Biology subjects

Pauken, K. E.

Publications and source records attributed to Pauken, K. E..

7 recordsLinked to original sources

bioRxiv2026

IGF1 modulates lesional skin inflammation in checkpoint inhibitor-induced lichen planus

Immune checkpoint inhibitor-induced lichen planus (ICI-LP) is a cutaneous immune related adverse event (irAE) that shares key clinicopathologic features with spontaneous lichen planus (LP) but differs histologically and in the sex distribution of its incidence, and may therefore reflect a distinct tissue inflammatory state. To define the cellular programs that distinguish ICI-LP from LP, we profiled lesional skin by single cell and spatial transcriptomic approaches. We found few differences in the T cell and keratinocyte compartments between ICI-LP and LP, which shared similar inflammatory signatures. Rather, the dominant transcriptional features differentiating these two eruptions occurred within the fibroblast and myeloid cell compartments. Fibroblasts in ICI-LP were enriched for IGF1, FGF7, and androgen-response-associated programs, whereas myeloid cells exhibited amplified JAK-STAT and interferon-responsive states spanning both type I and type II interferon signatures. The potential role of androgen response in shaping lichenoid inflammation was supported by a striking loss of androgen receptor expression in lesional keratinocytes by immunohistochemistry. Furthermore, using spatial RNA and transcriptomic approaches, we identified anatomically segregated IFNG, IL17A, and IL13 niches within lesional skin, suggesting that regional immune compartmentalization with differences in local immunoregulation may explain the mixed inflammatory features reported in both ICI-LP and LP. Collectively, these data indicate that ICI-LP is not simply a more inflamed form of LP, but a distinct form of the disease with more prominent inflammatory perturbations within stromal and innate immune cell populations.

immunology↗

bioRxiv2025

Bhlhe40 Coordinates T Cell Programs with Distinct CD4 and CD8 T Cell Requirements for Anti-PD-1 Versus Anti-CTLA-4

The transcriptional programs enabling T cells to mediate anti-tumor immunity remain incompletely defined. Here, we identify Bhlhe40 as a key transcriptional regulator that coordinates both CD4 and CD8 T cell effector programs, revealing divergent cell-specific requirements during anti-PD-1 versus anti-CTLA-4 immune checkpoint therapy (ICT). Using conditional knockout mice, we show that anti-PD-1 efficacy depends on CD8 T cell-intrinsic Bhlhe40, whereas anti-CTLA-4 remains effective through Bhlhe40-dependent CD4 T cell Th1 programs that buffer impaired effector function in Bhlhe40-deficient CD8 T cells. Mechanistically, loss of Bhlhe40 reduces IFN-{gamma} production and skews CD8 T cells toward TCF-1-expressing progenitor exhausted/stem-like states at the expense of effector differentiation, impairing glycolytic fitness under both therapies and mitochondrial function during anti-PD-1 treatment, thereby revealing a Bhlhe40-dependent coupling between effector differentiation, cytokine production, and metabolic fitness that is particularly critical for anti-PD-1 efficacy. CD8 T cell-intrinsic Bhlhe40 also promotes critical ICT-induced remodeling from M2-like CX3CR1 macrophages to inflammatory iNOS macrophages. Analysis of human cancer datasets supported our preclinical observations, revealing that BHLHE40 is enriched in tumor-reactive and activated/exhausted CD8 T cells, where its expression is inversely correlated with TCF7 (TCF-1) and positively associated with TOX, GZMB, and IFNG. Moreover, persistent CD8 T cell clones from basal cell carcinoma responders exhibited significantly higher BHLHE40 expression at pre-treatment than those from non-responders to PD-1 blockade. Together, these findings establish Bhlhe40 not only as a transcriptional coordinator of T cell effector programs, but also as a therapy-specific, subset-dependent determinant that differentially governs CD4 and CD8 T cell contributions to anti-PD-1 and anti-CTLA-4 efficacy.

