January 03, 2024

Hudson and Kheradmand labs awarded pilot grant to study lung cancer

We are excited to share that the Hudson lab has received a pilot grant from the Dan L. Duncan Comprehensive Cancer Center at Baylor College of Medicine. This grant will help us further our research into lung cancer, focusing on how the immune system interacts with cancer cells. Dr. Farrah Kheradmand, who leads the Lung Precision Oncology Program at the Michael E. DeBakey VA Medical Center, and Dr. Hudson, an Assistant Professor in the Department of Cell and Molecular Biology at Baylor College of Medicine, are co-principal investigators on the project.

This project is about studying the role of B cells in lung cancer, using the latest techniques to figure out how these responses affect the progression of the disease. While B cells are generally thought to promote immunity to pathogens by making antibodies, the goal of this research is to find out more about how certain B cell subsets and cancer cells work together to suppress anti-tumor immunity, which could point us toward new ways to treat lung cancer.

October 26, 2023

Hudson Lab Receives American Lung Association Grant for Lung Cancer Research

The Hudson Lab is excited to announce the receipt of a Lung Cancer Discovery Award from the American Lung Association to fund our research entitled “Mapping T Cell Exhaustion in Lung Tumors.” This project aims to uncover novel strategies to overcome resistance to immune checkpoint inhibitors in the treatment of lung cancer.

Immune checkpoint inhibitors – such as drugs targeting PD-1 – have ushered in a new era of lung cancer therapy, but not all tumors respond, and resistance remains a challenge. In our research, we will use advanced sequencing techniques to identify alternative inhibitory signaling mechanisms in lung tumor-infiltrating T cells. Additionally, we will create a spatial map of gene expression within lung adenocarcinoma tumors to gain insight into T cell function. This work has the potential to revolutionize lung cancer treatment and improve outcomes for patients.

We are grateful for the support from the American Lung Association and excited to advance our understanding of lung cancer.

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July 05, 2023

New award from the Cancer Research Institute

The Cancer Research Institute has granted the Hudson Laboratory a two-year Technology Impact Award to advance the adoption of spatial T cell receptor (TCR) sequencing technology for the analysis of preserved tissue samples.

This initiative aims to deepen our understanding of T cell function and antigen specificity within the tumor microenvironment. T cells, vital components of the immune system, detect foreign and mutated proteins present in cancer cells. Spatial TCR sequencing allows the evaluation of T cell specificity and their spatial distribution within tissues, shedding light on how the tumor environment influences T cell function and their response to immunotherapy. By extending this technique to preserved tissue, the project seeks to investigate T cell activity and location within tumors using a wider range of available samples. This advancement would lead to valuable insights into the distribution and behavior of T cell clones within the tumor microenvironment, aiding the evaluation of disease progression and response to immunotherapy.

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May 19, 2023

Exploring the immune effects of radiation in cancer

New Hudson Lab research was published today in Cell Reports Medicine!

In this report, we analyzed two brain tumors from the same patient – one tumor had received radiation, and the other was untreated. We performed advanced sequencing experiments to analyze gene and protein expression on more than 45,000 single cells from the two tumors and the patient’s blood immune cells. Because the two tumors are from the same patient, we could compare T cell receptor sequences – which are barcodes that track antigen-specific cells within a person – between the two samples.

Our results show that radiation is associated with dramatic immune changes in the tumor microenvironment. Despite similar mutational profiles between the untreated and irradiated samples, tumor-enriched T cells are nearly entirely depleted following radiation. These tumor-specific cells are instead replaced by T cells from the circulation, which are unlikely to contribute to tumor-specific immunity. Radiation also caused a depletion of tumor-associated macrophages and an influx of pro-inflammatory monocytes from the circulation. These findings indicate that radiation may deplete beneficial cells that contribute to anti-tumor immunity.

Read the full paper here.

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October 11, 2022

Research presentation at 10x Genomics Spatial Biology Symposium

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.

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October 06, 2022

Perspective article published in Cancer Cell

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.

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August 26, 2022

New paper: mapping escape mutations to SARS-CoV-2 antigen tests

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.

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June 09, 2022

Our protocol for localization of T cell clones using the Visium platform is published in STAR Protocols

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.

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