Biology subjects

Svane, I. M.

Publications and source records attributed to Svane, I. M..

7 recordsLinked to original sources

bioRxiv2025

Checkpoint receptors in circulating γδ T cells can discern the outcome of cancer immunotherapy

Gamma delta ({gamma}{delta}) T cells are innate-like lymphocytes that in humans can be broadly classified into two main subtypes based on their unique TCR{delta} chain, V{delta}1 and V{delta}2. Both subsets have potent anti-tumor properties and the presence of V{delta}1 cells in the tumor is often associated with positive prognosis. Herein, we investigated the molecular interplay between immune checkpoint receptors (ICRs), IC blockade (ICB) therapy and {gamma}{delta} T cells. We show that ICRs display differential expression and regulation by the JAK-STAT pathway in circulating V{delta}1 and V{delta}2 cells and identify constitutive (e.g. TIGIT, PD-1) and inducible (e.g. TIM-3, LAG-3, CTLA-4) ICRs. In melanoma, V{delta}1 cells, especially in patients who did not respond to ICB or required combination therapy, expressed high levels of ICR, TOX and inhibitory killer Ig-like receptors (KIR) transcripts, reminiscent of an exhaustion transcriptional signature. At the same time all {gamma}{delta} T cells had a prominent downregulation in AP-1 transcription factors. Patient derived cells were functionally competent, although induction of LAG-3 and CTLA-4 was impaired. In the context of anti-PD-1 monotherapy, V{delta}1 cells specifically bound high levels of therapeutic antibody but only in patients who responded to treatment, revealing a potential new prognostic marker for evaluating the efficacy of ICB therapy. Finally, expression of KIR genes in V{delta}1 cells was downregulated in response to successful ICB therapy. Collectively, our data indicate an intricate relationship between ICRs, putatively also KIRs, and {gamma}{delta} T cells and reveal novel approaches by which these cells can be harnessed in order to discern or improve cancer immunotherapy.

immunology↗

bioRxiv2024

A cancer immunotherapy modality based on dendritic cell reprogramming in vivo

Immunotherapy leads to long-term survival of cancer patients, yet generalized success has been hampered by insufficient antigen presentation and exclusion of immunogenic cells from the tumor microenvironment. Here, we developed an approach to reprogram tumor cells in vivo by adenoviral delivery of the transcription factors PU.1, IRF8, and BATF3, which enabled them to present antigens as type 1 conventional dendritic cells. Reprogrammed tumor cells remodeled their tumor microenvironment, recruited, and expanded polyclonal cytotoxic T cells, induced complete tumor regressions, and established long-term systemic immunity in different mouse melanoma models. In human tumor spheroids and xenografts, reprogramming to immunogenic dendritic-like cells progressed independently of immunosuppression, which usually limits immunotherapy. Our study paves the way for first-in-human trials and other applications of immune cell reprogramming in vivo. One-Sentence SummaryReprogramming of tumor cells to cDC1-like cells in vivo elicits systemic and long-term antitumor immunity.

immunology↗

bioRxiv2024

Identification and characterization of neoantigen-reactive CD8+ T cells following checkpoint blockade therapy in a pan-cancer setting