immunology↗

bioRxiv2025

Dietary methionine restriction primes T cell metabolism for activation and tumor inhibition and enhances the efficacy of immune checkpoint blockade

The proliferation of many cancer cells is methionine dependent and dietary methionine restriction (MR) has shown anti-tumor effects in a wide variety of immunodeficiency preclinical models. Yet, whether MR exerts an anti-tumor effect in the presence of an immune-competent background remains inconclusive. Accumulating evidence has shown an essential role of methionine in immune cell differentiation and function. Thus, competition for methionine between tumor cells and immune cells in the tumor microenvironment may drive tumor growth and tumor response to therapy. Here, we aim to define the impact of MR on tumor growth and associated immunity. We first assessed the effect of MR in a series of immunocompetent mouse models of melanoma, colorectal cancer, breast cancer, and lung. MR led to a broad tumor inhibition effect across these models and such tumor inhibition was not sex-or genetic background-dependent but appears to be fully or partially immune-dependent. Through flow cytometry analysis, we found a consistent increase in intratumoral activated CD8+ T cells across different tumor models and depletion of CD8+ T cells partially or completely reversed MR-induced tumor inhibition in a model dependent manner. Interestingly in young healthy non-tumor-bearing mice, MR increased spleen CD3+ and CD8+ T cell populations. Metabolomics and RNAseq analysis of spleen-derived CD8+ T cells revealed significant increase in purine metabolism and amino acid metabolism and that are in line with the metabolic feature of activated T cells. Furthermore, MR improved the efficacy of anti-PD1 immune checkpoint blockade. Together, MR primes T cell metabolism for its anti-tumor effect and improves the efficacy of anti-PD1 checkpoint blockade.

cell biology↗

bioRxiv2023

Overlapping and Distinct Mechanisms of Effective Neoantigen Cancer Vaccines and Immune Checkpoint Therapy

The goal of therapeutic cancer vaccines and immune checkpoint therapy (ICT) is to eliminate cancer by expanding and/or sustaining T cells with anti-tumor capabilities. However, whether cancer vaccines and ICT enhance anti-tumor immunity by distinct or overlapping mechanisms remains unclear. Here, we compared effective therapeutic tumor-specific mutant neoantigen (NeoAg) cancer vaccines with anti-CTLA-4 and/or anti-PD-1 ICT in preclinical models. Both NeoAg vaccines and ICT induce expansion of intratumoral NeoAg-specific CD8 T cells, though the degree of expansion and acquisition of effector activity was much more substantial following NeoAg vaccination. Further, we found that NeoAg vaccines are particularly adept at inducing proliferating and stem-like NeoAg-specific CD8 T cells. Single cell T cell receptor (TCR) sequencing revealed that TCR clonotype expansion and diversity of NeoAg-specific CD8 T cells relates to their phenotype and functional state associated with specific immunotherapies employed. Effective NeoAg vaccines and ICT required both CD8 and CD4 T cells. While NeoAg vaccines and anti-PD-1 affected the CD4 T cell compartment, it was to less of an extent than observed with anti-CTLA-4, which notably induced ICOS+Bhlhe40+ Th1-like CD4 T cells and, when combined with anti-PD-1, a small subset of Th2-like CD4 T cells. Although effective NeoAg vaccines or ICT expanded intratumoral M1-like iNOS+ macrophages, NeoAg vaccines expanded rather than suppressed (as observed with ICT) M2-like CX3CR1+CD206+ macrophages, associated with the vaccine adjuvant. Further, combining NeoAg vaccination with ICT induced superior efficacy compared to either therapy in isolation, highlighting the utility of combining these modalities to eliminate cancer. HighlightsO_LINeoAg cancer vaccines utilize distinct mechanisms from CTLA-4 or PD-1 ICT C_LIO_LINeoAg vaccines induce TCF1+ stem-like and proliferating NeoAg-specific CD8 T cells C_LIO_LICD8 TCR clonotype expansion relates to phenotype and functional state associated with immunotherapy C_LIO_LINeoAg vaccines induce partially distinct macrophage remodeling from ICT C_LIO_LINeoAg vaccines synergize with ICT, exceeding combination CTLA-4/PD-1 ICT efficacy C_LI

immunology↗

bioRxiv2021

Microenvironmental correlates of immune checkpoint inhibitor response in human melanoma brain metastases revealed by T cell receptor and single-cell RNA sequencing

