Biology subjects

Stahl, M.

Publications and source records attributed to Stahl, M..

18 recordsLinked to original sources

bioRxiv2026

Pre-chlorotic Mg2+ deficiency impairs guard-cell PSII and leaf gas exchange in Vicia faba

Magnesium deficiency impairs photosynthesis and transpiration before visible chlorosis, but whether guard cells themselves are affected at this early stage remains unresolved. We combined whole-leaf gas exchange and chlorophyll fluorescence with cell-specific fluorescence measurements of individual guard cell pairs, together with elemental analysis, metabolite profiling, adenosine triphosphate quantification, and proteome profiling of guard cell-enriched material in hydroponically grown Vicia faba. Magnesium deficiency reduced magnesium concentrations in both whole leaves and guard cell-enriched fractions. Under red light, magnesium-deficient leaves showed reduced effective quantum yield of photosystem II, CO2 assimilation, transpiration, and stomatal conductance, whereas intercellular CO2 concentration remained unchanged. Individual guard cell pairs likewise showed reduced effective quantum yield of photosystem II, demonstrating that the early deficiency response extended to guard cells. Electron transport rate and non-photochemical quenching in guard cells were not significantly altered. Only a small set of metabolites in guard cell-enriched material, mainly fatty acids and citrate, responded to magnesium deficiency, whereas ATP abundance and light-induced proton extrusion remained unchanged. In contrast, the guard cell-enriched proteome showed higher abundance of photosynthesis- and translation-related proteins despite reduced guard-cell PSII efficiency. Together, these findings identify guard cells as an early responsive cell type under magnesium deficiency and show that guard-cell photochemistry is impaired before visible chlorosis, alongside reduced whole-leaf carbon gain and water loss.

physiology↗

bioRxiv2026

CyChat: a conversational Cytoscape app for no-code, reproducible network analysis

Network-based analyses of molecular interactions are useful for interpreting high-throughput omics data and identifying therapeutic targets. Cytoscape is the standard platform for these tasks, but users face a trade-off between accessible graphical workflows that are difficult to document and reproducible automation in Python or R that requires programming expertise. General-purpose coding assistants can generate Cytoscape Automation scripts, but remain external to Cytoscape. We present CyChat, a Cytoscape Desktop app that integrates a chat interface and a large language model (LLM) agent into the application. CyChat translates natural language into executable Cytoscape Automation workflows, runs generated Python code, and exports chat sessions with executed code as standalone Jupyter notebooks. To reduce setup barriers, CyChat includes an embedded Python runtime and supports both cloud-based and locally hosted LLMs. CyChat was evaluated across ten Cytoscape workflows using seven LLM providers, each represented by one LLM. The strongest configuration achieves a pass rate above 99%. In a qualitative evaluation based on a published network visualization, CyChat completes the task in 1.5-5 minutes, compared with 15-20 minutes for manual GUI workflows by computational biologists. CyChat is available through the Cytoscape App Store at https://apps.cytoscape.org/apps/cychat.

bioinformatics↗

bioRxiv2025

Small Molecule Binding to EDS1/PAD4 in LRR-RP-Mediated Pattern-Triggered Immunity

Pattern-triggered immunity (PTI) is a key defense mechanism initiated when pathogen-associated molecular patterns are recognized by receptors, including leucine-rich repeat receptor proteins (LRR-RPs)1,2. EDS1 and PAD4 are crucial for LRR-RP-mediated PTI activation3. Small molecule (SM) phosphoribosyl-AMP/ADP, generated by TIR-domain NADase activity, promote the recruitment of helper NLRs into EDS1-PAD4 complex4,5. Here, we show that BAK1 recruitment to LRR-RP complexes is unaffected in eds1-2 or pad4-1 mutants, but is abolished in the sobir1-12 mutant, highlighting the essential role of SOBIR1 in surface immune receptor complex formation. Furthermore, SM-binding to EDS1 and PAD4 is critical for LRR-RP-mediated PTI, as SM-binding-deficient mutants fail to restore immune responses. De novo SM synthesis is required for late PTI responses, including PR1 expression and bacterial resistance, but not for early responses such as ROS and ethylene production. The TNL SADR1 functions only in late PTI responses, suggesting distinct roles of multiple TIR-domain proteins in PTI signaling.

