Pioneering Progress in Cancer Immunotherapy

Single-cell genomics advances T cell immunotherapies at MD Anderson Cancer Center

One of the nation’s preeminent cancer centers, MD Anderson has pioneered multidisciplinary interventional approaches to cancer treatment. The center hosts a dozen patient clinics and 40 research laboratories conducting studies in cancer prevention, early detection and treatment, personalized risk assessment and therapy, and patient care. 

MD Anderson’s Dr. Laurence Cooper leads the Pediatric Cell Therapy Program. His lab studies T cell-based adoptive immunotherapy to develop cells that target and destroy tumors. T cell adoptive immunotherapy is an emerging yet effective cancer therapy, where a patient’s immune cells are engineered to target tumors. The MD Anderson approach to the therapy is to genetically modify T cells so they express chimeric antigen receptors (CARs) with an antigen-binding domain and an intracellular signaling domain.1 In the presence of tumor antigen, the expressed chimeric complex combines antigen recognition with T cell activation to target and destroy tumor cells.

“The aim of this research is to understand the differences between individual cells, to identify the more robust subpopulation [of cells and] eliminate the tumor,” says Dr. Laurence Cooper.

T cell-based adoptive immunotherapy is broadly applicable to cancer and does not require sorting T cells first. Instead, T cells expressing CARs undergo a competitive repopulation in the patient’s body. The T cells that survive and grow out of the repopulation remain as effector memory cells that can help the patient by targeting the tumor.

"You want to understand what each individual cell’s contribution was to the whole and hence you need to understand single-cell analysis on the inoculum, and which of the cells that we put in propagated and sustained its proliferation in the patient," says Cooper.

That's why the C1™ and Biomark™ systems are critical tools in T cell-based adoptive immunotherapy. This integrated, single-cell gene expression workflow can be used to compare the genetics of infused T cells against the T cells that survived and killed tumor cells. Gene expression analysis can reveal up- and down-regulation of effector gene functions critical to survival and potency of the T cells. Cooper’s group employs a variety of Delta Gene™ assay panels to interrogate granzymes, cytokines, T cell activation markers and energetics/oxygen consumption. Through gene expression analysis, the T cells can be modified to generate more robust population of tumor targeting effector cells.

Sonny Ang, PhD, a research investigator in Cooper’s group, states,

“We believe the triple convergence of cancer biology, hypoxia and T cell biology is a unique niche we are well-positioned to explore using single-cell technology. Since using Fluidigm's single-cell genomic applications, we are finally getting meaningful answers.” Ang says, “We did not have the capacity to perform single-cell genomic applications prior to the C1 and Biomark HD systems. … Our main consideration for single-cell applications is technical reproducibility, and from this perspective the C1 and Biomark HD systems perform reliably.”

Integrating single-cell genomic and bioinformatics approaches, Cooper’s team refines its experimental methodologies to produce a desirable clinical outcome. Using an integrated bioinformatic approach, Cooper’s team uses the Fluidigm Singular™ Analysis Toolset to analyze its data coupled with the Circos software, a platform that allows a user to simultaneously visualize multilayered data side by side around the circumference of a circular plot to achieve a more targeted developmental pipeline of adoptive immunotransfer therapies.

Looking forward, Cooper’s group will include single-cell mRNA sequencing as an initial global screening method to profile patient T cells and targeted malignant cells. The global transcriptional profile of the recovered CAR-expressing T cells will guide customized informatics pipelines toward the identification of therapeutic T cell populations.

Selected Publications

1Singh, H. et al. “Manufacture of clinical-grade CD19-specific T cells stably expressing chimeric antigen receptor using Sleeping Beauty system and artificial antigen presenting cells.” PLoS One 8(5) (2013):e64138.