On AIRR - Immune receptors in the clinic

In Episode 20 of On AIRR, Dr. Lauren Williamson and Dr. Robert Carnahan, both from Vanderbilt University Medical Center, and Dr. Matthew Vogt, from the University of North Carolina, share extreme stories of sample collection that reveal how cutting-edge therapeutic antibody development depends as much on donor generosity and complex global logistics as on scientific innovation.

From dramatic efforts to secure the first U.S. donor samples in the early days of the COVID-19 pandemic, to rescuing lost samples from airport corridors and navigating international politics, these stories highlight the critical timing windows, global coordination, and human collaboration required to develop life-saving therapeutics. Throughout these extraordinary stories runs a thread of human generosity, demonstrating how crisis can bring out the best of human nature.

Comments are welcome to the inbox of [email protected] or on social media under the tag #onAIRR. Further information can be found here: https://www.antibodysociety.org/the-airr-community/airr-c-podcast.

The episode is hosted by Dr. Ulrik Stervbo and Dr. Zhaoqing Ding.

 Announcements and links

Lauren Williamson https://www.vumc.org/crowe-lab/person/lauren-williamson-phd 

Robert Carnahan https://www.vumc.org/crowe-lab/person/robert-carnahan-phd 

Matthew Vogt https://www.vogtviruslab.com 

Other:

ReVAMPP  https://revampp.org

Adaptive Immune Receptor Repertoire Community (AIRR-C) https://www.airr-community.org

The Antibody Society (TAbS) https://www.antibodysociety.org

AIRR-C Seminar Series: https://www.antibodysociety.org/the-airr-community/airr-community-seminar-series/

Episode 19 of onAIRR features a lively and insightful conversation with three outstanding scientists committed to advancing pandemic preparedness. Dr. Lauren Williamson and Dr. Robert Carnahan, both from Vanderbilt University Medical Center, and Dr. Matthew Vogt, from the University of North Carolina, share their passion for viral immunology and the art of discovering and developing therapeutic antibodies.

onAIRR’s guests provide a behind-the-scenes look at how collaborative research is shaping the future of global health. They introduce the Research and Development of Vaccines and Monoclonal Antibodies for Pandemic Preparedness (ReVAMPP) research network, a major NIH-funded initiative aimed at strengthening pandemic readiness. The conversation explores the use of prototype pathogen approaches to identifying broadly neutralizing antibodies against high-priority viral families, the challenges of balancing breadth versus potency in therapeutic antibodies, and innovative screening methodologies that could transform our ability to respond to future pandemics.

Comments are welcome to the inbox of [email protected] or on social media under the tag #onAIRR. Further information can be found here: https://www.antibodysociety.org/the-airr-community/airr-c-podcast.

The episode is hosted by Dr. Ulrik Stervbo and Dr. Zhaoqing Ding.

Announcements and links

Lauren Williamson https://www.vumc.org/crowe-lab/person/lauren-williamson-phd

Robert Carnahan https://www.vumc.org/crowe-lab/person/robert-carnahan-phd

Matthew Vogt https://www.vogtviruslab.com

ReVAMPP  https://revampp.org

ReVAMPP https://www.niaid.nih.gov/news-events/nih-awards-establish-pandemic-preparedness-research-network 

"Prototype Pathogen Approach for Vaccine and Monoclonal Antibody Development: A Critical Component of the NIAID Plan for Pandemic Preparedness” https://doi.org/10.1093/infdis/jiac296 

Adaptive Immune Receptor Repertoire Community (AIRR-C) https://www.airr-community.org

The Antibody Society (TAbS) https://www.antibodysociety.org

AIRR-C Seminar Series https://www.antibodysociety.org/the-airr-community/airr-community-seminar-series

In this episode of On AIRR, Dr. Paul Thomas, reviews advances in the field of TCR sequencing. Dr. Thomas is a faculty member in the Department of Immunology of St. Jude Children’s Research Hospital. His work has advanced our understanding of innate and adaptive immune responses and TCR specificity with a focus on responses to viral infections.

In Episode 18 of On AIRR, Dr. Thomas shares his journey from immunoparasitology to pioneering TCR repertoire sequencing. He began his scientific career studying innate immune responses to parasites during his graduate work in immunoparasitology. Motivated by a desire to use advanced molecular techniques, he moved to St. Jude for his postdoctoral research, where he contributed to the development of TCR repertoire sequencing methods. The discussion covers the evolution from single-chain TCR sequencing to the development of high-throughput paired sequencing methods, culminating in the TIRTL-seq approach. Dr. Thomas explains the technical and computational challenges in TCR pairing, the innovations that made large-scale studies possible, and the importance of data quality and curation in the field. The episode highlights the impact of these advances on understanding immune responses and the future of AIRR-based diagnostics.

Comments are welcome to the inbox of [email protected] or on social media under the tag #onAIRR. Further information can be found here: https://www.antibodysociety.org/the-airr-community/airr-c-podcast.

