Biology subjects

Hudson, W. H.

Publications and source records attributed to Hudson, W. H..

6 recordsLinked to original sources

bioRxiv2025

Decrypting cellular engagement and recruitment from spatially resolved transcriptomics

The recruitment of the various types of cells into the tissue microenvironment and how these cells engage with other cells in the tissue sites play critical biological roles. However, it is difficult to study these processes on a genome-wide scale using traditional low-throughput experiments. To address this gap, we developed a fully interpretable multi-instance deep learner, coined "spacer". Spacer digests the transcriptomics and spatial modalities of spatially resolved transcriptomics (SRT) data in alignment with the biological principles of the tissue spatial architecture. We deployed spacer to a panel of 17 high definition and 20 low definition SRT datasets, for studying how stromal and immune cells were recruited into tumors and heart during myocarditis. Spacer discovered novel biological insights not affordable by prior spatial data analysis tools, which were validated by orthogonal immuno-peptidomics, spatial T cell receptor (TCR) sequencing, and single cell sequencing experiments. We discovered genes that encode more immunogenic peptides and that are involved in developmental pathways are more potent in recruiting T cells to local tumor sites, while the recruitment of B cells and macrophages is stipulated by a different molecular program. On the other hand, expression of mucins in the tumor cells was found to repel T cell localization. For the engaging cell side, we also uncovered T cell-intrinsic features that determine their localization, validated by spatial-TCR-seq data. Spacer also unexpectedly revealed that CD4+ T cells, though fewer in numbers, are more responsive than CD8+ T cells in the heart during myocarditis. Collectively, this study establishes a new spatially resolved paradigm for studying cellular localization mechanisms in situ and shifts the paradigm from descriptive mapping to mechanistic discovery.

bioinformatics↗

bioRxiv2025

Single-cell, Spatially-Resolved TCR Profiling Links T Cell Phenotype and Clonality in Human Tumors

Despite remarkable success in melanoma and other cancers, immune checkpoint blockade has shown limited efficacy in head and neck squamous cell carcinoma (HNSCC), with durable responses in only [~]10% of patients. This is paradoxical given the abundant infiltration of CD8 T cells in HNSCC, suggesting that current T cell profiling methods fail to fully capture functional anti-tumor immunity and that key immunosuppressive mechanisms remain poorly understood. To uncover mechanisms regulating T cell function in situ, we developed a multimodal profiling framework integrating high-dimensional flow cytometry, single-cell RNA- and TCR-sequencing, and spatial transcriptomics, including spatially-resolved TCR profiling at single-cell resolution. Applying this approach to paired blood and tumor samples from 27 HNSCC patients enabled single-cell resolution mapping of T cell clonality, transcriptional state, and spatial localization within intact tumors. Tumors with similar clinical features and immune profiles by flow cytometry and scRNA-seq exhibited markedly different spatial immune architectures. Within the T cell compartment, stem- and memory-like T cells localized within immune-rich niches, while exhausted cells were broadly dispersed in tumor-rich regions. Targeted spatial TCR mapping revealed that tumor-enriched TCR clones were distributed throughout the tumor yet adopted distinct, location-dependent phenotypes, indicating that both antigen specificity and spatial cues shape T cell differentiation and function in human tumors. These findings reveal fundamental principles of T cell organization in solid tumors and establish a versatile platform for spatially-resolved, antigen-specific T cell profiling.

immunology↗

bioRxiv2024

Tobacco smoke exposure is a driver of altered oxidative stress response and immunity in head and neck cancer

PurposeExposomes are critical drivers of carcinogenesis. However, how they modulate tumor behavior remains unclear. Extensive clinical data link cigarette smoke as a key exposome that promotes aggressive tumors, higher rates of metastasis, reduced response to chemoradiotherapy, and suppressed anti-tumor immunity. We sought to determine whether smoke itself can modulate aggressive tumor behavior in head and neck squamous cell carcinoma (HNSCC) through reprogramming the cellular reductive state. Experimental designUsing established human and murine HNSCC cell lines and syngeneic mouse models, we utilized conventional western blotting, steady state and flux metabolomics, RNA sequencing, quantitative proteomics and flow cytometry to analyze the impact of smoke exposure on HNSCC tumor biology. ResultsCigarette smoke persistently activated Nrf2 target genes essential for maintenance of the cellular reductive state and survival under conditions of increased oxidative stress in HNSCC regardless of HPV status. In contrast to e-cigarette vapor, conventional cigarette smoke mobilizes cellular metabolism toward oxidative stress adaptation, resulting in development of cross-resistance to cisplatin. In parallel, smoke exposure modulates both expression of PDL1 and the secretory phenotype of HNSCC cells through activation of NF-{kappa}B resulting in an altered tumor immune microenvironment (TIME) in syngeneic mouse models and altered PBMC differentiation that includes downregulated expression of antigen presentation and costimulatory genes in myeloid cells. ConclusionCigarette smoke exposome is a potent activator of the Nrf2 pathway and is a likely primary trigger for the tripartite phenotype of aggressive HNSCC consisting of: 1) reduced chemotherapy sensitivity, 2) enhanced metastatic potential and 3) suppressed anti-tumor immunity. Statement of significanceThe smoke exposome drives aggressive tumor behavior, treatment resistance and suppressed immunity through coordinated metabolic reprogramming. Successfully targeting this adaptation is critical to improving survival in smokers with head and neck cancer.

