Biology subjects

Ailles, L.

Publications and source records attributed to Ailles, L..

11 recordsLinked to original sources

bioRxiv2026

Multimodal cell communication networks nominate immunotherapies for RCC subgroups with discrete T cell recruitment or expansion

Renal cell carcinoma (RCC) is amongst the most immune-infiltrated solid tumours, but only a small subset of patients achieves durable response to immune checkpoint blockade therapy. Efforts to characterize the immune microenvironment and molecular regulators responsible for treatment responses have explored numerous facets of disease biology using compartmentalized genomics, transcriptomics, and proteomics datasets, yielding many important yet context and data specific insights. Therefore, to provide a more integrated approach to informing future precision medicine strategies, we combined the complementary strengths of multiple technological platforms to profile multi-regional, spatially annotated surgical biospecimens from 65 RCC patients by single-cell RNA sequencing with paired TCR and BCR repertoire analysis, imaging mass cytometry, suspension mass cytometry, spatial transcriptomics and deconvolved bulk RNA sequencing. With this resource dataset, we explored patient subgroups and precision immunotherapy strategies using an integrated analysis of transcripts and proteins across single cell and spatial modalities. Proximal cell interactions and distinct receptor-ligand pairings identified 7 recurrent cellular communication networks. Robustly mapping reproducible gene signatures across technologies and to a variety of publicly available datasets, we show these highly refined immune subgroups stratify patients with tumour microenvironments associated with prognosis and immunotherapy response. Notably, this reveals that highly infiltrated environments with the potential for immunotherapy response may in fact comprise two distinct communication networks, with differing modes of T cell clonal expansion and immune evasion axes associated with T cell exhaustion or myeloid and NK reprogramming, which could inform targeted combination therapeutic strategies to improve outcomes. Overall, we provide a high-dimensional multi-modal resource dataset that enables cross-platform integration, links stages of T cell clonal expansion with enabling or suppressive RCC immune cell communication networks and nominates rational strategies for combinatorial precision immunotherapy. (Funded by University Health Network, Toronto; REMEDY ClinicalTrials.gov number, NCT04005183.)

cancer biology↗

bioRxiv2026

Humanized patient-derived xenografts preserve tumour-specific immune microenvironments

Defining the genetic and cellular programs that allow solid tumours to evade immune control requires preclinical models that preserve the complexity of the human tumour immune microenvironment. Most available systems capture only part of this biology. Organoid cultures and ex vivo tumour fragments can retain patient-derived tumour architecture and associated immune cells, but immune populations are typically maintained only for short periods. These models also cannot capture antitumour immune responses in the physiological setting of a living organism. Patient-derived xenografts propagated in humanized mice offer a potential path to overcome these limitations by combining patient-derived tumour tissue with a reconstituted human immune system. However, few studies have systematically tested whether these models reproduce the diverse immune cell phenotypes present in the parental tumours from which they are derived. This has limited their use for studying tumour-intrinsic mechanisms that shape immune composition and promote immune evasion. To address this gap, we profiled tumour-infiltrating, splenic, and bone marrow immune cells from ovarian, head and neck, and renal PDX models propagated in CD34+ hematopoietic stem cell (HSC)-derived huNOG-EXL mice expressing human IL-3 and GM-CSF. By comparing tumours grown across distinct HSC donor backgrounds with their matched primary tumour samples, we found that tumour-intrinsic factors are a dominant determinant of immune composition in humanized PDX tumours. Across models, these immune infiltrates generally resembled those of the corresponding parental tumours. These findings support humanized PDX models as a platform for functionally interrogating tumour-intrinsic drivers of immune composition and immune evasion in solid tumours.

cancer biology↗

bioRxiv2025

In vitro and in vivo derived macrophages occupy distinct phenotypic states

Monocyte-derived macrophages (MDMs) are widely used to model human macrophage biology in vitro and standardized polarization conditions were proposed to recapitulate the different macrophage activation states. Although surface markers specific for distinct MDM populations have been identified, a systematic analysis of surface marker expression on these consensus MDM populations has not previously been reported. Here, we use mass cytometry to perform an in-depth characterization of MDM surface profiles and determine how these markers evolve with time. We also compared the phenotypes found in vitro with patient-derived tumor-associated macrophages (TAMs) and found that although MDMs and TAMs shared most markers investigated, the cell-surface signatures markedly differed in terms of expression levels and combinations. Our high-dimensional, single-cell analyses clarifies the surface expression profile of the core in vitro differentiated macrophage populations and highlights some limitations of the in vitro system to represent the complexity of in vivo polarized tumor-associated macrophage phenotypes. These findings provide new opportunities to improve the models used to study macrophage biology and give a pathway to improve our understanding of the in vivo complexity of these systems.

