We use numerous immunological model systems to do so, but we place a particular emphasis on human immunology and bedside-to-bench research. Namely, we study immunological mechanisms of disease directly in samples isolated from patients, and thus, insights gained from this research are likely to be directly applicable to the design of improved immunotherapies for patients.


Single-Cell Genomics in Cancer Immunology

Cellular heterogeneity underlies all biological processes, for example, variability in immune responses or cancer relapse rates following immunotherapy. We develop and employ novel single-cell techniques to understand several key questions:

1) What are the cell types that underlie the immune responses to cancer and cancer immunotherapy?

2) What are the genetic pathways that regulate these cellular pathways?

3) How do single cells persist or change over time to promote effective anti-tumor immunity?

High-throughput Perturbation Technologies for Immune Cells

To functionally interrogate the molecular programs driving key immune cell types and activation states in disease, we utilize a toolbox of high-throughput perturbation technologies using CRISPR/Cas9 genome editing. These technologies enable us to ask several critical questions:

1)  What are the key molecular programs (i.e. genes, transcription factors, and enhancer elements) that control key cell type behaviors, such as T cell phenotypes within the tumor microenvironment?

2)  Which programs are shared between immune cell types, cancer types, and/or checkpoint blockade agents, and which programs are signal-specific?

3) Can these modules be altered to induce cells states associated with productive immunity, or to reverse dysfunctional cell states associated with therapy resistance?

Lineage Tracing of T cell clones

The T cell receptor (TCR) repertoire in each individual is highly diverse and allows for recognition of a wide array of foreign antigens. The TCR also serves as a molecular indicator of cellular origin as well as tumor response, since T cells expressing identical TCRab pairs likely arise from a common cellular ancestor, and T cells responding to tumors proliferate after antigen recognition. Our lab takes advantage of these properties of the TCR to trace the clonal response of individual tumor-specific T cell clones and to separate signals in tumor-specific T cells from noise in ‘bystander’ non-reactive T cells in the same patient. Using single cell technologies, paired with clonal history, we aim to study the origin and evolution of the T cell response during tumor progression, metastasis, and checkpoint blockade:

1) Which T cell types are clonally-expanded in the tumor site, and is clonal expansion linked to the molecular phenotype of each T cell? 

2) What is the clonal behavior of tumor-specific T cells over the course of disease and therapy progression? 

3) What is the origin of T cell clones that mediate response to checkpoint blockade?


Single-Cell Genomics

We develop high-throughput single-cell transcriptome and epigenome technologies for immune cell analysis (e.g. Satpathy, Granja et al, Nature Biotechnology, 2019, Yost, Satpathy et al, Nature Medicine, 2019).


To functionally interrogate the molecular programs associated with immune cell function, we utilize high-throughput perturbations using CRISPR/Cas9 genome editing, combined with phenotypic and molecular read-outs.

3D Chromosome Conformation

We utilize novel and highly-sensitive chromosome conformation technologies to measure the interactions between regulatory elements and gene promoters in primary immune cells.
(Mumbach, Satpathy et al, Nature Genetics, 2017)

Multi-omic Single-Cell Technologies

We envision that integration of multiple datatypes in single cells will enable new insights into the immune response to cancer and rationally-directed genome engineering strategies to improve immune cell function. We previously developed several strategies to combine datatypes in single cells, including:

1) paired epigenome and T cell receptor (TCR) profiling in single cells
(Satpathy, Saligrama, Buenrostro et al, Nature Medicine, 2018)

2) paired epigenome and CRISPR profiling in single cells
(Rubin, Parker, Satpathy et al, Cell, 2019)

3) paired transcriptome and TCR profiling in single cells
(Yost, Satpathy et al, Nature Medicine, 2019)

Immunological Methods

Genomic measurements are paired with immunological tools, including flow cytometry, fluorescence microscopy, and a variety of in vitro and in vivo immune cell differentiation and activation models.