BackgroundImmune checkpoint blockade (ICB) has been approved as first-line or second-line therapies for an expanding list of malignancies. T cells recognizing mutation-derived neoantigens are hypothesized to play a major role in tumor elimination. However, the dynamics and characteristics of such neoantigen-reactive T cells (NARTs) in the context of ICB are still limitedly understood. MethodsTo explore this, tumor biopsies and peripheral blood were obtained pre- and post-treatment from 20 patients with solid metastatic tumors, in a Phase I basket trial. From whole-exome sequencing and RNA-seq data, patient-specific libraries of neopeptides were predicted and screened with DNA barcode-labeled MHC multimers for CD8+ T cell reactivity, in conjunction with the evaluation of T cell phenotype. ResultsWe were able to detect NARTs in the peripheral blood and tumor biopsies for the majority of the patients; however, we did not observe any significant difference between the disease control and progressive disease patient groups, in terms of the breadth and magnitude of the detected NARTs. We also observed that the hydrophobicity of the peptide played a role in defining neopeptides resulting in NARTs response. A trend towards a treatment-induced phenotype signature was observed in the NARTs post-treatment, with the appearance of Ki67+ CD27+ PD-1+ subsets in the PBMCs and CD39+ Ki67+ TCF-1+ subsets in the TILs. Finally, the estimation of T cells from RNAseq was increasing post versus pre-treatment for disease control patients. ConclusionOur data demonstrates the possibility of monitoring the characteristics of NARTs from tumor biopsies and peripheral blood, and that such characteristics could potentially be incorporated with other immune predictors to understand further the complexity governing clinical success for ICB therapy.

immunology↗

bioRxiv2023

Fully automated workflow for integrated sample digestion and Evotip loading enabling high-throughput clinical proteomics

Protein identification and quantification is an important tool for biomarker discovery. With the increased sensitivity and speed of modern mass spectrometers, sample-preparation remains a bottleneck for studying large cohorts. To address this issue, we prepared and evaluated a simple and efficient workflow on the Opentrons OT-2 (OT-2) robot that combines sample digestion, cleanup and Evotip loading in a fully automated manner, allowing the processing of up to 192 samples in 6 hours. Our results demonstrate a highly sensitive workflow yielding both reproducibility and stability even at low sample inputs. The workflow is optimized for minimal sample starting amount to reduce the costs for reagents needed for sample preparation, which is critical when analyzing large biological cohorts. Building on the digesting workflow, we incorporated an automated phosphopeptide enrichment step using magnetic Ti-IMAC beads. This allows for a fully automated proteome and phosphoproteome sample preparation in a single step with high sensitivity. Using the integrated workflow, we evaluated the effects of cancer immune therapy on the plasma proteome in metastatic melanoma patients.

molecular biology↗

bioRxiv2019

Escape from nonsense mediated decay associates with anti-tumor immunogenicity

Frameshift insertion/deletions (fs-indels) are an infrequent but potentially highly immunogenic mutation subtype. Although fs-indel transcripts are susceptible to degradation through the non-sense mediated decay (NMD) pathway, we hypothesise that some fs-indels escape degradation and lead to an increased abundance of tumor specific neoantigens, that are highly distinct from self. We analysed matched DNA and RNA sequencing data from TCGA, and five separate melanoma cohorts treated with immunotherapy. Using allele-specific expression analysis we show that expressed fs-indels were enriched in genomic positions predicted to escape NMD, and associated with higher protein expression, consistent with degradation escape ("NMD-escape"). Across four independent cohorts, fs-indel NMD-escape mutations were found to be significantly associated with clinical benefit to checkpoint inhibitor (CPI) therapy (Pmeta=0.0039), a stronger association than either nsSNV (Pmeta=0.073) or fs-indel (Pmeta=0.064) count. NMD-escape mutations were additionally shown to have independent predictive power in the "low-TMB" setting, and may serve as a biomarker to rescue patients judged ineligible for CPI based on overall TMB, but still with a high chance of response (low-TMB cohort: NMD-escape-positive % clinical benefit=53%, NMD-escape-negative % clinical benefit=16%, P=0.0098). Furthermore, in an adoptive cell therapy (ACT) treated cohort, NMD-escape mutation count was the most significant biomarker associated with clinical benefit (P=0.021). Analysis of functional T-cell reactivity screens from recent personalized vaccine and CPI studies shows direct evidence of fs-indel derived neoantigens eliciting patient anti-tumor immune response (n=15). We additionally observe a subset of fs-indel mutations, with highly elongated neo open reading frames, which are found to be significantly enriched for immunogenic reactivity in these patient studies (P=0.0032). Finally, consistent with the potency of NMD-escape derived neo-antigens and ongoing immune-editing, NMD-escape fs-indels appear to be under negative selective pressure in untreated TCGA cases. Given the strongly immunogenic potential, and relatively rare nature of NMD-escape fs-indels, these alterations may be attractive candidates in immunotherapy biomarker optimisation and neoantigen ACT or vaccine strategies.

