Biology subjects

Valladeau-Guilemond, J.

Publications and source records attributed to Valladeau-Guilemond, J..

9 recordsLinked to original sources

bioRxiv2025

Refined cellular activity expression signatures provide a targeted framework to quantify phenotypic intra-tumor heterogeneity in single-cell data

Single cell RNA-seq (scRNA-seq) now allows deeper insight into cellular biology at both the individual and population level. Measuring cell-to-cell variations in the population enables quantification of phenotypic heterogeneity in populations in which cell states and identities deviate from healthy transcriptomic profiles. Cellular activities quantifiable using gene set enrichment analyses can provide useful grounds to quantify phenotypic heterogeneity, but the specificity and adequacy of existing molecular signatures for scRNA-seq data is still insufficient. Here we induced 6 activities in vitro, for which we refined existing expression signatures to enhance specificity and detection in scRNA-seq data: epithelial-mesenchymal transition (EMT), DNA repair, responses to interferons and {gamma} (IFN and IFN{gamma}, respectively), glycolysis, oxidative phosphorylation (OxPhos). We report new signatures, with much lower redundancy between IFN and IFN{gamma}, and glycolysis and OxPhos signatures, achieving average AUCs of 0.85 across bootstrapped datasets for each activity. We could use these signatures to quantify phenotypic intra-tumor heterogeneity (ITH) in 20 patient samples and 14 cell lines, observing high correlation with diversity indices in classified healthy cells (p<0.001). Focusing on cancer cells only, we furthermore report higher phenotypic ITH in patients than in cell lines (p<0.001), and in basal tumors (p=0.028).

cancer biology↗

bioRxiv2025

Spatial tumour-immune ecosystems shape the efficacy of anti-PD1 immunotherapy in primary cutaneous melanoma

Intra-tumoral heterogeneity in melanoma arises from dynamic cancer cell plasticity and underlies various mechanisms of immune escape. Here, we combined high-plex immunofluorescence imaging with spatially resolved transcriptomics to map the architecture of melanoma cell states and their interactions with the immune microenvironment in primary cutaneous tumours prior to adjuvant anti-PD1 immune checkpoint inhibitor (ICI) treatment. Computational analyses showed that melanoma cells organise into spatially restricted patches, with a preferential organisation of undifferentiated cells associated with poor ICI efficacy. Neighbouring immune cell composition varied according to cancer cell states, with a crucial involvement of specific subsets of tumour-associated macrophages, driven by signalling pathways involving tumour-derived and microenvironmental cues such as IFN-{gamma} and hypoxia. Integrated spatial analyses further revealed tumour-immune ecosystems that stratify patient outcomes, delineating configurations either associated with ICI efficacy or metastatic relapse. These results uncover the spatial landscape of tumour ecosystems and identify signalling pathways as potential targets for improving the efficacy of ICI in melanoma. HighlightsO_LIMelanoma cell states spatial organization is associated with aPD1 therapy efficacy C_LIO_LISpatial organization of TAM subsets is a crucial determinant of ICI outcome C_LIO_LIMelanoma cells in different states co-localise with functionally distinct TAM subsets C_LIO_LIIdentification of cell-cell communication pathways that underlie tumour-TAM crosstalk C_LIO_LIA balance between tumour-immune ecosystems is associated with aPD1 therapy efficacy C_LI

cancer biology↗

bioRxiv2025

IntegrAlign: A comprehensive tool for multiimmunofluorescence panel integration through image alignment

