Biology subjects

Huber, A.

Publications and source records attributed to Huber, A..

15 recordsLinked to original sources

bioRxiv2026

An MLL-Independent Function of Menin Promotes Resistance to MAPK-Targeted Therapy

BRAF mutant colorectal cancer (CRC) remains difficult to treat despite the clinical use of combined BRAF and EGFR inhibition, highlighting a need to define tumour-intrinsic mechanisms that limit therapeutic response. Here, using genome-wide CRISPR-Cas9 screening in BRAF-mutant CRC cells, we identify MEN1, encoding the chromatin-associated protein Menin, as a selective determinant of sensitivity to combined encorafenib and cetuximab (EC). MEN1 loss markedly enhanced EC-mediated inhibition of cell proliferation and ERK activity while having comparatively little effect in untreated cells, and re-expression of Menin restored resistance. Transcriptomic and chromatin profiling revealed that Menin supports the transcriptional response associated with MAPK signalling. Menin occupied promoters of MAPK/BRAF-responsive genes and EC treatment caused widespread displacement of Menin from chromatin. Phosphoproteomic analysis demonstrated extensive remodelling of MAPK signalling following EC treatment, whereas proximity proteomics showed that the Menin-associated protein complexes remained largely intact despite loss of Menin chromatin occupancy. Importantly, MLL1 loss did not reproduce the sensitising effect of MEN1 deletion, and pharmacological Menin inhibition with revumenib failed to phenocopy either genetic MEN1 loss or acute Menin degradation, indicating that this phenotype is independent of Menin-MLL activity. Together, these findings identify a previously unrecognised, MLL-independent role for Menin in buffering the response of BRAF-mutant CRC cells to MAPK pathway inhibition and suggest targeting Menin, rather than disruption of its interaction with MLL, may provide a strategy for enhancing the response to BRAF-targeted therapy for CRC.

cancer biology↗

bioRxiv2026

A p32 family RNA editing factor acts in mitochondrial ribosome biogenesis

Biogenesis of mitochondrial ribosomes (mitoribosomes) in the unicellular parasite Trypanosoma brucei requires an exceptionally large toolkit of assembly factors, identified in stable precursors of large and small mitoribosomal subunits (mtLSU and mtSSU) by cryoEM. Here, using genetic modifications and proteomic characterization of the immunoprecipitated assemblosome, the earliest characterized mtSSU precursor, we determined that a cap of its distinctive protrusion of hitherto unknown composition consists of a p22 homotrimer. This protein was previously implicated in the uridine-insertion editing of the cytochrome c oxidase subunit II transcript. Our functional analysis confirmed this role but revealed that its ablation also causes a loss of mtSSU and a systemic reduction in mitochondrial translation, phenocopying the depletion of established mitoribosomal assembly factors. Consequently, the oxidative phosphorylation system and mitochondrial function are compromised. The p22 protein belongs to the p32 family. We showed that five of its six trypanosomal members are involved in mtSSU biogenesis. Notably, p32 proteins are associated with mitoribosomes in two other distant eukaryotic lineages. A eukaryote-wide mapping of p32 proteins documented that their presence correlates with the retention of mitochondrial genomes. Together, our findings redefine trypanosomal p22 as a dual-function coordinator of mitochondrial gene expression and reveal that the ancestral role of the p32 family is associated with mitochondrial translation.

molecular biology↗

bioRxiv2026

Deep Visual Proteomics links vascular smooth muscle cell phenotypes to atherosclerotic plaque stability

Vascular smooth muscle cells (VSMCs) drive atherosclerosis through phenotypic switching, yet their spatial organization and protein signatures within plaques remain poorly characterized. Here, we applied Deep Visual Proteomics (DVP) to dissect more than 500 VSMC neighborhoods across 24 human carotid plaques and profile VSMC plasticity in disease. To functionally interpret these tissue proteomes, we built a reference atlas of primary VSMCs driven toward five phenotypes by TGF-{beta}, PDGF-BB, osteogenic stimuli, IL-1{beta}, or cholesterol, quantifying over 10,000 proteins. We integrated tissue and reference proteomes with a deep-learning framework that assigns functional phenotypes to each neighborhood. This revealed spatially distinct phenotype distributions and a shift toward dedifferentiated states in unstable plaques. Knockdown of four candidates (TNC, TNFAIP2, AEBP1, PLK1) validated operational roles during phenotypic switching. Our approach functionally annotates spatial proteomes and links VSMC plasticity to plaque instability in carotid artery disease.

