Biology subjects

Merces, G.

Publications and source records attributed to Merces, G..

5 recordsLinked to original sources

bioRxiv2025

Clinical and molecular characterisation of primary refractoriness to atezolizumab plus bevacizumab in patients with unresectable hepatocellular carcinoma.

BackgroundDespite improved outcomes with atezolizumab plus bevacizumab (A+B) in hepatocellular carcinoma (HCC), primary refractoriness (PRef), characterised by early progression or short-lived disease stabilisation following treatment, remains a significant and poorly understood clinical challenge. MethodsWe analysed 1296 patients with HCC and Child-Pugh A liver cirrhosis treated with frontline A+B (AB-real) and validated findings in 645 trial participants recruited to IMbrave150 and GO30140. PRef was defined by Society for the Immunotherapy of Cancer (SITC) criteria as progressive disease in the first 6 months after treatment initiation. Patients who achieved complete response, partial response or stable disease for [≥] 6 months were classified as responders. We performed a multi-parametric analysis of pre-treatment tumour tissue including machine learning-based quantification of tumour-infiltrating lymphocytes, imaging mass cytometry and RNA sequencing (RNAseq) to evaluate differences in the tumour microenvironment (TME) of PRef versus responding patients. We employed conditional inference tree analyses to provide a hierarchical organisation of determinants of PRef. ResultsAmong 677 AB-real and 378 trial patients evaluable by SITC criteria, PRef identified inferior median OS in comparison with responding patients (AB-real: 7.3 vs. 31.5 months, HR 3.7, 95%CI 2.8-8.5, p<0.001; Trials: 10.8 vs. NR, HR 4.6, 95%CI 3.3-6.3, p<0.001). PRef patients exhibited higher baseline systemic inflammation (neutrophil-to-lymphocyte ratio, NLR [≥]3), a distinctively immunosuppressive TME enriched in CD163+ tumour-associated macrophages and a higher Treg/Teff ratio. RNAseq of tumour tissue demonstrated lower intrinsic immunogenicity in PRef samples, characterised by repressed IFN-{gamma} and Teff signatures, with elevated myeloid infiltration. Conditional inference tree analysis identified IFN-{gamma} signature downregulation combined with NLR [≥]3 as the strongest contributor of PRef. ConclusionsPRef to A+B identifies a distinct biological entity characterised by unopposed systemic inflammation, myeloid cell infiltration and T-cell depletion. Targeting myeloid-mediated immunosuppression, particularly in patients with low IFN-{gamma} signature expression and elevated NLR might enhance responsiveness to A+B. HighlightsO_LIPrimary refractoriness to atezolizumab plus bevacizumab in hepatocellular carcinoma, as defined by SITC criteria, is associated with poor clinical outcomes. C_LIO_LITumour microenvironment profiling reveals an immunosuppressive phenotype characterized by high myeloid infiltration, reduced interferon-{gamma} signalling, and T-cell depletion. C_LIO_LIThe combination of systemic inflammation and low IFN-{gamma} signature expression strongly predicts primary refractoriness and may inform therapeutic decision-making. C_LI

cancer biology↗

bioRxiv2025

A Slc5a6 Deficient Mouse Model Reveals a Metabolically Driven Dilated Cardiomyopathy with Therapeutic Potential for Vitamin-Based Intervention

