Biology subjects

Viuff, M. C.

Publications and source records attributed to Viuff, M. C..

3 recordsLinked to original sources

bioRxiv2026

Impaired HPV driven CD8 T cells recognition and Immune suppression in HPV-Induced Cervical Cancer

Human papillomavirus (HPV) remains the leading cause of cervical cancer, yet the mechanisms underlying its immune evasion remain poorly defined. We performed an integrated analysis of HPV-specific CD8 T cell responses and the immune microenvironment in cervical cancer, high-grade intraepithelial neoplasia (CIN3), and healthy controls using flow cytometry, transcriptomics, and DNA-barcoded peptide-MHC multimer screening across cervical biopsies, peripheral blood, and liquid-based cytology (LBC). Cervical cancer tissues exhibited a profoundly immunosuppressive milieu, with enrichment of exhausted CD8 and CD4 T cells, increased regulatory T cells, and PD-L1-expressing myeloid subsets. Conventional dendritic cells and macrophages showed reduced frequencies, while plasmacytoid dendritic cells and intermediate monocytes were elevated. Interestingly, LBC samples reliably reflected T cell exhaustion signatures observed in biopsies, supporting their use as a minimally invasive tool for T cell immune monitoring; however, they were not suitable for detailed myeloid profiling. Transcriptomic analysis revealed distinct gene expression profiles in tumor tissues with elevated signatures of immune checkpoints and regulatory immune cell infiltration. Importantly, HPV-specific CD8 T cell responses were significantly reduced in cancer patients compared to CIN3 and controls, with decreased breadth and frequency of HPV peptides recognition. HPV peptides screening identified HPV-specific CD8 T cell responses toward 109 unique peptide-MHC complexes, including 37 novel HPV-derived peptide from E2, E6, and E7 proteins. These findings reveal impaired HPV immune recognition and a suppressive tumor microenvironment in cervical cancer, underscoring the need to enhance HPV-specific T cell responses and target immune suppression in therapeutic strategies.

immunology↗

bioRxiv2025

ITRAP2, a flexible and robust strategy to assign antigen recognition of T-cells in a coupled single-cell TCR-pMHC assay

Determining T-cell specificity forms a crucial step toward understanding T-cell involvement in health and disease. Single-cell sequencing technologies allow for co-capture of TCR alpha and beta chains, and their antigen specificity can be determined through peptide-MHC (pMHC) multimer binding and capture of a co-attached barcode oligo. However, SC sequencing often includes a high level of dropouts and risk of cross-contamination. Similarly, barcoded pMHC readouts often suffer from significant background noise. These issues complicate the automatic assignment of pMHC recognition to TCR clonotypes. To overcome these challenges, we developed a method for data denoising - Improved T-cell Receptor Antigen Paring 2 (ITRAP2). This approach significantly reduces noise in single-cell pMHC readouts and allows for accurate identification of TCR specificity. ITRAP2 incorporates statistical tests and confidence metrics for each TCR-pMHC pairing, offering user flexibility in pairing rigor, and allows multiple pMHC assignments to the same T-cell clone in the event of cross-binding within the pMHC multimer library. We tested this method on an in-house generated dataset of 8141 single cells, screened for CD8 T-cell binding using a panel of 100 different barcode-labelled pMHC multimers holding virus-derived peptides, and on a larger public dataset from 10x Genomics with 208,589 T-cells evaluated for recognition using a panel of 50 different pMHCs. In both datasets, ITRAP2 was able to recover TCR-pMHC hits that were missed either when investigating the raw data or analyzing the data using alternative tools. Importantly, we demonstrate that the size of the pMHC multimer library is crucial for accurate pMHC-TCR pairing and that a minimum of 25 pMHC multimer should be included to optimally determine background characteristic, and assigning true positive events.

bioinformatics↗

bioRxiv2024

De novo designed pMHC binders facilitate T cell induced killing of cancer cells

The recognition of intracellular antigens by CD8+ T cells through T-cell receptors (TCRs) is central to adaptive immunity, enabling responses against infections and cancer. The recent approval of TCR-gene-edited T cells for cancer therapy demonstrates the therapeutic advantage of using pMHC recognition to eliminate cancer. However, identification and selection of TCRs from patient material is complex and influenced by the TCR repertoire of the donors used. To overcome these limitations, we here present a rapid and robust de novo binder design platform leveraging state-of-the-art generative models, including RFdiffusion, ProteinMPNN, and AlphaFold2, to engineer minibinders (miBds) targeting the cancer-associated pMHC complex, NY-ESO-1(157-165)/HLA-A*02:01. By incorporating in silico cross-panning and molecular dynamics simulations, we enhanced specificity screening to minimise off-target interactions. We identified a miBd that exhibited high specificity for the NY-ESO-1-derived peptide SLLMWITQC in complex with HLA-A*02:01 and minimal cross-reactivity in mammalian display assays. We further demonstrate the therapeutic potential of this miBd by integrating it into a chimeric antigen receptor, as de novo Binders for Immune-mediated Killing Engagers (BIKEs). BIKE-transduced T cells selectively and effectively killed NY-ESO-1+ melanoma cells compared to non-transduced controls, demonstrating the promise of this approach in precision cancer immunotherapy. Our findings underscore the transformative potential of generative protein design for accelerating the discovery of high-specificity pMHC-targeting therapeutics. Beyond CAR-T applications, our workflow establishes a foundation for developing miBds as versatile tools, heralding a new era of precision immunotherapy.

immunology↗