systems biology↗

bioRxiv2026

Fatty acids in the tumor microenvironment reprogram neutrophils to induce immunosuppression via adenosine

As solid tumors progress, the tumor microenvironment (TME) becomes increasingly immunosuppressive, impairing cytotoxic T-cell activity and limiting the efficacy of the immune checkpoint blockade. However, the mechanistic drivers of this immunosuppression remain poorly understood. Here, we identify a tumor-derived lipid-neutrophil-adenosine axis as a critical regulator of immune suppression in advanced colorectal cancer (CRC). We show that fatty acids enriched in tumor interstitial fluid reprogram neutrophils to generate adenosine via PPAR activation, leading to T-cell suppression. Using AB928, a dual A2aR/A2bR adenosine receptor antagonist currently in clinical trials, we restored T-cell proliferation, effector function, and tumor-killing capacity in vitro and in vivo. Importantly, AB928 synergized with anti-PD-1 therapy to enhance survival in an autochthonous model of metastatic CRC. Our findings define a metabolic immune evasion mechanism in the TME and provide a rationale for targeting neutrophil-derived adenosine signaling to improve immunotherapy responses in CRC and other solid tumors.

cancer biology↗

bioRxiv2025

VMAT2 dysfunction impairs vesicular dopamine uptake, driving its oxidation and α-synuclein pathology in DJ-1-linked Parkinson's disease neurons

Parkinsons disease (PD) is characterized by -synuclein accumulation and dopaminergic neuron degeneration, with dopamine (DA) oxidation emerging as a key pathological driver. However, the mechanisms underlying this neurotoxic process remain unclear. Using PD patient-derived and CRISPR-engineered iPSC midbrain dopaminergic neurons lacking DJ-1, we identified defective sequestration of cytosolic DA into synaptic vesicles, which culminated in DA oxidation and -synuclein accumulation. In-depth proteomics, state-of-the-art imaging, and ultrasensitive DA probes uncovered that decreased VMAT2 protein and function impaired vesicular DA uptake, resulting in reduced vesicle availability and abnormal vesicle morphology. Furthermore, VMAT2 activity and vesicle endocytosis are processes dependent on ATP, which is notably reduced in DJ-1-deficient dopaminergic neurons. ATP supplementation restored vesicular function and alleviated DA-related pathologies in mutant dopaminergic neurons. This study reveals an ATP-sensitive mechanism that regulates DA homeostasis through VMAT2 and vesicle dynamics in midbrain dopaminergic neurons, highlighting enhanced DA sequestration as a promising therapeutic strategy for PD. TeaserLoss of DJ-1 interferes with VMAT2 function and vesicle dynamics, leading to DA oxidation and -synuclein pathology in PD neurons.