cancer biology↗

bioRxiv2021

Localization of T cell clonotypes using spatial transcriptomics

Spatial transcriptomics is an emerging technology that measures gene expression while preserving spatial information. Here, we present a method to determine localization of specific T cell clones by obtaining T cell receptor (TCR) sequences from spatial transcriptomics assays. Our method uses an existing commercial spatial transcriptomics platform and open-source software for analysis, allowing simple and inexpensive integration with archived samples and existing laboratory workflows. Using human brain metastasis samples, we show that TCR sequences are readily obtained from human tumor tissue and that these sequences are recapitulated by single-cell sequencing methods. This technique will permit detailed studies of the spatial organization of the human T cell repertoire, such as the identification of tumor-infiltrating and tumor-excluded T cell clones.

immunology↗

bioRxiv2021

The CD8+ T cell landscape of human brain metastases

Despite improved outcomes with checkpoint blockade immunotherapy, patients with brain metastases have the worst prognosis among patients with metastatic cancer. Immune checkpoint blockade agents target inhibitory receptors, such as PD-1, on exhausted CD8+ T cells to restore their anti-cancer function. Many patients, however, either do not respond or progress after an initial response to immune checkpoint blockade, and distant intracranial failure is common despite excellent options for local treatment of brain metastasis. To develop more effective therapeutic strategies for the treatment of brain metastases, an understanding of the phenotype of brain metastasis-infiltrating CD8+ T cells is essential. Here we performed a detailed characterization of the CD8+ T cells contained in brain metastases. Brain metastases were densely infiltrated by CD8+ T cells; blood contamination of tumor samples was rare. Compared to patient-matched circulating cells, brain metastasis-infiltrating CD8+ T cells had a distinct phenotype characterized by more frequent expression of PD-1, with subpopulations defined by expression of additional co-inhibitory molecules and the residence marker CD69. Single cell RNA-sequencing identified four phenotypic subpopulations within brain metastasis-infiltrating PD-1+ CD8+ T cells. Two of these populations -- a terminally-differentiated and a dividing population -- were characterized by high expression of co-inhibitory molecules and lacked expression of progenitor markers such as TCF-1. There was significant T cell receptor (TCR) overlap between the terminally-differentiated and dividing populations, suggesting that the dividing cells give rise to the terminally-differentiated cells. There was minimal TCR overlap between these two populations and other brain metastasis-infiltrating PD-1+ CD8+ T cells. T cell clones from brain metastasis-infiltrating CD8+ T cells were rare in circulation, particularly clones from the terminally-differentiated and dividing populations. We systematically identified bystander CD8+ T cells specific for microbial antigens; these cells infiltrated brain metastases and expressed genes shared with exhausted progenitor CD8+ T cells, such as TCF7 and IL7R. We performed spatial transcriptomics on brain metastases and used a novel method to obtain TCR sequences from spatial transcriptomics data. These data revealed distinct niches within the TME defined by their gene expression patterns and cytokine profiles. Terminally-differentiated CD8+ T cells preferentially occupied niches within the tumor parenchyma. Together, our results show that antigen-specificity restricts the spatial localization, phenotypic states, and differentiation pathways available to CD8+ T cells within the brain metastasis TME.

immunology↗

bioRxiv2021

Reduced binding and neutralization of infection- and vaccine-induced antibodies to the B.1.351 (South African) SARS-CoV-2 variant

The emergence of SARS-CoV-2 variants with mutations in the spike protein is raising concerns about the efficacy of infection- or vaccine-induced antibodies to neutralize these variants. We compared antibody binding and live virus neutralization of sera from naturally infected and spike mRNA vaccinated individuals against a circulating SARS-CoV-2 B.1 variant and the emerging B.1.351 variant. In acutely-infected (5-19 days post-symptom onset), convalescent COVID-19 individuals (through 8 months post-symptom onset) and mRNA-1273 vaccinated individuals (day 14 post-second dose), we observed an average 4.3-fold reduction in antibody titers to the B.1.351-derived receptor binding domain of the spike protein and an average 3.5-fold reduction in neutralizing antibody titers to the SARS-CoV-2 B.1.351 variant as compared to the B.1 variant (spike D614G). However, most acute and convalescent sera from infected and all vaccinated individuals neutralize the SARS-CoV-2 B.1.351 variant, suggesting that protective immunity is retained against COVID-19.

immunology↗