Biology subjects

Keane, C.

Publications and source records attributed to Keane, C..

6 recordsLinked to original sources

bioRxiv2026

Rethinking Syndecan-1 as a Marker of Trauma-Induced Endothelial Injury

Syndecan-1 (SDC1), a transmembrane proteoglycan and component of the glycocalyx, is widely considered the key circulating biomarker of endothelial dysfunction in trauma and critical illness. However, the tissue distribution of SDC1 and the cellular origin of plasma SDC1 in health and disease are incompletely understood. This series of experiments integrates immunostaining, spatial transcriptomics (GeoMx Digital Spatial Profiler (DSP) and Xenium), and single-cell atlases to map SDC1, as well as the other three members of the syndecan family, syndecan-2 (SDC2), syndecan-3 (SDC3), and syndecan-4 (SDC4), across mouse and human tissues, including the lung, gastrointestinal tract, and brain. Across modalities, SDC1 primarily localizes to epithelial compartments, as demonstrated by colocalization with epithelial markers and enrichment in epithelial cell types in the lung and gut. Spatial profiling further identifies SDC1 and SDC4 enrichment in airway epithelial niches, SDC3 in endothelial-rich regions, and SDC2 distributed more broadly across compartments. Mouse and human single-cell atlases confirm epithelial predominance of SDC1. These findings define the cellular and spatial landscape of syndecan expression in healthy tissues and support SDC1 as an epithelial-enriched proteoglycan. These results also challenge the specificity of circulating SDC1 as a biomarker of endotheliopathy and raise the possibility that epithelial injury contributes substantially to circulating SDC1 after trauma and critical illness.

cell biology↗

bioRxiv2026

Tumour microenvironments impose translational repression that limits natural killer cell persistence

Natural killer (NK) cells infiltrate many solid tumours, yet the mechanisms that determine their functional heterogeneity across tumour types remain poorly understood. Differences in tumour immunogenicity, inhibitory signalling, and nutrient availability have all been implicated, but unifying explanations are lacking. Here, we compared four syngeneic tumour models implanted at identical anatomical sites to isolate tumour-intrinsic effects on NK-cell fate. Tumour-infiltrating NK cells displayed striking tumour-specific differences in cytokine production, cytotoxic protein expression, and persistence. These differences were not explained by cytokine availability or global features of the tumour metabolic environment. Instead, quantitative proteomics and time-resolved in vivo labelling revealed that NK cells enter tumours in a functionally competent state but rapidly diverge thereafter. In suppressive tumour microenvironments, NK cells undergo early mitochondrial loss, translational repression, and impaired proteostatic responses, accompanied by increased apoptotic priming. These defects result in reduced effector function and failure of intratumoural persistence despite preserved recruitment. In contrast, permissive tumours sustain NK-cell translational capacity, cytokine responsiveness, and long-term residency. Together, these findings identify disruption of translational and mitochondrial homeostasis as a central mechanism limiting NK-cell persistence in solid tumours. This work establishes early tumour-induced defects in protein synthesis and cellular fitness as key constraints on durable NK-cell immunity and provides a framework for restoring effective innate anti-tumour responses.

immunology↗

bioRxiv2026

Spatial multi-omics identify an immunosuppressive lipid-laden macrophage niche in primary CNS lymphoma

Primary central nervous system lymphoma (PCNSL) is histologically a subtype of diffuse large B-cell lymphoma (DLBCL), sharing genetic and transcriptomic similarity, but with distinct clinical features, particularly its confinement to the CNS and higher relapse risk. The microenvironmental basis for its divergence from systemic DLBCL remains unclear. Using spatial transcriptomic approaches (Xenium/GeoMx digital spatial profiling) in a comparative study of PCNSL (n=17) and DLBCL (n=76), we found that PCNSL, unlike systemic DLBCL, is dominated by an immunosuppressive macrophage compartment enriched for cholesterol-metabolism programs. In independent cohorts of PCNSL profiled by single-cell RNA sequencing, we validated the presence of a recurrent population of lipid-laden macrophages (LLMs): TREM2/GPNMB-expressing, lipid-remodeled cells transcriptionally distinct from resident microglia and consistent with an infiltrating monocyte origin, not previously characterized in CNS lymphoma. LLMs formed immunosuppressive niches with regulatory T cells, and using Cellscape hyperplex proteomic imaging we demonstrate that LLM-Treg spatial interactions are associated with chemotherapy response. To test whether LLMs are lymphoma-driven and functionally important, we developed an immunocompetent syngeneic PCNSL mouse model, driven by Myd88L252P and Cd79b mutations with Bcl2 overexpression. Monocyte-derived macrophages in lymphoma-bearing brain regions acquired an LLM-like state, not seen in lymphoma-free brain regions or in splenic tumors driven by the same oncogenic lesions. TREM2-SYK signaling sustained this state, and SYK inhibition reversed its tumor-supportive activity ex vivo. These findings identify the LLM program as a targetable immunosuppressive myeloid state in CNS lymphoma.

