Biology subjects

Johanns, T. M.

Publications and source records attributed to Johanns, T. M..

4 recordsLinked to original sources

bioRxiv2025

Mapping CD4+ T Cell Landscapes in Glioblastoma Reveals Effectors and Bystanders

The tumor immune microenvironment (TME) has been demonstrated to significantly shape glioblastoma (GBM) progression and therapeutic response, yet the role of CD4+ T cells remains incompletely defined. Here, by integrating single-cell RNA, surface-protein, and TCR profiling of 39,788 T cells from 16 high-grade gliomas with five matched blood samples, we mapped 23,550 CD4+ T cells across 11 states and revealed predominance of CD4+ T cells in primary, but not recurrent, tumors, alongside pronounced tumor-blood discordance. Clonal analyses revealed expansion of cytotoxic effector CD4+ T cells within tumors and TEMRA CD4+ T cells in blood. A small set of dominant clonotypes (0.2% of unique TCR{beta} sequences) accounted for >6% of all CD4+ T cells across both compartments and were shared across different transcriptional subsets, suggesting diverse transcriptional development stemming from a shared progenitor. In contrast, virally annotated clonotypes were broadly dispersed and largely unexpanded, consistent with bystander populations. Collectively, we investigated the cellular and clonal architecture of human CD4+ T cells in GBM and highlight the contrast between PBMC and TIL compartments.

immunology↗

bioRxiv2023

Glioblastoma-infiltrating CD8+ T cells are predominantly a clonally expanded GZMK+ effector population

Recent clinical trials have highlighted the limited efficacy of T cell-based immunotherapy in patients with glioblastoma (GBM). To better understand the characteristics of tumor-infiltrating lymphocytes (TIL) in GBM, we performed cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-cell RNA sequencing (scRNA-seq) with paired V(D)J sequencing, respectively, on TIL from two cohorts of patients totaling 15 patients with high grade glioma, including GBM or astrocytoma, IDH mutant, grade 4 (G4A). Analysis of the CD8+ TIL landscape reveals an enrichment of clonally expanded GZMK+ effector T cells in the tumor compared to matched blood, which was validated at the protein level. Furthermore, integration with other cancer types highlights the lack of a canonically exhausted CD8+ T cell population in GBM TIL. These data suggest that GZMK+ effector T cells represent an important T cell subset within the GBM microenvironment and which may harbor potential therapeutic implications. SignificanceIn order to understand the limited efficacy of immune checkpoint blockade in GBM, we endeavor to understand the TIL landscape through a multi-omics approach. In this study, by highlighting the enrichment of GZMK+ effector T cells and lack of exhausted T cells, we provide a new potential mechanism of resistance to immunotherapy in GBM.

immunology↗

bioRxiv2021

The conventional dendritic cell 1 subset primes CD8+ T cells and traffics tumor antigen to drive anti-tumor immunity in the brain

The central nervous system (CNS) antigen presenting cell (APC) which primes anti-tumor CD8+ T cell responses remains undefined. Elsewhere, the conventional dendritic cell 1 (cDC1) performs this role. However, steady-state brain cDC1 are rare; cDC localize to choroid plexus and dura. Using preclinical glioblastoma models and cDC1-deficient mice, we explored the role of cDC1 in CNS anti-tumor immunity. We determined that cDC1 mediate checkpoint blockade-induced survival benefit and prime neoantigen-specific CD8+ T cells against brain tumors. We observed that cDC, including cDC1, isolated from the tumor, the dura, and the CNS-draining cervical lymph nodes harbored a traceable fluorescent tumor-antigen. In patient samples, we observed several APC subsets (including the CD141+ cDC1-equivalent) infiltrating glioblastomas, meningiomas, and dura. In these same subsets, we identified a tumor-specific fluorescent metabolite of 5- aminolevulinic acid, which labels tumor cells during fluorescence-guided glioblastoma resection. Together, these data elucidate the specialized behavior of cDC1 and suggest cDC1 play a significant role in CNS anti-tumor immunity. One Sentence SummaryCNS cDC1 engage in previously undefined behavior to establish immune responses against brain tumors.

immunology↗

bioRxiv2020

Accurate neoantigen prediction depends on mutation position relative to patient allele-specific MHC anchor location

Neoantigens are novel peptide sequences resulting from sources such as somatic mutations in tumors. Upon loading onto major histocompatibility complex (MHC) molecules, they can trigger recognition by T cells. Accurate neoantigen identification is thus critical for both designing cancer vaccines and predicting response to immunotherapies. Neoantigen identification and prioritization relies on correctly predicting whether the presenting peptide sequence can successfully induce an immune response. As the majority of somatic mutations are single nucleotide variants, changes between wildtype and mutated peptides are typically subtle and require cautious interpretation. A potentially underappreciated variable in neoantigen-prediction pipelines is the mutation position within the peptide relative to its anchor positions for the patients specific MHC molecules. While a subset of peptide positions are presented to the T-cell receptor for recognition, others are responsible for anchoring to the MHC, making these positional considerations critical for predicting T-cell responses. We computationally predicted high probability anchor positions for different peptide lengths for 328 common HLA alleles and identified unique anchoring patterns among them. Analysis of 923 tumor samples shows that 6-38% of neoantigen candidates are potentially misclassified and can be rescued using allelespecific knowledge of anchor positions. A subset of anchor results were orthogonally validated using protein crystallography structures. Representative anchor trends were experimentally validated using peptide-MHC stability assays and competition binding assays. By incorporating our anchor prediction results into neoantigen prediction pipelines, we hope to formalize, streamline and improve the identification process for relevant clinical studies. One Sentence SummaryNeoantigen prediction accuracy is significantly influenced by the mutation position within the neoantigen and its relative position to the patients allele-specific MHC anchor locations.

bioinformatics↗