neuroscience↗

bioRxiv2025

A TAK1Cytokine Toxicity Checkpoint Controls Anti-Cancer Immunity

The success of cancer immunotherapies is currently limited to a subset of patients, which underscores the urgent need to identify the processes by which tumours evade immunity. Through screening a kinome-wide CRISPR/Cas9 sgRNA library we identified MAP3K7 (TAK1) as a suppressor of CD8+ T cell mediated killing. We demonstrate that TAK1 acts as a cancer-intrinsic checkpoint by integrating signals from T cell-secreted TNF and IFNy effector cytokines to elicit a cytoprotective response. This cytoprotective response profoundly limits the anti-cancer activity these key effector molecules and completely abrogates bystander killing by perforin deficient T cells. Inhibition of the TAK1 checkpoint effectively redirects the combined TNF/IFNy pathway activation to promote inflammatory cell death via RIPK1 and Caspase-8 and simultaneously amplifies the output of the IFNy pathway, thereby priming cells for cytokine-induced cell death. Mechanistically, TAK1 deficiency led to proteasomal degradation of cFLIP, enhancing the formation of Complex II and subversion of other cytoprotective responses. Targeting the TAK1 checkpoint led to profound attenuation of tumour growth in immune competent mice, with minimal impact in immune deficient counterparts. Adoptive cell therapy led to preferential elimination of TAK1 deficient clones. Collectively, our study uncovers a cancer-intrinsic checkpoint controlled by TAK1 activity that switches TNF and IFNy responses from cytoprotective to apoptosis. Cancer cells exploit this to limit cell death in the presence of the cytotoxic lymphoctye cytokines TNF and IFN{gamma} and therapeutic intervention can fully unleash the impact of these effector molecules both on the direct target and bystander cells. These findings highlight the clinical development of TAK1 biologics as a potential strategy to improve cancer immunotherapies through harnessing and enhancing the cytotoxic potential of CTL-derived cytokines. In BriefDjajawi et al. identify TAK1 as a cancer-intrinsic cytokine toxicity checkpoint that limits the efficacy of anti-cancer immune responses. Cancer cells exploit TAK1 activity to confers resistance to CD8+ T cell-derived TNF and IFN{gamma}-induced apoptosis, limiting both direct and bystander killing. Mechanistically, TAK1 loss acts through 1. cFLIP and RIPK1 to promote cell death, 2. The inactivation of pro-survival signals and 3. Via amplification of the IFNy response. Targeting of this TAK1 checkpoint enhanced anti-tumour immunity in vivo and improved adoptive cellular therapy. These findings identify a strategy employed by transformed cells to avoid destruction by inflammatory cytokines and provide new therapeutic vulnerabilities for enhancing immunotherapies. HighlightsO_LICRISPR screens identify TAK1 as a tumour-intrinsic survival checkpoint limiting destruction by CD8+ T cells. C_LIO_LITAK1 protects tumour cells from combined TNF and IFN{gamma}-induced apoptosis. C_LIO_LITAK1 loss destabilizes cFLIP, priming cells for STAT1 and RIPK1-dependent cell death. C_LIO_LITAK1 loss promotes tumour control in immune competent animals and enhances the efficacy of adoptive cell therapy. C_LI

cancer biology↗

bioRxiv2025

Unraveling dendritic-cell diversity in blood of pigs: welcome tDC and DC3

Dendritic cells (DC) are professional antigen presenting cells playing a major role in orchestrating adaptative immune responses. To adapt to various immune challenges, such as different classes of pathogens, specialized subsets of DC have evolved across species. To date, DC are classified as conventional DC (cDC1, cDC2) and plasmacytoid DC (pDC), with the more recent addition of DC3 and transitional DC (tDC) that were discovered in human and mouse thanks to high-dimensional phenotyping and single-cell sequencing technologies. Here, by combining flow cytometry and RNA-seq on the bulk- and single-cell level, we identified the porcine equivalent of tDC in blood as CD14-CADM1-CD172a+CD4-cells expressing both Flt3 and CD123 (IL-3RA). This new subset forms a well-defined cluster when mapped onto scRNA-seq data of enriched DC and shares transcriptomic features and abundance with porcine blood cDC2 and pDC. Moreover, we describe putative porcine DC3 as transcriptionally overlapping cells in-between cDC2 and monocytes. With the core functions of tDC and DC3 remaining to be elucidated, our datasets provide a valuable resource for cross-species research on DC heterogeneity in various lymphoid and non-lymphoid tissues.

immunology↗

bioRxiv2024

In vitro genotoxic and mutagenic potentials of combustion particles from marine fuels with different sulfur contents