Melanoma-derived brain metastases (MBM) represent an unmet clinical need due to central nervous system (CNS) progression as a frequent, end-stage site of disease. Immune checkpoint inhibition (ICI) represents a clinical opportunity against MBM; however, the MBM tumor microenvironment (TME) has not been fully elucidated in the context of ICI. To dissect unique MBM-TME elements and correlates of MBM-ICI response, we collected 32 fresh MBM and performed single cell RNA sequencing of the MBM-TME and T cell receptor clonotyping on T cells from MBM and matched blood and extracranial lesions. We observed myeloid phenotypic heterogeneity, most notably multiple distinct neutrophil states including an IL-8 expressing population that correlated with malignant cell epithelial-to-mesenchymal transition. Additionally, we observe significant relationships between intracranial T cell phenotypes and the distribution of T cell clonotypes intracranially and peripherally. We found that the phenotype, clonotype, and overall number of MBM-infiltrating T cells were associated with response to ICI, suggesting that ICI-responsive MBMs interact with peripheral blood in a manner similar to extracranial lesions. These data demonstrate unique features of the MBM-TME, which may represent potential targets to improve clinical outcomes for patients with MBM.

cancer biology↗

bioRxiv2021

Repertoire analyses reveal TCR sequence features that influence T cell fate

T cells acquire a regulatory phenotype when their T cell receptors (TCRs) experience an intermediate-high affinity interaction with a self-peptide presented on MHC. Using TCR sequences from FACS-sorted human cells, we identified TCR features that shape affinity to these self-peptide-MHC complexes, finding that 1) CDR3{beta} hydrophobicity and 2) certain TRBV genes promote Treg fate. We developed a scoring system for TCR-intrinsic regulatory potential (TiRP) and found that within the tumor microenvironment clones exhibiting Treg-Tconv plasticity had higher TiRP than expanded clones maintaining the Tconv phenotype. To elucidate drivers of these predictive TCR features, we examined the two elements of the Treg TCR ligand separately: the self-peptide via murine Tregs, and the human MHC II molecule via human memory Tconvs. These analyses revealed that CDR3{beta} hydrophobicity promotes reactivity to self-peptides, while TRBV gene usage shapes the TCRs general propensity for MHC II-restricted activation.

immunology↗

bioRxiv2020

Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment

The ability to monitor anti-tumor CD8+ T cell responses in the blood has tremendous therapeutic potential. Here, we used paired single-cell RNA sequencing and T cell receptor (TCR) sequencing to detect and characterize "tumor matching" (TM) CD8+ T cells in the blood of mice with MC38 tumors and melanoma patients using the TCR as a molecular barcode. TM cells showed increased activation compared to non-matching T cells in blood, and appeared less exhausted than matching counterparts in tumor. Importantly, PD-1, which has been used to identify putative circulating anti-tumor CD8+ T cells, showed poor sensitivity for identifying TM cells. By leveraging the transcriptome we identified candidate cell surface marker panels for TM cells in mice and melanoma patients, and validated NKG2D, CD39, and CX3CR1 in mice. These data demonstrate that the TCR can be used to identify tumor-relevant populations for comprehensive characterization, reveal unique transcriptional properties of TM cells, and develop marker panels for tracking and analysis of these cells. SummaryUsing single-cell RNA-sequencing coupled with TCR sequencing, we detected CD8+ T cell clones shared between blood and tumor in mice and melanoma patients, characterized these matching clones in blood and tumor, and identified potential biomarkers for their isolation in blood.

immunology↗