plant biology↗

bioRxiv2025

Resistance Training Reshapes the Gut Microbiome for Better Health

ObjectivesThe gut microbiome plays a critical role in metabolism, immunity, and aging. While endurance training has been shown to beneficially modulate the microbiome, the effects of resistance training remain less clear, with some studies reporting minimal changes. This project aims to investigate whether structured resistance training elicits significant changes in gut microbiome composition and diversity in sedentary, healthy adults. Methods150 participants completed an 8-week supervised resistance training program. Session-level training data, including weights and repetitions, were recorded alongside metrics like load and compliance. Fecal samples were collected throughout the study period at designated timepoints for 16S rRNA gene amplicon sequencing to assess microbiome composition and for metabolomics analyses to evaluate microbial metabolic activity. ResultsNo differences in microbial diversity were observed, and there were no significant changes in microbial community composition or fecal metabolomics across all participants post-training. However, within-individual microbial community changes significantly correlated with strength improvement, and significantly stronger shifts in beta diversity were observed in participants with high average strength gains compared to those with smaller gains. In these high responders, differential abundance analysis revealed time-dependent microbial changes, with more taxa enriched or depleted by week 8 of training. Notably, Faecalibacterium and Roseburia hominis--both associated with a healthier, anti-inflammatory microbiome--were significantly enriched. Many differentially abundant taxa belonged to the Lachnospiraceae family. ConclusionResistance training drives significant, time-dependent gut microbiome changes, particularly in those demonstrating greater improvements in strength. These shifts mirror endurance training effects and may reflect improved overall health. SummaryWhile endurance training has been consistently shown to enhance gut microbiome composition, the effects of resistance training remain less well defined, with findings to date being variable. Our results indicate that resistance training can induce meaningful, time-dependent shifts in the gut microbiome, particularly among sedentary individuals who experience substantial strength gains. Notably, we observed enrichment of key health-associated taxa, including Faecalibacterium and Roseburia hominis, both linked to anti-inflammatory effects and improved gut function. These findings suggest that resistance training may contribute to gut health in conjunction with physical fitness, supporting its broader application in health promotion strategies and future microbiome-focused research.

microbiology↗

bioRxiv2025

Emergent loss of microbial biodiversity with increasing resource diversity

The origin of biodiversity is arguably the most fundamental question in ecology -- especially how countless microbial species coexist within a single community. A prevailing hypothesis holds that microbial species coexist by specializing on different resources, thereby reducing competition. Accordingly, increasing resource diversity is expected to promote species coexistence and boost biodiversity. Surprisingly, we observe the opposite: microbial biodiversity often declines as resource diversity increases. This unexpected result emerges from a widespread physiological response across diverse microbial taxa, in which more complex environments trigger higher overall resource uptake. This intensifies competition and drives biodiversity loss. Updating a central ecological model to include this physiological trait accurately reproduces the observed decline. Our findings demonstrate that physiological changes at the individual level can overturn classical ecological principles and scale up to restructure entire ecosystems.

microbiology↗

bioRxiv2025

Refinement Strategies for Tangram for Reliable Single-Cell to Spatial Mapping

MotivationSingle-cell RNA sequencing (scRNA-seq) provides comprehensive gene expression data at a single-cell level but lacks spatial context. In contrast, spatial transcriptomics captures both spatial and transcriptional information but is limited by resolution, sensitivity, or feasibility. No single technology combines both the high spatial resolution and deep transcriptomic profiling at the single-cell level without trade-offs. Spatial mapping tools that integrate scRNA-seq and spatial transcriptomics data are crucial to bridge this gap. However, we found that Tangram, one of the most prominent spatial mapping tools, provides inconsistent results over repeated runs. ResultsWe refine Tangram to achieve more consistent cell mappings and investigate the challenges that arise from data characteristics. We find that the mapping quality depends on the gene expression sparsity. To address this, we (1) train the model on an informative gene subset, (2) apply cell filtering, (3) introduce several forms of regularization, and (4) incorporate neighborhood information. Evaluations on real and simulated mouse datasets demonstrate that this approach improves both gene expression prediction and cell mapping. Consistent cell mapping strengthens the reliability of the projection of cell annotations and features into space, gene imputation, and correction of low-quality measurements. Our pipeline, which includes gene set and hyperparameter selection, can serve as guidance for applying Tangram on other datasets, while our benchmarking framework with data simulation and inconsistency metrics is useful for evaluating other tools or Tangram modifications. AvailabilityThe refinements for Tangram and our benchmarking pipeline are available in https://github.com/daisybio/Tangram_Refinement_Strategies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/634996v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@5ef8a8org.highwire.dtl.DTLVardef@11707d7org.highwire.dtl.DTLVardef@103e1f2org.highwire.dtl.DTLVardef@1e713e9_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Systemic effects of cystic fibrosis transmembrane conductance regulator (CFTR) modulators on the blood proteome

