The TCR Shuffle: How your genes help determine your immune response

From the Dr. Frederick “Erick” Matsen and Dr. Philip Bradley labs, Biostatistics and Computational Biology Program, Cancer Consortium.

Arguably the most critical characteristic of the immune system is its ability to adapt following immune exposures. T cells are an exquisitely specific cells that are “trained” to hunt down infection and illness based on the clues presented to them by other cells in the body. An activated T cell will only lock onto and kill a target when its T cell receptor (TCR) recognizes surface proteins displayed on the other cell. T cells expressing TCRs that home in on a component of an active infection will rapidly expand, making identical copies of themselves into an army large enough to fight off the infection. But how does the immune system ensure a TCR diversity sufficient to recognize a pathogen it has never encountered in the first place? The sequences that encode TCRs are determined through a complex and random genetic process called recombination, wherein the DNA molecules of a regions called V D and J for variable, diversity and joining, are physically broken apart and reassembled. While the DNA ends are exposed they can be randomly chewed back by DNA digesting enzymes or have additional short sequences pasted on, though this process isn’t completely understood. At the end of this process, a T cell finally expresses its own unique TCR and undergoes selective “quality-control” testing in the thymus to make sure it can interface correctly with other immune recognition machinery and won’t over-react to “self” markers. TCR repertoires can vary hugely between individuals and are the result of randomized recombination as well as prior immune exposures. Graduate student Maggie Russell recently led the Bradley and Matsen labs in a heroic effort to characterize how an individual’s genetic background might contribute to variability in their TCR repertoire, a study published in eLife.

“Broadly, our work raises questions about how the TCR generation process varies mechanistically across individuals and what functional effects this variation may have on the immune response,” explained Russell. The group wanted to figure out whether an individual’s genetic background could influence the process of TCR generation, and to what extent. Led by Russell, the team figured they could answer their questions by pairing a previously published dataset of TCR sequences with genome-wide genotyping data from almost 400 people. “Using [these data], we extend the current literature by providing the first genome-wide genomic mapping to V(D)J recombination probabilities,” explained Russell. “This approach has allowed us to refine our understanding of genetically-determined T cell receptor repertoire biases and provide specific examples of genetic variants which are associated with modifying the extent of nucleotide trimming and N-insertion”. Essentially, the group found that mutations in genes encoding two proteins, Artemis (which chews the DNA ends) and TdT (which pastes on short sequences) could bias V(D)J recombination and which way the DNA ends get modified before being stuck back together. This is exciting because these aren’t mutations in the V(D)J region itself – they’re mutations in proteins that act on the region. This work shows that genetic differences in areas outside of the TCR-encoding regions can affect the molecular properties of the TCRs.

Additionally, their work helps shed light on the entire process of trimming and pasting that occurs while the V(D)J region’s DNA ends are exposed. “To me, the most exciting part of this work was identifying an independent line of evidence, in addition to existing biochemical evidence, to support that Artemis is the nuclease responsible for trimming nucleotides during VDJ recombination,” said Russell. “As we continue to learn more about this process of junctional diversification, we can begin to explore how the VDJ recombination mechanism, and the trimming process specifically, varies across individuals to promote diverse T cell receptor repertoires and possibly differences in immune responses”.

A graphic with boxes labeled "genetic variant", "population-level differences", "TCR repertoire feature" and "gene usage". There are arrows pointing from "population level differences" to "genetic variant" and "TCR repertoire features", from "genetic variant" to "gene usage" and "TCR repertoire feature", and from "gene usage" to "TCR repertoire feature".
In this publication, Russell et al directly inferred connections between genetic variants and T-cell receptor (TCR) repertoire features while correcting for gene-usage and population-level differences that may have confounded the connection. Figure provided by Maggie Russell.

As for what’s next, Russell is excited to tease apart how these mutations, particularly within the Artemis protein, change the protein’s function. “We are hoping to explore how genetic variants within the gene encoding the Artemis protein could be mediating a change in trimming. Answering this question will first require us to learn more about how the Artemis protein functions during VDJ recombination in healthy humans,” said Russell. “To do this, we are currently using statistical inference and large T-cell receptor repertoire datasets to design mechanistically-inspired probabilistic models of the trimming process that will allow us to learn about the mechanism in a quantitative way”.

In a way, the Cancer Consortium promotes “scientific recombination”, wherein researchers can come together and contribute expertise to a complex problem, creating uniquely suited teams to tackle each question: this study is no different. “This study built on a wonderful pre-existing collaboration with John Hansen and Paul Martin, here at the Hutch, and Dave Levine at UW,” said Dr. Phil Bradley. “Their team facilitated our access to the genotyping data and provided valuable insight and advice”. Dr. John Hansen, a former director of the Clinical Research Division at Fred Hutch, passed away in 2019. Russell added that “collaborations across the Cancer Consortium have allowed us to gain access to the unique, paired genotype and repertoire sequencing dataset that enabled this project… [and researchers] who have enhanced the statistical rigor of our work”.

ML Russell, A Souquette, DM Levine, SA Schattgen, EK Allen, G Kuan, N Simon, A Balmaseda, A Gordon, PG Thomas, FA Matsen IV, and P Bradley. 2022. Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities. eLife. 11:e73475.

This work was funded by the National Institutes of Health, National Institute of Allergy and Infectious Diseases, National Cancer Institute, National Heart, Lund, and Blood Institute, the Simons Foundation, and the Howard Hughes Medical Institute.

Cancer Consortium members Dr. Erick A Matsen and Dr. Phil Bradley contributed to this work.