About
Brian Rudd, MPH, PhD, is a Professor of Immunology in the Department of Microbiology and Immunology at Cornell University College of Veterinary Medicine. His research focuses on understanding why individuals in early life are more susceptible to infection and respond poorly to vaccination. He investigates the underlying basis for this increased susceptibility, which is attributed to quantitative and qualitative differences in neonatal T lymphocytes. His work explores how altered programs of T cell production and maintenance during early development contribute to immune system differences, including a higher proportion of immature recent thymic emigrants, more extensive homeostatic proliferation of naïve T cells, different hematopoietic precursors, and a smaller T cell repertoire. Using neonatal mouse models of infectious diseases, Dr. Rudd aims to determine the contribution of these differences to impaired adaptive immune responses. His ultimate goal is to identify primary defects in neonatal T cells and uncover mechanisms underlying these defects to inform the design of more effective therapeutic interventions and vaccines suitable for early life.
Research topics
- Genetics
- Cell biology
- Immunology
- Biology
- Chemistry
- Medicine
- Geology
Selected publications
bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-09
articleOpen accessAbstract There is growing evidence that neonates harbor innate-like CD8a + T cell subsets that contribute to both protection and hyper-inflammatory states. It remains unclear, however, where these innate-like features are found among the many conventional and unconventional T cell populations that can upregulate the CD8 receptor. Further delineation of these unique populations and functions, with a focus on CD8ab co-expression, will enable studies that seek to understand the unique immune features in conventional T cell populations that are present during fetal and early postnatal life. We used cord blood from infants across the full viable gestational age range to examine phenotypic and transcriptional heterogeneity, with a particular focus on the naïve T cell pool. We report a set of fetally-derived and innate-like naïve CD8αβ + T cells (‘FITs’) that are marked by their KLRG1 + CD161 + phenotype, unique transcriptomic features and which are sparsely detected in adult peripheral blood. Additionally, using T cell receptor repertoire profiling, we can distinguish FITs from well-described and semi-invariant unconventional T cell populations such as mucosa-associated invariant T cells. Our delineation of FITs’ unique features will enable future investigation into their ontogeny and tissue distribution, and ultimately their role in immune-related outcomes in preterm infants.
Proceedings of the National Academy of Sciences · 2026-01-26 · 4 citations
articleOpen accessThe spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we introduce AIR-SPACE, an integrative approach that combines high-resolution spatial transcriptomics with paired, high-fidelity long-read sequencing of T and B cell receptors. This method enables the simultaneous analysis of cellular transcriptomes and adaptive immune receptor (AIR) repertoires within their native spatial context. We applied AIR-SPACE to mouse popliteal lymph nodes at five distinct time points after Vaccinia virus footpad infection and constructed a comprehensive map of the developing adaptive immune response. Our analysis revealed heterogeneous activation niches, characterized by Interferon-gamma (IFN-γ) production, during the early stages of infection. At later stages, we delineated subanatomical structures within the germinal center (GC) and observed evidence that antibody-producing plasma cells differentiate and exit the GC through the dark zone. Furthermore, by combining clonotype data with spatial lineage tracing, we demonstrate that B cell clones are shared among multiple GCs within the same lymph node, reinforcing the concept of a dynamic, interconnected network of GCs. Overall, our study demonstrates how AIR-SPACE can be used to gain insight into the spatial dynamics of infection responses within lymphoid organs.
iScience · 2026-04-02
articleOpen accessSenior authorRTEs and found that they exhibit distinct phenotypes and functions. Paired single-cell transcriptomics and T cell receptor (TCR) sequencing showed that neonatal RTEs exhibit a more effector-like gene expression profile than adult RTEs, and the most pronounced effector-gene bias was found in neonatal RTEs that utilize germline-encoded TCRs. Collectively, these data reveal how the RTE pool changes during development and how TCR usage contributes to phenotypic heterogeneity in the neonatal and adult RTE pools.
