Biology subjects

Cubillos-Ruiz, J. R.

Publications and source records attributed to Cubillos-Ruiz, J. R..

3 recordsLinked to original sources

bioRxiv2024

High-grade serous ovarian cancer development and anti-PD-1 resistance is driven by IRE1α activity in neutrophils

High-grade serous ovarian cancer (HGSOC) is an aggressive malignancy that remains refractory to current immunotherapies. While advanced stage disease has been extensively studied, the cellular and molecular mechanisms that promote early immune escape in HGSOC remain largely unexplored. Here we report that primary HGSO tumors program neutrophils to inhibit T cell anti-tumor function by activating the endoplasmic reticulum (ER) stress sensor IRE1. We found that intratumoral neutrophils exhibited overactivation of ER stress response markers compared with their counterparts at non-tumor sites. Selective deletion of IRE1 in neutrophils delayed primary ovarian tumor growth and extended the survival of mice with HGSOC by enabling early T cell-mediated tumor control. Notably, loss of IRE1 in neutrophils sensitized tumor-bearing mice to PD-1 blockade, inducing HGSOC regression and long-term survival in [~]50% of treated hosts. Hence, neutrophil-intrinsic IRE1 facilitates early adaptive immune escape in HGSOC and targeting this ER stress sensor might be used to unleash endogenous and immunotherapy-elicited immunity that controls metastatic disease.

immunology↗

bioRxiv2022

Inflammatory ER Stress Responses Dictate the Immunopathogenic Progression of Systemic Candidiasis

Recognition of pathogen-associated molecular patterns can trigger the IRE1 arm of the endoplasmic reticulum (ER) stress response in immune cells. IRE1 activation has been shown to maintain ER homeostasis while simultaneously coordinating diverse immunomodulatory programs in the setting of bacterial and viral infections. However, the role of IRE1 signaling in innate immune responses to fungal pathogens is unknown. Here we report that systemic infection with the fungus Candida albicans causes severe renal immunopathology by triggering inflammatory IRE1 hyperactivation in host myeloid cells. Mechanistically, sensing of fungal {beta}-glucans by the C-type lectin receptor Dectin-1 induced Src-Syk-NOX-dependent accumulation of intracellular reactive oxygen species and the ensuing generation of lipid peroxidation byproducts that sustained IRE1 activation. Selective deletion of IRE1 in leukocytes, or treatment with an IRE1 pharmacological inhibitor, reduced detrimental inflammatory responses in the kidney and extended survival in mice systemically infected with C. albicans. Hence, controlling IRE1 overactivation may be useful to impede the fatal immunopathogenic progression of disseminated candidiasis. One sentence summaryInnate IRE1 signaling in disseminated candidiasis

immunology↗

bioRxiv2018

High throughput droplet single-cell Genotyping of Transcriptomes (GoT) reveals the cell identity dependency of the impact of somatic mutations

Defining the transcriptomic identity of clonally related malignant cells is challenging in the absence of cell surface markers that distinguish cancer clones from one another or from admixed non-neoplastic cells. While single-cell methods have been devised to capture both the transcriptome and genotype, these methods are not compatible with droplet-based single-cell transcriptomics, limiting their throughput. To overcome this limitation, we present single-cell Genotyping of Transcriptomes (GoT), which integrates cDNA genotyping with high-throughput droplet-based single-cell RNA-seq. We further demonstrate that multiplexed GoT can interrogate multiple genotypes for distinguishing subclonal transcriptomic identity. We apply GoT to 26,039 CD34+ cells across six patients with myeloid neoplasms, in which the complex process of hematopoiesis is corrupted by CALR-mutated stem and progenitor cells. We define high-resolution maps of malignant versus normal hematopoietic progenitors, and show that while mutant cells are comingled with wildtype cells throughout the hematopoietic progenitor landscape, their frequency increases with differentiation. We identify the unfolded protein response as a predominant outcome of CALR mutations, with significant cell identity dependency. Furthermore, we identify that CALR mutations lead to NF-{kappa}B pathway upregulation specifically in uncommitted early stem cells. Collectively, GoT provides high-throughput linkage of single-cell genotypes with transcriptomes and reveals that the transcriptional output of somatic mutations is heavily dependent on the native cell identity.

cancer biology↗