MotivationTyramide-based multiplex-immunofluorescence (mIF) enables the simultaneous analysis of up to seven protein markers on a whole slide, providing a comprehensive approach to study the tumor microenvironment. Integrating multiple mIF panels through image alignment of serial slide significantly expands the number of cell populations analyzed in a single space. IntegrAlign was developed to optimize this integration on serial whole slides, enhancing the value and applicability of mIF for comprehensive spatial analyses and enabling biomarker discovery at scale. ResultsIntegrAlign, leveraging the SimpleITK toolkit, applies a two-step alignment using rigid and B-spline transformations to integrate serial mIF whole slides. Validation on simulated and real datasets demonstrated alignment accuracy below the diameter of a cell nucleus ([~]6 {micro}m), outperforming existing methods. This precision enhances spatial analyses by combining extended phenotypic data, supporting novel insights into tissue architecture and cellular interactions. Availability and ImplementationIntegrAlign is open-source, implemented in Python, and freely available under the MIT license at https://github.com/CAUXlab/IntegrAlign.

bioinformatics↗

bioRxiv2024

HERV-derived epitopes represent new targets for T-cell based immunotherapies in ovarian cancer

BackgroundOvarian cancer represents the most lethal gynecological cancer with poor results of checkpoint inhibitors. Human endogenous retroviruses (HERVs) are aberrantly expressed by tumor cells and may represent a source of shared T cell epitopes for cancer immunotherapy regardless of the tumor mutational burden. MethodsA transcriptomic analysis based on RNA-sequencing (RNA-seq) was developed to quantify the expression of HERV-K sequences containing the selected epitopes. The presence of HERV-K/HML-2 Gag antigen was then assessed by immunohistochemistry (IHC) on tumor microarrays from ovarian cancer samples and normal ovarian tissues. A specific immunopeptidomics approach was developed to detect epitopes on HLA molecules. Epitope-specific CD8+ T cells were quantified by multimer staining and in vitro target cell killing was evaluated using xCELLigence technology. In vivo antitumor efficacy of HERV-specific T cells was assessed in an avian embryo model. ResultsEpitope-containing HERV transcripts were significantly higher in ovarian cancers compared to normal tissues. The presence of HERV-K/HML-2 Gag antigen was confirmed by IHC in 20/40 (50%) ovarian cancers while no Gag expression was found in normal ovarian tissue samples. Immunopeptidomics analysis showed the presence of epitopes on HLA molecules on the surface of ovarian tumor cell lines but not on normal primary cells from critical tissues. HERV-specific T cells were detected among tumor infiltrating lymphocytes (TILs) from ovarian cancers, confirming the immunogenicity of these epitopes in patients. In vitro, HERV-specific T cells specifically killed ovarian cancer cells in an HLA class I-restricted manner while sparing normal HLA-A2-positive primary cells derived from critical tissues. Epitope-specific CD8+ T cells exhibited a strong anti-tumoral activity in vivo, inducing a highly significant decrease in tumor volume in comparison with control groups. ConclusionThese results provide the preclinical rationale for developing T-cell based approaches against HERV-K-derived epitopes in ovarian cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/603392v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1c889b8org.highwire.dtl.DTLVardef@c9b0c5org.highwire.dtl.DTLVardef@1748100org.highwire.dtl.DTLVardef@1c129cc_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LISome HERVs are specifically overexpressed in ovarian cancer compared to normal tissues. C_LIO_LIHERV-K/HML-2 Gag antigen is detected by immunohistochemistry in ovarian cancers but not in normal ovarian tissues. Furthermore, HERV-K-derived epitopes are presented on HLA molecules on the surface of ovarian cancer cells but not on normal cells. C_LIO_LIThese epitopes are immunogenic in patients and induce high-avidity CD8+ T cells that specifically kill ovarian cancer cells in vitro and in vivo while sparing normal cells. C_LI

immunology↗

bioRxiv2024

Targeting a shared neoepitope derived from non-canonical translation of c-MYC oncogene in cancer cells

Cancer cells rely on alternative modes of translation for protein synthesis, promoting internal ribosome entry site (IRES)-dependent translation of mRNA encoding pro-oncogenic factors. Furthermore, ribosomes translate mRNA with lower fidelity in tumor cells. We proposed that these translational modifications in cancer produce shared tumor-specific epitopes derived from IRES-containing oncogenes. To identify such neoepitopes, we developed an in silico-based method that we applied to c-MYC. We showed that the non-canonical translation of c-MYC mRNA in cancer cells, involving a (+1) ribosomal frameshift, generates a shared neoepitope which induces high-avidity T cells able to kill tumor cells in vitro and in vivo while sparing normal cells. Our data provide preclinical rationale for developing immunotherapies targeting this c-MYC-derived neoepitope and validate a new type of shared translation-associated neoantigens.