Cystic fibrosis (CF), resulting from a dysfunction in the cystic fibrosis transmembrane conductance regulator (CFTR), affects multiple organs through mucus obstruction and differences in secretion. The CFTR modulator drug combination elexacaftor/tezacaftor/ivacaftor (ELX/TEZ/IVA, ETI) has markedly improved clinical symptoms, but its broader molecular and systemic effects remain to be fully elucidated. We employed mass spectrometry-based proteomics to compare the blood proteomes of CF patients treated with the earlier, less effective lumacaftor/ivacaftor (LUM/IVA) combination against those receiving the more potent ELX/TEZ/IVA therapy. Our analysis revealed both specific and common pharmacodynamic signatures associated with inflammation and metabolic processes under each treatment regimen. Notably, ELX/TEZ/IVA therapy exhibited more consistent alterations across patients that were directed towards profiles observed in healthy individuals. Furthermore, by comparing sputum and blood proteomes of ELX/TEZ/IVA treated patients we identified counter-directional changes in the pulmonary surfactant-associated protein B, SFTPB, a potential biomarker of lung tissue repair, which also correlated with lung function improvements. This study provides a comprehensive resource that enhances our understanding of CFTR modulator-driven proteome alterations, offering insights to both systemic and local protein regulation in CF. Our findings indicate that ELX/TEZ/IVA promotes broader systemic health improvements, providing critical insights that could shape future therapeutic strategies in CF.

molecular biology↗

bioRxiv2024

Metabolic conservation by protein quality control in Campylobacter jejuni underlies the antibiotic tolerance

Bacterial persistence enables survival during lethal antibiotic exposure and is implicated in recurrent infections, yet the physiology underlying bacterial persistence in many pathogens remains poorly defined. Here we show that exposure of Campylobacter jejuni to ampicillin or ciprofloxacin generates an antibiotic-persistent subpopulation. Rather than undergoing global metabolic shutdown, persister cells adopted a metabolically constrained state characterized by selective maintenance of oxidative phosphorylation and bioenergetic metabolism through coordinated proteostasis control. The ATP-dependent protease ClpP was essential for entry into this persistent state. Loss of ClpP disrupted proteostasis of the electron transport chain, specifically impaired bd-like terminal oxidase integrity, and reduced survival in vivo and in macrophages. These findings identify ClpP-dependent maintenance of redox and bioenergetic homeostasis as critical determinants of C. jejuni persistence and highlight metabolic remodeling as a defining feature of antibiotic tolerance. These insights may inform future therapeutic strategies aimed at disrupting persistence and improving antibiotic efficacy.

microbiology↗

bioRxiv2023

Cultural use of tropane alkaloids of Brugmansia species and cultivars in Colombia depends on local plant growth environment rather than genetic diversity

Borracheros or Angel Trumpets (Brugmansia spp.) of the Solanaceae plant family are known for producing scopolamine and other tropane alkaloids and are widely used by indigenous communities in the Andes for medicinal and ritual purposes. Growing different varieties has increased the popularity of Brugmansia species in recent years, leading to the promotion of hybridization to get new morphotypes. However, so far no medical or cultural use of plant extracts could be linked to selected Brugmansia species or cultivars. Moreover, until now there is only limited knowledge about the effect of hybridization on tropane alkaloid contents and/or diversity of Brugmansia species or cultivars. Here, a liquid chromatography-mass spectrometry (LC-MS) approach was applied to identify and characterize secondary metabolite contents in various Brugmansia species and hybrids from different geographic origins in Colombia. The analysis of the metabolic data sets revealed that tropane alkaloids and other secondary metabolites accumulate in a leaf and flower specific manner. Although some minor differences were found between Brugmansia subgroups, the only significant difference exists between plants collected in the Sibundoy Valley, where they have been domesticated by indigenous communities since a long time and those, which so far have not been used by humans at all. The different genetic constitutions of Brugmancia species and cultivars are not the dominating reason for their differences in tropane alkaloid contents and medical and cultural usages, as there is no clear taxonomical signature based on the metabolite properties for species segregation. Instead, their use by indigenous communities during ceremonies and for medical treatment such as wound healing, infection control, rheumatism and arthritis is rather caused by the plasticity of the individual plants to react to the local abiotic and biotic environments by the variation of secondary metabolite composition and by the differences in the bioavailability of the active compounds as result of the extraction method.

plant biology↗

bioRxiv2023

In planta exploitation of leaf apoplastic compounds: a window of opportunity for spatiotemporal studies of apoplastic metabolites, hormones and physiology