Ship emissions cause serious environmental impacts and adverse effects toward human health. Therefore, the International Maritime Organization (IMO) restricted the fuel sulfur content (FSC) of marine fuels: FSC must be <0.5% m/m or <0.1% m/m in sulfur emission control areas, covering a range of fuels from distillate diesel-like fuels to low-sulfur heavy fuel oils (HFOs). As a result, ship emissions, e.g., sulfur oxides and particulate matter (PM) have been reduced. However, how FSC correlates with the toxicological potential of ship emissions is still uncertain. The objective of this study was to understand how the physical and chemical properties of particulate emissions from a marine engine operating on five marine fuels with different FSCs influence their toxicological outcome. For this scope, cytotoxic, genotoxic, mutagenic, and pro-inflammatory potentials of collected particles were evaluated in lung cell model systems. The involvement of intracellular reactive oxygen species and xenobiotic metabolism was also explored. While PM from different fuels combustion resulted in up to approximately 20% of reduction of cytotoxicity at the highest concentration, other toxicological outcomes, including clonogenic and genotoxic potentials, showed a stronger trend with the polycyclic aromatic hydrocarbon contents in PM compared with FSC. This trend was supported by evidence of a significant increase in gene mutation frequency and alterations in cellular mechanisms induced by an aromatic-rich HFO with an intermediate FSC. In conclusion, apart from reducing FSC in marine fuels, additional particle abatement systems should be considered to reduce the adverse effects of particulate emissions from shipping operations on human health.

pharmacology and toxicology↗

bioRxiv2024

Mutant TP53 switches therapeutic vulnerability during gastric cancer progression within Interleukin-6 family cytokines

Although aberrant activation of the KRAS and PI3K pathway alongside TP53 mutations account for frequent aberrations in human gastric cancers, neither the sequence nor the individual contributions of these mutations have been clarified. Here, we establish an allelic series of mice to afford conditional expression in glandular epithelium of KrasG12D; Pik3caH1047R or Trp53R172H and/or ablation of Pten or Trp53. We find that KrasG12D;Pik3caH1047Ris sufficient to induce adenomas, and that lesions progress to carcinoma when also harboring Pten-deletions. Additional challenge with either Trp53 loss- or gain-of-function alleles further accelerated tumor progression and triggered metastatic disease. While tumor-intrinsic STAT3 signaling in response to gp130 family cytokines remained as a gatekeeper for all stages of tumor development, metastatic progression required a mutant Trp53-induced interleukin (IL)-11 to IL-6 dependency switch. Consistent with poorer survival of patients with high IL6 expression, we identify IL6/STAT3 signaling as a therapeutic vulnerability for TP53-mutant gastric cancer.

cancer biology↗

bioRxiv2023

Ornithological and molecular evidence of a reproducing Hyalomma rufipes population under continental climate in Europe

BackgroundReports on adult Hyalomma ticks in certain regions of the Carpathian Basin date back to the 19th century. These ticks were thought to emerge from nymphs dropping from birds, then molting to adults. Although the role of migratory birds in carrying ticks of this genus is known from all parts of Europe, in most countries no contemporaneous multiregional surveillance of bird-associated ticks was reported which could allow the recognition of hotspots in this context. MethodsIxodid ticks were collected from birds at seven ringing stations in Hungary, including both the spring and autumn migration period in 2022. Ixodes and Haemaphysalis species were identified morphologically, whereas Hyalomma species molecularly. ResultsFrom 38 passeriform bird species 957 ixodid ticks were collected. The majority of developmental stages were nymphs (n=588), but 353 larvae and 16 females were also present. On most birds (n=381) only a single tick was found and the maximum number of ticks removed from the same bird was 30. Tick species were identified as Ixodes ricinus (n=598), Ixodes frontalis (n=18), Ixodes lividus (n=6), Haemaphysalis concinna (n=322), and D. reticulatus (n=1). All twelve Hyalomma sp. ticks (11 engorged nymphs and an unengorged larva) were identified as Hyalomma rufipes based on three mitochondrial markers. This species was only found in the Transdanubian region and along its southeastern border. The Common Blackbird (Turdus merula) and the European Robin (Erithacus rubecula) were the two main hosts of I. ricinus and I. frontalis, whereas H. concinna was almost exclusively collected form long-distance migrants. The predominant hosts of H. rufipes were reed-associated bird species, the Sedge Warbler (Acrocephalus schoenobaenus) and the Bearded Reedling (Panurus biarmicus), both harboring these ticks at the end of June (i.e., the nesting period) in southwestern Hungary. ConclusionsThis study provides ornithological explanation for the regional, century-long presence of adult Hyalomma ticks under continental climate in the Transdanubian Region of the Carpathian Basin. More importantly, the autochthonous occurrence of a H. rufipes population was revealed for the first time in Europe, based on the following observations: (1) the bird species infested with H. rufipes are not known to migrate during their nesting period; (2) one larva was not yet engorged; (3) the larva and the nymphs must have belonged to different local generations; and (4) all H. rufipes found in the relevant location were identical in their haplotypes based on three maternally inherited mitochondrial markers, probably reflecting founder effect. This study also demonstrated that the species of ticks carried by birds were significantly different between collection sites even within a geographically short distance (200 km). Therefore, within a country multiregional monitoring is inevitable to assess the overall epidemiological significance of migratory birds in importing exotic ticks, and also in maintaining newly established tick species.