immunology↗

bioRxiv2025

Surface proteomics reveals arginine metabolism as a vulnerability in high grade serous ovarian cancer

The significant lethality of high-grade serous ovarian cancer (HGSC) is driven by the lack of long-term efficacy of current treatments, underscoring the need for developing additional therapeutics. Cell surface proteins represent attractive therapeutic targets yet remain underexplored in high-grade serous ovarian cancer. Here, we employed cell surface N-glycoproteomics to elucidate the cell surface proteomes of HGSC cells alongside normal epithelial and cancer-associated stromal cells, uncovering new opportunities for therapeutic intervention. Integration of cell surface N-glycoproteomics and functional screening revealed multiple minimally characterized, HGSC-enriched surface proteins that are critical for HGSC proliferation, most notably, SLC7A1. Multi-omic and functional characterization indicated that SLC7A1 is necessary for HGSC migration, protein synthesis and mitochondrial functions likely linked to its role as an arginine transporter. Finally, we demonstrate that elevated surface expression of SLC7A1 in HGSC reflects dysregulated arginine metabolism, pointing to a putative therapeutic vulnerability. Our work identifies SLC7A1 and arginine metabolism as a previously unrecognized molecular vulnerability in HGSC and provides a framework to guide future therapeutic development.

cancer biology↗

bioRxiv2024

Pan-cancer N-glycoproteomic atlas of patient derived xenografts uncovers FAT2 as a therapeutic target for head and neck cancers

Cell surface proteins offer significant cancer therapeutic potential attributable to their accessible membrane localization and central role in cellular signaling. Despite this, their promise remains largely untapped due to the technical challenges inherent to profiling cell surface proteins. Here, we employed N-glycoproteomics to analyze 85 patient-derived xenografts (PDX), constructing Glyco PDXplorer - an in vivo pan-cancer atlas of cancer-derived cell surface proteins. We developed a target discovery pipeline to prioritize proteins with favorable expression profiles for immunotherapeutic targeting and validated FAT2 as a head and neck squamous cancer (HNSC) enriched surface protein with limited expression in normal tissue. Functional studies revealed that FAT2 is essential for HNSC growth and adhesion through regulation of surface architecture and integrin-PI3K signaling. Chimeric antigen receptor (CAR) T cells targeting FAT2 demonstrated potent anti-tumor activity in HNSC models. This work lays the foundation for developing FAT2-targeted therapies and represents a pivotal resource to inform therapeutic target discovery for multiple cancers. HIGHLIGHTSO_LIPan-cancer landscape of cancer-derived cell surface proteins detected in vivo C_LIO_LIDevelopment of a multi-omic discovery pipeline to prioritize proteins with optimal expression profiles as immunotherapy targets C_LIO_LIIdentification and validation of FAT2 as a head and neck squamous cancer enriched surface protein with minimal expression in normal tissues C_LIO_LIFAT2 coordinates cell surface organization, adhesion, growth and survival through the integrin-PI3K-AKT pathway C_LIO_LIFAT2 CAR T cells demonstrate anti-tumour activity in pre-clinical models C_LI

cancer biology↗

bioRxiv2023

Heparan-6-O-endosulfatase 2 promotes invasiveness of head and neck squamous carcinoma cell lines in co-cultures with cancer associated fibroblasts