2025-11-24
articleOpen access<p>Tyr-CreER, LSL-BrafV600E, Ptenflox/flox genetically engineered mouse model (TBP GEMM).</p>
bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-06 · 3 citations
preprintOpen accessThe spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we introduce AIR-SPACE, an integrative approach that combines high-resolution spatial transcriptomics with paired, high-fidelity long-read sequencing of T and B cell receptors. This method enables the simultaneous analysis of cellular transcriptomes and adaptive immune receptor (AIR) repertoires within their native spatial context. We applied AIR-SPACE to mouse popliteal lymph nodes at five distinct time points after Vaccinia virus footpad infection and constructed a comprehensive map of the developing adaptive immune response. Our analysis revealed heterogeneous activation niches, characterized by Interferon-gamma (IFN-γ) production, during the early stages of infection. At later stages, we delineated sub-anatomical structures within the germinal center (GC) and observed evidence that antibody-producing plasma cells differentiate and exit the GC through the dark zone. Furthermore, by combining clonotype data with spatial lineage tracing, we demonstrate that B cell clones are shared among multiple GCs within the same lymph node, reinforcing the concept of a dynamic, interconnected network of GCs. Overall, our study demonstrates how AIR-SPACE can be used to gain insight into the spatial dynamics of infection responses within lymphoid organs.
2025-11-24
articleOpen access<p>Different resistance phenotypes observed with and without Ccr2+ macrophages.</p>
The Journal of Immunology · 2025-11-01
articleOpen accessAbstract Description The spatial organization of adaptive immune cells within lymph nodes is essential for understanding immune responses during infection and disease. Here, we sought to investigate the spatial and temporal changes to the adaptive immune receptor repertoire (AIRR) in the draining lymph node after footpad infection with Vaccinia virus in mice. We developed a novel method that combines high-resolution spatial transcriptomics (Slide-seq) with high-fidelity long-read adaptive immune receptor sequencing from tissue sections. This integration enables simultaneous analysis of whole transcriptomes and the AIRR in their spatial context. Applying our method to the model, we demonstrated its capability to map the spatial distribution and capture temporal dynamics of the AIRR at 3, 7, 10, 14, and 21 days post-infection. Our approach revealed heterogenous niches of activation from Interferon-gamma (IFN-γ) during early stages of infection. We also observed sub-anatomical structures within the germinal center (GC), providing evidence that antibody-producing plasma cells differentiate and exit the GC from the dark zone. Additionally, we traced the spatial lineage trajectory of B cell clones and found evidence to suggest that their maturation occurs across multiple GCs. Thus, our methodology offers valuable insights into the spatial dynamics of immune responses, presenting a powerful tool for studying the immune system and disease pathogenesis. Topic Categories Technological Innovations in Immunology (TECH)
2025-11-24
articleOpen access<p>Lymphocyte and myeloid population profiles from resistant control and Ccr2RFP/RFP tumors.</p>
Gene-regulatory programs that specify age-related differences during thymocyte development
Cell Reports · 2025-06-25 · 2 citations
articleOpen accessT cell development is fundamental to immune system establishment, but how this development changes with age remains poorly understood. Here, we construct a transcriptional and chromatin accessibility atlas of T cell developmental programs in neonatal and adult mice, revealing the ontogeny of divergent gene-regulatory programs and their link to age-related differences. Specifically, we identify a gene module that diverges with age from the earliest stages of genesis and includes programs that govern the effector response and cell cycle. Moreover, we reveal that neonates possess more accessible chromatin during early thymocyte development, likely establishing poised gene expression programs that manifest later in thymocyte development. Finally, we leverage this atlas, employing a CRISPR-based perturbation approach coupled with single-cell RNA sequencing readout, to uncover a conserved transcriptional regulator, Zbtb20, that contributes to age-dependent differences in T cell development. In summary, our study defines gene-regulatory programs that regulate age-specific differences in T cell development.
2025-11-24
articleOpen access<p>Antibodies used for immunostaining and flow cytometry</p>
Recent grants
The developmental layers in the CD8+ T cell response to chronic infection
NIH · $4.1M · 2014–2024
Mechanisms Limiting Neonatal Immunity
NIH · $4.0M · 2014–2025
Roles for DevelopmentallyRegulated microRNAs in Neonatal Immunity
NIH · $2.2M · 2017–2022
Impact of microbial exposure on immune development
NIH · $1.4M · 2018–2021
NIH · $714k · 2014
Frequent coauthors
- 42 shared
Viviana I. Maymí
Cornell University
- 36 shared
Jiwon Moon
- 36 shared
Andrew C. White
- 36 shared
Dahihm Kim
- 36 shared
Luye An
- 36 shared
Deborah J. Fowell
- 36 shared
Alexander I. McGurk
- 31 shared
Norah L. Smith
Cornell University
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