zoology↗

bioRxiv2021

Glutamatergic dysfunction leads to a hyper-dopaminergic phenotype through deficits in short-term habituation: a mechanism for aberrant salience.

Psychosis in disorders like schizophrenia is commonly associated with aberrant salience and elevated striatal dopamine. However, the underlying cause(s) of this hyper-dopaminergic state remain elusive. Various lines of evidence point to glutamatergic dysfunction and impairments in synaptic plasticity in the aetiology of schizophrenia, including deficits associated with the GluA1 AMPAR subunit. GluA1 knockout (Gria1-/-) mice provide a model of impaired synaptic plasticity in schizophrenia and exhibit a selective deficit in a form of short-term memory which underlies short-term habituation. As such, these mice are unable to reduce attention to recently presented stimuli. In this study we used fast-scan cyclic voltammetry to measure phasic dopamine responses in the nucleus accumbens of Gria1-/- mice to determine whether this behavioral phenotype might be a key driver of a hyper-dopaminergic state. There was no effect of GluA1 deletion on electrically-evoked dopamine responses in anaesthetized mice, demonstrating normal endogenous release properties of dopamine neurons in Gria1-/- mice. Furthermore, dopamine signals were initially similar in Gria1-/- mice compared to controls in response to both sucrose rewards and neutral light stimuli. They were also equally sensitive to changes in the magnitude of delivered rewards. In contrast, however, these stimulus-evoked dopamine signals failed to habituate with repeated presentations in Gria1-/- mice, resulting in a task-relevant, hyper-dopaminergic phenotype. Thus, here we show that GluA1 dysfunction, resulting in impaired short-term habituation, is a key driver of enhanced striatal dopamine responses, which may be an important contributor to aberrant salience and psychosis in psychiatric disorders like schizophrenia.

neuroscience↗

bioRxiv2020

The SPIRE1 actin nucleator coordinates actin/myosin functions in the regulation of mitochondrial motility

Subcellular localisation of mitochondria provides a spatial and temporal organisation for cellular energy demands. Long-range mitochondrial transport is mediated by microtubule tracks and associated dynein and kinesin motor proteins. The actin cytoskeleton has a more versatile role and provides transport, tethering, and anchoring functions. SPIRE actin nucleators organise actin filament networks at vesicle membranes, which serve as tracks for myosin 5 motor protein-driven transport processes. Following alternative splicing, SPIRE1 is targeted to mitochondria. In analogy to vesicular SPIRE functions, we have analysed whether SPIRE1 regulates mitochondrial motility. By tracking mitochondria of living fibroblast cells from SPIRE1 mutant mice and splice-variant specific mitochondrial SPIRE1 knockout mice, we determined that the loss of SPIRE1 function increased mitochondrial motility. The SPIRE1 mutant phenotype was reversed by transient overexpression of mitochondrial SPIRE1, which almost completely inhibited motility. Conserved myosin 5 and formin interaction motifs contributed to this inhibition. Consistently, mitochondrial SPIRE1 targeted myosin 5 motors and formin actin filament generators to mitochondria. Our results indicate that SPIRE1 organises an actin/myosin network at mitochondria, which opposes mitochondrial motility. Summary statementThe mitochondrial SPIRE1 protein targets myosin 5 motor proteins and formin actin-filament nucleators/elongators towards mitochondria and negatively regulates mitochondrial motility.

cell biology↗

bioRxiv2019

Distinct roles for DAT and COMT in regulating dopamine transients and reward-guided decision making