Local invasiveness of head and neck squamous cell carcinoma (HNSCC) is a complex phenomenon supported by interaction of the cancer cells with the TME. We and others have shown that CAFs are a component of the TME that can promote local invasion in HNSCC and other cancers. Here we report that the secretory enzyme Sulf-2 directly affects the CAF-supported invasion of HNSCC cell lines SCC35 and Cal33 into Matrigel. The Sulf-2 knockout (KO) cells differ from their wild type counterparts in their spheroid growths and formation, and the Sulf-2-KO leads to decreased invasion in a spheroid co-culture model with the CAF. Next, we investigated whether a fucosylated chondroitin sulfate isolated from the sea cucumber Holothuria Floridana (HfFucCS), affects activity of the Sulf-2 enzyme. Our results show that HfFucCS not only inhibits efficiently the Sulf-2 enzymatic activity but, like the Sulf-2 knockout, inhibits Matrigel invasion of the SCC35 and Cal33 cells co-cultured with the primary HNSCC CAF. These findings suggest that the heparan 6-O-endosulfatases regulate local invasion and could be therapeutically targeted with the inhibitory activity of a marine glycosaminoglycan. Simple SummaryLocal invasion of cancer cells is an early step in the cascade of metastasis that requires cooperation of multiple factors and cell types in the tumor microenvironment (TME). One important factor is the crosstalk of cancer cells with cancer associated fibroblasts (CAF). Here we explore the impact of a secretory enzyme heparan-6-O-endosulfatase 2 (Sulf-2) on the CAF-assisted invasion of head and neck squamous carcinoma cells into matrigel. We show that Sulf-2 knock out inhibits cancer cell invasion in a spheroid co-culture model and we identified a novel Sulf-2 inhibitor that, in the same model, limits cancer cell invasion.

cancer biology↗

bioRxiv2023

EHMT2/G9a-Inhibition Reprograms Cancer-Associated Fibroblasts (CAFs) to a More Differentiated, Less Proliferative and Invasive State

Cancer-associated fibroblasts (CAFs) have previously been shown to play a pivotal role in multiple cancer dynamics, including mediating tumor cell invasion: their pro-invasive secretory profile and ability to remodel the extracellular matrix (ECM) architecture particularly promote tumor progression through tumor cell invasion into surrounding tissue areas and beyond. Given that reduced CAF abundance in tumors correlates with improved outcomes in various cancers, we set out to identify epigenetic targets involved in CAF activation in the tumor-stromal margin to reduce overall tumor aggressiveness. Using the GLAnCE (Gels for Live Analysis of Compartmentalized Environments) co-culture platform, we performed an image-based, phenotypic screen and identified EHMT2 (also known as G9a), an epigenetic enzyme that targets the methylation of histone 3 lysine 9 (H3K9), as the most potent modulator of CAF abundance and CAF-mediated tumor cell invasion. Transcriptomic and functional analysis of EHMT2-inhibited CAFs revealed the involvement of EHMT2 in driving CAFs towards a pro-invasive phenotype. Further, EHMT2 signaling mediated CAF hyperproliferation, a feature that is typically associated with activated fibroblasts present in tumors, but the molecular basis for which has not thus far been identified. This study suggests a role for EHMT2 as a regulator of CAF hyperproliferation within the tumor mass, which in turn magnifies CAF-induced pro-invasive effects on tumor cells.

cancer biology↗

bioRxiv2023

PRMT1 is a critical dependency in clear cell renal cell carcinoma through its role in post-transcriptional regulation of DNA damage response genes

Biallelic inactivation of the Von Hippel-Lindau (VHL) tumor suppressor gene occurs in almost all cases of clear cell renal cell carcinoma (ccRCC) and leads to disrupted oxygen sensing and the upregulation of hypoxia-related genetic programs. Although the loss of VHL appears to be a necessary oncogenic driver event in the majority of ccRCC instances, it is not always a sufficient one. Large genomics studies have revealed that co-deletions of VHL with genes involved in chromatin regulation are common and important co-drivers of tumorigenesis. Several conserved evolutionary subtypes have been described clinically and the majority implicate disruptions in epigenetic regulators. It is now clear that impairments in cellular epigenetic mechanisms are important co-drivers of disease and signal a potential vulnerability in the epigenetic network of ccRCC cells relative to their normal counterparts. Using a clinically relevant panel of ccRCC models, we herein sought to exploit this potential vulnerability by screening a library of small molecule inhibitors that target a spectrum of epigenetic regulators. We identified MS023, an inhibitor of type I protein arginine methyltransferases (PRMTs) as an agent with antitumor activity. Using orthogonal genetic technologies, we further validated PRMT1 as the specific critical dependency for cancer growth. Mechanistically, our transcriptomic and functional analyses suggest that MS023 treatment results in substantial impairments to cell cycle and DNA damage repair (DDR) pathways, while spawning an accumulation of DNA damage over time. Our PRMT1 specific proteomics analysis revealed an interactome rich in RNA binding proteins including the specific regulator of DDR mRNA metabolism: the BCLAF1/THRAP3 complex. Further investigation suggests that MS023 treatment may result in impairments to DDR specific mRNA activities including nucleocytoplasmic transport and RNA splicing. Together, our data supports PRMT1 as a compelling target in ccRCC and informs a potential mechanism-based strategy for translational development.