immunology↗

bioRxiv2024

Spatial architecture of CD8+ T cells and DC subsets is critical for the response to immune checkpoint inhibitors in melanoma

BackgroundDendritic cells (DCs) are promising targets for cancer immunotherapies owing to their central role in the initiation and the control of immune responses. Their functions encompass a wide range of mechanisms mediated by different DC subsets. Several studies have identified human tumor- associated DC (TA-DC) populations through limited marker-based technologies, such as immunostaining or flow cytometry. However, tumor infiltration, spatial organization and specific functions in response to immunotherapy of each DC subset remain to be defined. MethodsHere, we implemented a multiplexed immunofluorescence analysis pipeline coupled with bio-informatic analyses to decipher the tumor DC landscape and its spatial organization within melanoma patients lesions, and its association with patients response to immune checkpoint inhibitors (ICI). For this aim, we analyze a cohort of 41 advanced melanoma patients treated with anti- PD1 alone or associated with anti-CTLA4. Distance and cell network analyses were performed to gain further insight into the spatial organization of tumor-associated DCs. A Digital Spatial Profiling analysis further characterized ecosystem of tumor-infiltrating DCs. ResultsPlasmacytoid DCs (pDCs) were the most abundant DC population, followed by conventional cDC1 and mature DCs, present in equal proportions. In contrast to CD8+ T cell frequency, and despite varying densities, all DC subsets were associated with a favorable response to ICI. Distance and cell network analyses demonstrated that tumor-infiltrating DCs were largely organized in dense areas with high homotypic connections, except for cDC1 that exhibited a more scattered distribution. We identified four patterns of ecosystems with distinct preferential interactions between DC subsets. Significantly, the proximity and interactions between CD8+ T cells and cDC1 were positively associated with patients response to ICI. ConclusionsOur study unravels the complex spatial organization of DC subsets and their interactions in melanoma patient lesions, shedding light on their pivotal role in shaping the response to ICI. Our discoveries regarding the spatial arrangement of cDC1, especially with CD8+ T cells, provide valuable clues for improving immunotherapeutic strategies in melanoma patients. What is already known on this topicDendritic cells (DCs) are promising targets for cancer immunotherapies owing to their central role in the initiation and the control of immune responses. Although conventional type 1 dendritic cells (cDC1) were proposed to contribute to immunotherapy response, their precise functions and interactions with other immune populations in human cancers are largely unknown. What this study addsThis study provides a precise characterization of the spatial distribution and organization of tumor- infiltrating DCs in a large cohort of advanced melanoma patients, and in correlation with response to immunotherapy. While DCs are organized in dense areas with high homotypic connections, cDC1 exhibit a more scattered distribution and form heterotypic aggregates with other DC subsets. More importantly, a close connection between cDC1 and CD8 T cell is uniquely correlated with the patients response to immunotherapy. How this study might affect research, practice or policyThis study improves our understanding of CD8-DC spatial organization within the tumor microenvironment and will have a broad spectrum of implications in the design of anti-tumor immune-activating compounds and the design of biomarkers of response to immunotherapy for melanoma patients.

cancer biology↗

bioRxiv2023

IL-33 drives polyfunctionality and antitumor activity of a unique ST2+ NK cell population