Dopamine plays a crucial role in adaptive behavior, and dysfunctional dopamine is implicated in multiple psychiatric conditions characterized by inflexible or inconsistent choices. However, the precise relationship between dopamine and flexible decision making remains unclear. One reason is that, while many studies have focused on the activity of dopamine neurons, efficient dopamine signaling also relies on clearance mechanisms, notably the dopamine transporter (DAT), which predominates in striatum, and catechol-O-methyltransferase (COMT), which predominates in cortex. The exact locus, extent, and timescale of the effects of DAT and COMT are uncertain. Moreover, there is limited data on how acute disruption of either mechanism affects flexible decision making strategies mediated by cortico-striatal networks. To address these issues, we combined pharmacological modulation of DAT and COMT with electrochemistry and behavior in mice. DAT blockade, but not COMT inhibition, regulated sub-second dopamine release in the nucleus accumbens core, but surprisingly neither clearance mechanism affected evoked release in prelimbic cortex. This was not due to a lack of sensitivity, as both amphetamine and atomoxetine changed the kinetics of sub-second release. In a multi-step decision making task where mice had to respond to reversals in either reward probabilities or the choice sequence to reach the goal, DAT blockade selectively impaired, and COMT inhibition improved, performance after reward reversals, but neither manipulation affected the adaptation of choices after actionstate transition reversals. Together, our data suggest that DAT and COMT shape specific aspects of behavioral flexibility by regulating striatal and cortical dopamine, respectively, at fast and slow timescales.

neuroscience↗

bioRxiv2019

Glucocorticoids regulate cancer cell dormancy

The glucocorticoid receptor directly regulates thousands of genes across the human genome in a cell-type specific manner, governing various aspects of homeostasis. The influence of the glucocorticoid receptor is also seen in various pathologies, including cancer, where it has been linked to tumorigenesis, metastasis, apoptosis resistance, and therapy bypass. Nonetheless, the direct genetic and molecular underpinnings of glucocorticoid action in cancer remain elusive. Here, we dissected the glucocorticoid receptor signalling axis and uncovered the mechanism of glucocorticoid-mediated cancer cell dormancy. Upon glucocorticoid receptor activation cancer cells undergo quiescence, subserved by cell cycle arrest through CDKN1C and reprogramming of signalling orchestrated via FOXO1/IRS2. Strikingly, co-expression of these three genes, directly regulated by glucocorticoid-induced chromatin looping, correlates with a benign molecular phenotype across human cancers, whereas triple loss is associated with increased expression of proliferation/aggressiveness markers. Finally, we show that the glucocorticoid receptor signalling axis is inactivated by alterations of either the chromatin remodelling complex or TP53 in vitro and in vivo. Our results indicate that the activation of the glucocorticoid receptor leads to cancer cell dormancy, which has several implications in terms of glucocorticoid use in cancer therapy.

cancer biology↗

bioRxiv2019

Multilevel regulation of the glass locus during Drosophila eye development

Development of eye tissue is initiated by a conserved set of transcripton factors termed retinal determination network (RDN). In the fruit fly Drosophila melanogaster, the zinc-finger transcription factor Glass acts directly downstream of the RDN to control idendity of photoreceptor as well as non-photoreceptors cells. Tight control of spatial and temporal gene expression is a critical feature during development, cell-fate determination as well as maintainance of differentiated tissues. The molecular mechanisms that control expression of glass, however remain largely unknown. We here identify complex regulatory mechanisms controlling expression of the glass locus. All information to recapitulate glass expression are contained in a compact 5.2 kb cis-acting genomic element by combining different cell-type specific and general enhancers with repressor elements. Moreover, the immature RNA of the locus contains an alterantive small open reading frame (smORF) upstream of the actual glass translation start, resulting in a small peptide instead of the three possible glass protein isoforms. CRISPR/Cas9-based mutagenesis shows that the smORF is not required for the formation of functioning photoreceptors, but to attenuate effects of glass misexpression. Furthermore, editing the genome to generate glass loci eliminating either one or two isoforms shows that only one of the three proteins is critical for formation of functioning photoreceptors, while removing the two other isoforms did not cause defects in developmental or photoreceptor function. Our results show that eye development and function is surprisingly robust and appears buffered to targeted manipulations of critical features of the glass transcript, suggesting a strong selection pressure to allow the formation of a functioning eye.

developmental biology↗