The episode is hosted by Dr. Ulrik Stervbo and Dr. Zhaoqing Ding.

 Announcements and links

Paul Thomas Lab https://www.stjude.org/research/labs/thomas-lab.html 

Other:

TIRTL-seq: Deep, quantitative, and affordable paired TCR repertoire sequencing https://doi.org/10.1101/2024.09.16.613345  

TIRTL-seq repository: https://github.com/pogorely/TIRTL

Adaptive Immune Receptor Repertoire Community (AIRR-C) https://www.airr-community.org

The Antibody Society (TAbS) https://www.antibodysociety.org

AIRR-C Seminar Series s https://www.antibodysociety.org/the-airr-community/airr-community-seminar-series/

In this episode of On AIRR, Dr. Bjoern Peters, Professor at the La Jolla Institute for Immunology (LJI), explores how high-quality data serves as the foundation for advancing AI-based immunological predictions and diagnostics.

Originally from Germany, Dr. Peters began his academic journey in theoretical physics at Hamburg, focusing on quantum optics, before pivoting to biophysics during his PhD at Humboldt University. This shift was inspired by the challenge of understanding epitope presentation pathways and the limitations of epitope-prediction algorithms, which led him to work with Dr. Alessandro Sette at LJI to develop the Immune Epitope Database (IEDB) — the world’s largest resource for immune epitope data.

Throughout the conversation, Dr. Peters traces the evolution of epitope research, starting with his work on MHC-peptide binding predictions and expanding into broader immunological data collection. He emphasizes that high-quality datasets often outcompete algorithmic improvements and shares the story of how the IEDB was established to consolidate immune epitope data. The conversation explores the status of data standardization and use of ontologies in structuring biomedical data, particularly in immunology. Dr. Peters highlights how work done by the IEDB and the Adaptive Immune Receptor Repertoire Community (AIRR-C) in these areas is critical for advancing immunology and enabling prediction and diagnostics. Finally, the discussion covers challenges of predicting epitopes from immune repertoires, the growing interest in using AIRR sequencing for diagnostics, and the importance of rigorous, unbiased validation of prediction models for clinical applications. 

Comments are welcome to the inbox of [email protected] or on social media under the tag #onAIRR. Further information can be found here: https://www.antibodysociety.org/the-airr-community/airr-c-podcast.

The episode is hosted by Dr. Ulrik Stervbo and Dr. Zhaoqing Ding.

 Announcements and links

Peters Lab https://www.lji.org/labs/peters-lab

Tools mentioned:

Immune Epitope Database (IEDB) https://www.iedb.org 

Ontology for Biomedical Investigations (OBI) https://obi-ontology.org 

Other:

Adaptive Immune Receptor Repertoire Community (AIRR-C) https://www.airr-community.org

The Antibody Society (TAbS) https://www.antibodysociety.org

Antibody News Podcast, by TAbS https://www.antibodysociety.org/antibody-news-podcast

Sette Lab https://www.lji.org/labs/sette-lab

Dr. Thierry Mora and Dr. Aleksandra Walczak co-lead the Statistical biophysics group within Laboratoire de physique de l'ENS (LPENS) at the Ecole normale supérieure (Paris, France). Physicists by training, Dr. Mora and Dr. Walczak entered the field of the analysis of the immune system in a time when the first AIRR-seq datasets were becoming available. They have applied biophysics, neuroscience, and information theory perspectives to understand V(D)J recombination and quantify diversity. The group has published many software tools for the analysis of immune repertoires, including IGoR (to infer V(D)J recombination related processes from sequencing data), Sonia (infer selection pressures on features of amino acid CDR3 sequences), ALICE (detect TCR involved in immune responses from single RepSeq datasets), and PUBLIC (for analyzing sharing of TCRs, and predict public clones).

In this episode of On AIRR, Dr. Mora and Dr. Walczak discuss the relevance and challenges of quantifying diversity and the questions that remain unanswered. They think of immune repertoire diversity in the same way as one could think of English language sentences, and try to learn the grammar of the combinations and quantify it. They also provide an overview of some of the software tools developed by their group.

Comments are welcome to the inbox of [email protected]  or on social media under the tag #onAIRR. Further information can be found here: https://www.antibodysociety.org/the-airr-community/airr-c-podcast.
 
The episode is hosted by Dr. Ulrik Stervbo and Dr. Zhaoqing Ding.

Announcements and links

Statistical biophysics @ ENS. The website of the group. https://sites.google.com/view/statbiophysens/home

Tools mentioned:

IGoR: https://github.com/statbiophys/IGoR

Sonia: https://github.com/statbiophys/SONIA

SoNNia: https://github.com/statbiophys/sonnia

ALICE: https://github.com/pogorely/ALICE

PUBLIC: https://github.com/yuvalel/PUBLIC