Despite increasing recognition of NK cell diversity, their functional heterogeneity and its relevance to cancer remain incompletely understood. Here, we show that IL-12 promotes the emergence of a distinct ST2/IL33R+ NK cell state poised for robust activation by IL-33. Human ST2 NK cells exhibit a unique transcriptional program, an intermediate differentiation state between CD56bright and CD56dim NK cells, and enhanced polyfunctionality combining proliferation, cytokine production, and cytotoxicity. ST2 NK cells were identified across human and murine tumor datasets. In murine breast cancer models, IL-33 and IL-12 cooperated to elicit potent antitumor responses dependent on IFN-{gamma} and ST2 NK cells. In cancer patients, IL-12 unleashed tumor-infiltrating ST2 NK cells' potential to produce IFN-g in response to IL-33, an IL33hi-NKhi score was associated with prolonged survival, and ST2 NK cells correlated with improved immunotherapy response. Collectively, these findings identify ST2 NK cells as a therapeutically actionable NK cell state promoting antitumor immunity.

cancer biology↗

bioRxiv2023

CD4 T cells and neutrophils contribute to epithelial-mesenchymal transition in breast cancer

Epithelial-mesenchymal transition (EMT) is a central oncogenic mechanism, contributing both to transformation and metastatic dissemination. Inflammation and innate immune cells are known to favor EMT induction, but the role of adaptive immunity still remains unclear. Using an original murine mammary tumor model in immune cell subpopulation depletion experiments, we demonstrated that tumor cells maintain their epithelial phenotype in mice deficient for adaptive immune response, but undergo EMT in the presence of T-cells. This phenotypic conversion involves the major contribution of CD4 T cells, but not CD8 T cells nor B cells, undoubtedly demonstrating the pro-EMT role of CD4 T cells specifically among adaptive immune cells. Moreover, combined intra-tumor immune infiltrate and transcriptomic analyses of murine mammary tumors with various EMT phenotype revealed an inverse correlation between mesenchymal tumor cell and intratumoral neutrophil proportions, due to the reduced ability of mesenchymal cells to recruit neutrophils. Last, selective in vivo depletion of neutrophils and transcriptomic analysis of human breast tumor cohorts demonstrated the pro-EMT role of neutrophils and suggest a cooperation with CD4 T cells in EMT promotion. Collectively, our data highlight a novel mechanism of EMT regulation by both innate and adaptive immune compartments.

cancer biology↗

bioRxiv2020

cDC1 and interferons promote spontaneous CD4+ and CD8+ T cell protective responses to breast cancer

Here we show that efficient breast cancer immunosurveillance relies on cDC1, conventional CD4+ T cells, CD8+ cytotoxic T lymphocytes (CTL) and later NK/NK T cells. For this process, cDC1 were required constitutively, but especially during the T cell priming phase. In the tumor microenvironment, cDC1 interacted physically and jointly with both CD4+ T cells and tumorspecific CD8+ T cells. We found that interferon (IFN) responses were necessary for the rejection of breast cancer, including cDC1-intrinsic signaling by IFN-{gamma} and STAT1. Surprisingly, cell-intrinsic IFN-I signaling in cDC1 was not required. cDC1 and IFNs shaped the tumor immune landscape, notably by promoting CD4+ and CD8+ T cell infiltration, terminal differentiation and effector functions. XCR1, CXCL9, IL-12 and IL-15 were individually dispensable for breast cancer immunosurveillance. Consistent with our experimental results in mice, high expression in the tumor microenvironment of genes specific to cDC1, CTL, helper T cells or interferon responses are associated with a better prognosis in human breast cancer patients. Our results show that immune control of breast cancer depends on cDC1 and IFNs as previously reported for immunogenic melanoma or fibrosarcoma tumor models, but that the underlying mechanism differ. Revisiting cDC1 functions in the context of spontaneous immunity to cancer should help defining new ways to mobilize cDC1 functions to improve already existing immunotherapies for the benefits of patients. SynopsisType 1 conventional dendritic cells cross-present tumor antigens to CD8+ T cells. Understanding the regulation of their antitumor functions is important. Cell-intrinsic STAT1/IFN-{gamma} signaling licenses them for efficient CD4+ and CD8+ T cell activation during breast cancer immunosurveillance.

immunology↗