cancer biology↗

bioRxiv2018

Collagen density regulates the activity of tumor-infiltrating T cells

BackgroundTumor progression is accompanied by dramatic remodeling of the surrounding extracellular matrix leading to the formation of a tumor-specific ECM, which is often more collagen-rich and of increased stiffness. The altered ECM of the tumor supports cancer growth and metastasis, but it is unknown if this effect involves modulation of T cell activity. To investigate if a high-density tumor-specific ECM could influence the ability of T cells to kill cancer cells, we here studied how T cells respond to 3D culture in different collagen densities.\n\nMethodsT cells cultured in 3D conditions surrounded by a high or low collagen density were imaged using confocal fluorescent microscopy. The effects of the different collagen densities on T cell proliferation, survival, and differentiation were examined using flow cytometry. Cancer cell proliferation in similar 3D conditions was also measured. Triple-negative breast cancer specimens were analyzed for the number of infiltrating CD8+ T cells and for the collagen density. Whole-transcriptome analyses were applied to investigate in detail the effects of collagen density on T cells. Computational analyses were used to identify transcription factors involved in the collagen density-induced gene regulation. Observed changes were confirmed by qRT-PCR analysis.\n\nResultsT cell proliferation was significantly reduced in a high-density matrix compared to a low-density matrix and prolonged culture in a high-density matrix led to a higher ratio of CD4+ to CD8+ T cells. The proliferation of cancer cells was unaffected by the surrounding collagen-density. Consistently, we observed a reduction in the number of infiltrating CD8+ T-cells in mammary tumors with high collagen-density indicating that collagen-density has a role in regulating T cell abundance in human breast cancer.\n\nWhole-transcriptome analysis of 3D-cultured T cells revealed that a high-density matrix induces downregulation of cytotoxic activity markers and upregulation of regulatory T cell markers. These transcriptional changes were predicted to involve autocrine TGF-B signaling and they were accompanied by an impaired ability of tumor-infiltrating T cells to kill autologous cancer cells.\n\nConclusionsOur study identifies a new immune modulatory mechanism, which could be essential for suppression of T cell activity in the tumor microenvironment.

immunology↗

bioRxiv2018

Differential effects of corticosteroids and anti-TNF on tumor-specific immune responses - implications for the management of irAEs

Up to 60% of patients treated with cancer immunotherapy develop severe or life threatening immune-related adverse events (irAEs). Immunosuppression with high doses of corticosteroids or, in refractory cases, with tumor necrosis factor (TNF) antagonists, are the mainstay of treatment for irAEs. It is currently unknown what is the impact of corticosteroids and anti-TNF on the activity of antitumor T cells. In this study, the influences of clinically relevant doses of dexamethasone (corresponding to an oral dose of 10 to 125 mg prednisolone) and infliximab (anti-TNF) on the activation and killing ability of tumor-infiltrating lymphocytes (TILs) was tested in vitro. Overall, dexamethasone at low or intermediate/high dose impaired the activation (respectively -46% and -62%) and tumor-killing ability (respectively -48% and -53%) of tumor-specific TILs. In contrast, a standard clinical dose of infliximab only had a minor effect on T cell activation (-20%) and tumor killing (-10%). A brief resting following exposure to dexamethasone was sufficient to rescue the in vitro activity of TILs. In conclusion, clinically-relevant doses of infliximab only influenced to a lesser extent the activity of tumor-specific TILs in vitro, whereas even low doses of corticosteroids markedly impaired the antitumor activity of TILs. These data support steroid-sparing strategies and early initiation of anti-TNF for the treatment of irAEs in immuno-oncology.

cancer biology↗