News

We recently presented our work on spatial T cell receptor sequencing at the 10x Genomics Spatial Biology Symposium in Boston! You can check out the recording on demand here.

We have a new publication in Cancer Cell! In this perspective article, we discuss the role of various -omics technologies in studying T cells within the tumor microenvironment. In particular, we focus on the opportunities these techniques present to deepen our understanding of T cell biology and also describe the challenges that arise in the interpretation and analysis of these experiments.

Our work describing a new assay for antibody epitope mapping was published today in Cell. This work was a collaboration with the Ortlund Lab at Emory University.

New SARS-CoV-2 mutations are emerging continually, threatening not only to evade immune responses but also to escape binding of antibodies used in antigen tests (also known as rapid tests) to detect COVID-19 infection. In this work, we describe a new method to identify SARS-CoV-2 mutations that escape commonly-used antigen tests.

Most antigen tests detect the SARS-CoV-2 nucleoprotein. To map epitopes of anti-nucleoprotein antibodies, we induced nucleoprotein expression on the surface of cells by adding a secretion leader sequence to the N-terminus and a transmembrane domain to the C-terminus. We then created a deep mutational library that expressed every possible single nucleoprotein mutation. By incubating this library of surface-expressed nucleoprotein with antibodies used in rapid tests and sorting cells without antibody binding, we could identify every single mutation that eliminated nucleoprotein detection by rapid test antibodies.

The results from this assay showed that current variants of concern are unlikely to evade currently-available antigen tests. Additionally, these data provide a useful resource for predicting the detectability of future SARS-CoV-2 variants with antigen tests. Finally, this method is generalizable to map interaction and functional surfaces of proteins in a wide variety of contexts.

Our protocol for localization of T cell clones using the Visium platform is published in STAR Protocols. This protocol is a step-by-step guide on how to use a popular spatial transcriptomics platform to visualize the location of antigen-specific T cells directly within tissue. See our recent work in Cell Reports Medicine for our implementation of this technique in brain tumors.

The Cancer Prevention and Research Institute of Texas (CPRIT) has awarded a $2 million grant to the Hudson Lab! This five-year award will fund research in the laboratory to characterize CD8+ T cell responses in human tumors and develop new immunotherapies to improve immune responses to cancer. Read more here.

Our work describing the CD8+ T cell infiltrate of brain metastases is published today in Cell Reports Medicine! We show that metastatic brain tumors harbor lots of T cells, making them excellent targets for immunotherapy. Our work is also the first to use spatial TCR sequencing, allowing us to track individual T cell clones within tumor tissue! See also Emory University’s press release here.

Dr. Hudson was interviewed by 10X Genomics on the Cell Intel podcast; the episode dropped today- listen here! Our work was previously featured on 10X Genomics’ Innovators blog here.

We are proud to contribute to the publication of a review article on the role of non-coding RNAs in T cell function. Non-coding RNAs are an abundant gene class that are actively regulated and transcribed but do not generate proteins. We discuss the roles of these genes in the generation of T cell memory.