cancer biology↗

bioRxiv2022

Extracellular heparan 6-O-endosulfatases SULF1 and SULF2 in HNSC and other malignancies

SULF1 and SULF2 are oncogenic in a number of human malignancies, including head and neck squamous cell carcinoma (HNSC). The function of these two heparan sulfate editing enzymes was previously considered largely redundant but the biology of cancer suggests differences that we explore in our RNAseq and RNAScope studies of HNSC and in a pan cancer analysis using the TCGA and CPTAC (proteomics) data. Our studies document a consistent upregulation of SULF1 and SULF2 in HNSC which is associated with poor survival outcomes. SULF2 expression increases in multiple malignancies but less consistently than SULF1, which uniformly increases in the tumor tissues and negatively impacts survival in several types of cancer. Meanwhile, SULF1 showed low expression in cancer cell lines and a scRNAseq study of HNSC shows that SULF1 is not supplied by epithelial tumor cells, like SULF2, but is secreted by cancer associated fibroblasts. Our RNAScope and PDX analysis of the HNSC tissues fully confirm the stromal source of SULF1 and explain the uniform impact of this enzyme on the biology of multiple malignancies. In summary, the SULF1 enzyme, supplied by a subset of cancer associated fibroblasts, is upregulated and negatively impacts HNSC survival at an early stage of the disease progression while the SULF2 enzyme, supplied by tumor cells, impacts survival at later stages of HNSC. This paradigm is common to multiple malignancies and suggests a potential for diagnostic and therapeutic targeting of the heparan sulfatases in cancer diseases.

cancer biology↗

bioRxiv2019

Gels for Live Analysis of Compartmentalized Environments (GLAnCE): A Tissue Model to Probe Tumour Phenotypes at Tumour-Stroma Interfaces

The interface between a tumour and the adjacent stroma is a site of great importance for tumour development. At this site, carcinoma cells are highly proliferative, undergo invasive phenotypic changes, and directly interact with surrounding stromal cells, such as cancer-associated fibroblasts (CAFs) which further exert pro-tumorigenic effects. Here we describe the development of GLAnCE (Gels for Live Analysis of Compartmentalized Environments), an easy-to-use hydrogel-culture platform for investigating CAF-tumour cell interaction dynamics in vitro at a tumour-stroma interface. GLAnCE enables observation of CAF-mediated enhancement of both tumour cell proliferation and invasion at the tumour-stroma interface in real time, as well as stratification between phenotypes at the interface versus in the bulk tumour tissue compartment. We found that CAF presence resulted in the establishment of an invasion-permissive, interface-specific matrix environment, that leads to carcinoma cell movement outwards from the tumour edge and tumour cell invasion. Furthermore, the spatial stratification capability of GLAnCE was leveraged to discern differences between tumour cell epithelial-to-mesenchymal (EMT) transition genes induced by paracrine signaling from CAFs versus genes induced by interface-specific, CAF-mediated microenvironment. GLAnCE combines high usability and tissue complexity, to provide a powerful in vitro platform to probe mechanisms of tumour cell movement specific to the microenvironment at the tumour-stroma interface.

bioengineering↗

bioRxiv2019

Molecular and functional heterogeneity of cancer associated fibroblasts in high-grade serous ovarian cancer

Recent studies indicate that cancer-associated fibroblasts (CAFs) are phenotypically and functionally heterogeneous. However, little is known about CAF subtypes and the roles they play in cancer progression. Here we identify and characterize two CAF subtypes that coexist within high grade serous ovarian cancers: Fibroblast activation protein (FAP)-high (FH) CAFs resemble the classical myofibroblast-type CAF, whereas FAP-low (FL) CAFs possesses a preadipocyte-like molecular signature. Patients with predominantly FH CAFs have significantly worse outcomes than patients with predominantly FL CAFs. FH CAFs contract collagen gels and aggressively promote proliferation, invasion and therapy resistance of cancer cells, whereas FL CAFs do not. Overexpression of the FL-specific transcription factor TCF21 in FH CAFs decreases their ability to promote gel contraction, invasion, and in vivo tumor growth. Understanding CAF subtypes in more detail could lead to better patient stratification and novel therapeutic strategies.

cancer biology↗