cancer biology↗

bioRxiv2025

PASTA: Versatile Tyramine-oligonucleotide Amplification for Multi-modal Spatial Biology

Spatial proteomics techniques have revolutionized our understanding of tissue architecture, but are frequently limited by detection sensitivity, bioconjugation limitations, multiplexing capacity, and multi-modal integration. Here we present Protein and nucleic Acid Serial Tyramine Amplification (PASTA), a novel signal amplification approach that significantly enhances detection sensitivity while maintaining compatibility with diverse spatial profiling methodologies. PASTA utilizes horseradish peroxidase (HRP) recruitment pathways to generate tyramine radicals that deposit oligonucleotides, enabling adaptable signal amplification across multiple biomarkers at high-plex via cyclical imaging using complementary fluorophore-labeled oligonucleotides. We demonstrate that PASTA achieves up to 100-fold signal enhancement for markers with minimal background in blank controls. The method is compatible with in situ hybridization for DNA/RNA detection, proximity ligation assays for protein-protein interactions, sequential antibody staining protocols, or any modular combination thereof. PASTA enables antibody rescue of markers with suboptimal signal-to-noise ratios and is versatile in its applications to unconjugated antibodies, and multi-round probe-based RNA detection systems beyond current capabilities. This technique addresses key limitations in spatial-omics by enhancing sensitivity for challenging targets while maintaining compatibility with established multiplexing strategies, providing a versatile, cost-efficient, and valuable tool for comprehensive spatial tissue analysis in both research and clinical applications.

molecular biology↗

bioRxiv2021

EEG biomarkers of free recall

Brain activity in the moments leading up to spontaneous verbal recall provide a window into the cognitive processes underlying memory retrieval. But these same recordings also subsume neural signals unrelated to mnemonic retrieval, such as response-related motor activity. Here we examined spectral EEG biomarkers of memory retrieval under an extreme manipulation of mnemonic demands: subjects either recalled items after a few seconds or after several days. This manipulation helped to isolate EEG components specifically related to long-term memory retrieval. In the moments immediately preceding recall we observed increased theta (4-8 Hz) power (+T), decreased alpha (8-20 Hz) power (-A), and increased gamma (40-128 Hz) power (+G), with this spectral pattern (+T-A+G) distinguishing the long-delay and immediate recall conditions. As subjects vocalized the same set of studied words in both conditions, we interpret the spectral +T-A+G as a biomarker of episodic memory retrieval.

neuroscience↗

bioRxiv2019

Enhanced cytokine responsiveness in natural killer cells from a pilot cohort of uninfected seronegative women exposed to hepatitis C virus contaminated anti-D immunoglobulin

BackgroundSome people exposed to hepatitis C virus (HCV) appear to be capable of preventing infection in the absence of detectable antibody responses. These exposed seronegative (ESN) people appear naturally resistant to HCV infection. Here, we aimed to examine innate immune mechanisms in ESN individuals amongst rhesus negative Irish women exposed to HCV via contaminated anti-D immunoglobulin between 1977-79 and 1991-94.\n\nMethodsA total of 16 ESN individuals were recruited, along with 9 age- and gender-matched healthy controls. All tested negative for HCV-specific antibodies using conventional diagnostic assays. Peripheral blood cells were analysed for presence of adaptive immune response markers, innate immune responsiveness and natural killer cell phenotype and function.\n\nResultsThe innate immune cell profile of ESN women in the present study was characterised by a significant decrease in monocyte frequency and elevated levels of interleukin-8 and -18 compared to age- and gender-matched healthy controls. NK cells from ESN women had normal expression of NK cell receptors but increased IFN{gamma}-production upon cytokine and target cell stimulation as well as enhanced natural killer (NK) cell STAT3 phosphorylation in response to Type I IFN.\n\nConclusionsWe describe for the first time ESN individuals amongst Irish women with past exposure to HCV via contaminated anti-D immunoglobulin. NK cells from these ESN individuals are more responsive to cytokine signalling compared with age- and gender-matched controls. Human ESN cohorts can provide unique insights into the biological mechanisms associated with antigen-independent natural resistance to viral infection.

immunology↗