optimally is that the T cells need to traffic to the tumor sites. Unlike hematological malignancies, T cell trafficking to, and infiltration into tumor sites, is often greatly limited by the immunosuppressive microenvironment of the tumor. To understand how CAR-T cells interact with the tumor cells, Dr. Ryan Golden, resident physician in the lab of Prof. Carl June at the University of Pennsylvania, used GeoMx DSP to finely dissect gene expression across small regions of tumor tissue.

They asked the question: “What molecules drive or inhibit a T cell response in the tumor microenvironment?” They used a mouse xenograft model to study human ovarian and pancreatic cancers. Tumor sections with high and low CAR-T cell infiltration were selected based on morphological markers. They did a cluster analysis for RNA expression between these regions and noticed many differences. They are now excited to take this further to human biopsies collected pre-infusion, and post-CAR-T cell therapy from ongoing clinical trials. Two new CAR constructs targeted against a GPI anchored protein, called Mesothelin, are being tested for solid tumors (Mesothelioma, Pancreatic, Ovarian, and Lung Cancers) in these clinical trials.

To learn more about these studies, watch the webinar on-demand.

For Research Use Only. Not for Use in Diagnostic Procedures.

References

  1. CAR-T TREK through the lymphoma universe, to boldly go where no other therapy has gone before. Ghilardi G. et al Br J Haematol . 2021 May;193(3):449-465. doi: 10.1111/bjh.17191.
  2. CAR-T Cell Therapy. Ahmad A. Int J Mol Sci. 2020 Jun 17;21(12)
  3. CAR T-Cell Therapy in Hematological Malignancies: A Voyage in Progress. Holstein S.A and Lunning M.A. Clin Pharmacol Ther 2020 Jan;107(1):112-122.
  4. New development in CAR-T cell therapy. Wang Z, Wu Z, Liu Y, Han W.J Hematol Oncol. 2017 Feb 21;10(1)
  5. Mechanisms of resistance to CAR-T cell therapy. Shah N.N and Fry T.J. Nat Rev Clin Oncol 2019  Jun;16(6)
Post by Nirupama Deshpande