Background and AimsThe sodium-dependent multivitamin transporter, encoded by SLC5A6, mediates cellular uptake of the vitamins, biotin and pantothenic acid, both of which are essential cofactors for energy metabolism. Here, we report two families with SLC5A6 mutations presenting with early-onset dilated cardiomyopathy (DCM). To investigate the link between vitamin deficiency and DCM, we generated a novel cardiac-specific Slc5a6 knockout (Slc5a6cKO) mouse model and tested the therapeutic potential of vitamin supplementation. MethodsCardiac function in Slc5a6cKO mice was assessed by cardiac magnetic resonance imaging and ECG measurements. Histological, biochemical, and proteomic analyses were conducted to identify structural and metabolic changes. The impact of dietary biotin and pantothenic acid supplementation on disease progression was evaluated. ResultsSlc5a6cKO mice developed progressive cardiac dysfunction, manifesting as DCM with cardiac dilation, cardiomyocyte hypertrophy, fibrosis, impaired Coenzyme A synthesis, and metabolic imbalance, culminating in premature death by 26 weeks. Proteomic analysis revealed early mitochondrial metabolic disruption and extracellular matrix protein upregulation at 8 weeks, preceding overt cardiac dysfunction. Strikingly, vitamin supplementation from preconception onwards, prevented the cardiac phenotype, preserving cardiac structure, function, morphology and survival. This parallels the clinical outcome in one patient who received early vitamin treatment, compared to another who required a heart transplant following delayed vitamin treatment. ConclusionsThis study establishes a direct link between SLC5A6-mediated vitamin transport, mitochondrial function, and cardiac health. It highlights how vitamin deficiency contributes to DCM pathogenesis and supports early vitamin supplementation as a potential therapeutic strategy for metabolic cardiomyopathies. Translational perspectiveThis study highlights the therapeutic potential of vitamin supplementation in treating dilated cardiomyopathy (DCM) caused by mitochondrial abnormalities. Using a cardiac-specific Slc5a6 knockout mouse model, we demonstrated that deficiencies in key vitamins, biotin and pantothenic acid, impair mitochondrial energy metabolism, leading to DCM progression. Remarkably, vitamin supplementation preserved cardiac function, morphology, and survival, suggesting that restoring vitamin levels could be a promising therapeutic strategy for DCM and other cardiomyopathies linked to metabolic deficiencies. These findings could inform newborn screening programmes and clinical approaches for treating mitochondrial-related cardiac diseases by targeting specific vitamin deficiencies. Key QuestionWhat is the underlying molecular cause of early-onset dilated cardiomyopathy in patients with SLC5A6 mutations, and can insights from a cardiac-specific knockout mouse model reveal potential metabolic mechanisms and therapeutic strategies involving vitamin supplementation? Key FindingCardiac-specific deletion of Slc5a6 in mice caused early mitochondrial dysfunction, metabolic derangement, and progressive dilated cardiomyopathy. Strikingly, early and continuous supplementation with biotin and pantothenic acid completely preserved cardiac structure, function, and survival, paralleling successful outcomes in patients treated early. Take Home MessageThis study establishes a mechanistic link between SLC5A6 mutations, vitamin deficiency and mitochondrial abnormalities as a cause of dilated cardiomyopathy. Early vitamin supplementation prevents disease onset, highlighting the potential of targeted vitamin therapy in metabolic cardiomyopathies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/658273v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@cf8e8corg.highwire.dtl.DTLVardef@97c74borg.highwire.dtl.DTLVardef@9d0e41org.highwire.dtl.DTLVardef@112eb77_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

An evolutionarily conserved laterally acquired toolkit enables microbiota targeting by Trichomonas

Trichomonas species are a diverse group of obligate extracellular symbionts associated with or attributed to various inflammatory diseases. They colonise mucosal surfaces across a wide range of hosts, all of which harbour a resident microbiota. Their evolutionary history likely involved multiple host transfers, including zoonotic events from columbiform birds to mammals. Using comparative transcriptomics, this study examines Trichomonas gallinae co-cultured with Escherichia coli, identifying a molecular toolkit that Trichomonas species may use to interact with bacterial members of the microbiota. Integrating transcriptomic data with comparative genomics and phylogenetics revealed a conserved repertoire of protein-coding genes likely acquired through multiple lateral gene transfers (LGT) in a columbiform-infecting ancestor. These LGT-derived genes encode muramidases, glucosaminidases, and antimicrobial peptides--enzymes and effectors capable of targeting bacterial cell walls, potentially affecting the bacterial microbiota composition across both avian and mammalian hosts. This molecular toolkit suggests that Trichomonas species can actively compete with and exploit their surrounding microbiota for nutrients, potentially contributing to the dysbiosis associated with Trichomonas infections. Their ability to target bacterial populations at mucosal surfaces provides insight into how Trichomonas species may have adapted to diverse hosts and how they could influence inflammatory mucosal diseases in birds and mammals.

molecular biology↗

bioRxiv2023

OPTIMAL: An OPTimsed Imaging Mass cytometry AnaLysis framework for Segmentation and Data Exploration

Analysis of Imaging Mass Cytometry (IMC) data and other low-resolution multiplexed tissue imaging technologies is often confounded by poor single cell segmentation and sub-optimal approaches for data visualisation and exploration. This can lead to inaccurate identification of cell phenotypes, states or spatial relationships compared to reference data from single cell suspension technologies. To this end we have developed the "OPTIMAL" framework to benchmark any approaches for cell segmentation, parameter transformation, batch effect correction, data visualisation/clustering and spatial neighbourhood analysis. Using a panel of 27 metal-tagged antibodies recognising well characterised phenotypic and functional markers to stain the same FFPE human tonsil sample Tissue Microarray (TMA) over 12 temporally distinct batches we tested several cell segmentation models, a range of different arcsinh cofactor parameter transformation values, five different dimensionality reduction algorithms and two clustering methods. Finally we assessed the optimal approach for performing neighbourhood analysis. We found that single cell segmentation was improved by the use of an Ilastik-derived probability map but that issues with poor segmentation were only really evident after clustering and cell type/state identification and not always evident when using "classical" bi-variate data display techniques. The optimal arcsinh cofactor for parameter transformation was 1 as it maximised the statistical separation between negative and positive signal distributions and a simple Z-score normalisation step after arcsinh transformation eliminated batch effects. Of the five different dimensionality reduction approaches tested, PacMap gave the best data structure with FLOWSOM clustering out-performing Phenograph in terms of cell type identification. We also found that neighbourhood analysis was influenced by the method used for finding neighbouring cells with a "disc" pixel expansion outperforming a "bounding box" approach combined with the need for filtering objects based on size and image-edge location. Importantly OPTIMAL can be used to assess and integrate with any existing approach to IMC data analysis and, as it creates .FCS files from the segmentation output, allows for single cell exploration to be conducted using a wide variety of accessible software and algorithms familiar to conventional flow cytometrists.

bioinformatics↗

bioRxiv2022

Molecular determinants of the Bacillus subtilis chromosome origin basal unwinding system

Genome duplication is essential for cell proliferation and DNA synthesis is generally initiated by dedicated replication proteins at specific loci termed origins. During DNA replication initiation in bacteria, the ubiquitous DnaA protein engages both double-strand DNA (dsDNA) and single-stranded DNA (ssDNA) at the chromosome origin (oriC) to promote DNA duplex unwinding. While the molecular basis for DnaA binding to a specific dsDNA element ("DnaA-box") has been established, the mechanism for DnaA binding to a specific ssDNA motif ("DnaA-trio") is unclear. Here we define specific steps of DnaA-trio engagement by Bacillus subtilis DnaA. Single-molecule total internal reflection fluorescence microscopy indicates that DnaA proteins are loaded onto DnaA-trios using DnaA-boxes located on a shared DNA polymer. Chemical modification of either the phosphodiester backbone or the nucleobases revealed that three DnaA-trio repeats proximal to DnaA-boxes are necessary and sufficient to promote DnaA-dependent strand separation, and that the amino group from the central nucleobase of the DnaA-trio is critical for this reaction. Finally, based on electrophoretic mobility shift assays, we propose that during replication initiation DnaA progresses from DnaA-boxes to nucleobase recognition at DnaA-trios before engaging the phosphodiester backbone and destabilizing the DNA duplex. These results provide new molecular insight into DnaA-dependent Bacterial Unwinding System (BUS) activity at a bacterial chromosome origin.

microbiology↗