Processes in the leaf apoplast are relevant for development, cell wall rheological properties, plant nutrition, sink-source portioning, microbe-host plant-interactions or intercellular information exchange and signaling and are therefore regulated or influenced by the composition of the leaf apoplastic solute. In contrast to the traditional methods for the extraction of apoplastic solutes that are more or less destructive, we propose a new method that allows extraction of leaf apoplastic solutes (i) non-invasively and, thus, (ii) over time. Moreover, the method has (iii) a high spatial resolution that allows identification of solute-microdomains in the leaf apoplast. The method was established for Arabidopsis thaliana and Vicia faba leaves but should also be applicable to other plants species with similar leaf morphologies. It is based on the infiltration of an aqueous extraction solution into the apoplast followed by its recovery seconds later, both through the stomata. By this, the apoplast (and its solutes) of an identical leaf can be sampled on successive days with negligible symplastic contamination. A spatiotemporal mapping of leaf apoplastic ion and metabolite patterns within the identical leaf opens a window of opportunity for understanding apoplast biology. As for example, the existence of apoplastic abscisic acid gradients within a leaf in response to salinity was witnessed in this study, as was the unsuspected accumulation of kaempferol glycosides in the leaf apoplast. The presented method is relevant for plant developmental biologists, phytopathologists, plant physiologists, plant nutritionists and others that need to integrate apoplast biology into their research approaches.

plant biology↗

bioRxiv2022

Deep thermal proteome profiling for detection of proteoforms and drug sensitivity biomarkers

The complexity of the functional proteome extends significantly beyond the protein coding genome resulting in millions of proteoforms. Investigation of proteoforms and their functional roles is important to understand cellular physiology and its deregulation in diseases, but challenging to perform systematically. Here, we apply thermal proteome profiling with deep peptide coverage to detect functional proteoforms in acute lymphoblastic leukemia cell lines with different cytogenetic aberrations. We detect 15,846 proteoforms, capturing differently spliced, post-translationally modified, and cleaved proteins expressed from 9,290 genes. We identify differential coaggregation of proteoform pairs and establish links to disease biology. Moreover, we systematically make use of measured biophysical proteoform states to find specific biomarkers of drug sensitivity. Our approach thus provides a powerful and unique tool for systematic detection and functional annotation of proteoforms.

biochemistry↗

bioRxiv2022

Integrated Single-Cell Genotyping and Chromatin Accessibility Charts JAK2V617F Human Hematopoietic Differentiation

In normal somatic tissue differentiation, changes in chromatin accessibility govern priming and commitment of precursors towards cellular fates. In turn, somatic mutations can disrupt differentiation topologies leading to abnormal clonal outgrowth. However, defining the impact of somatic mutations on the epigenome in human samples is challenging due to admixed mutated and wildtype cells. To chart how somatic mutations disrupt epigenetic landscapes in human clonal outgrowths, we developed Genotyping of Targeted loci with single-cell Chromatin Accessibility (GoT-ChA). This high-throughput, broadly accessible platform links genotypes to chromatin accessibility at single-cell resolution, across thousands of cells within a single assay. We applied GoT-ChA to CD34+ cells from myeloproliferative neoplasm (MPN) patients with JAK2V617F-mutated hematopoiesis, where the JAK2 mutation is known to perturb hematopoietic differentiation. Differential accessibility analysis between wildtype and JAK2V617F mutant progenitors revealed both cell-intrinsic and cell state-specific shifts within mutant hematopoietic precursors. An early subset of mutant hematopoietic stem and progenitor cells (HSPCs) exhibited a cell-intrinsic pro-inflammatory signature characterized by increased NF-{kappa}B and JUN/FOS transcription factor motif accessibility. In addition, mutant HSPCs showed increased myeloid/erythroid epigenetic priming, preceding increased erythroid and megakaryocytic cellular output. Erythroid progenitors displayed aberrant regulation of the {gamma}-globin locus, providing an intrinsic epigenetic basis for the dysregulated fetal hemoglobin expression observed in MPNs. In contrast, megakaryocytic progenitors exhibited a more specialized inflammatory chromatin landscape relative to early HSPCs, with increased accessibility of pro-fibrotic JUN/FOS transcription factors. Notably, analysis of myelofibrosis patients treated with JAK inhibitors revealed an overall loss of mutant-specific phenotypes without modifying clonal burden, consistent with clinical responses. Finally, expansion of the multi-modality capability of GoT-ChA to integrate mitochondrial genome profiling and cell surface protein expression measurement enabled genotyping imputation and discovery of aberrant cellular phenotypes. Collectively, we show that the JAK2V617F mutation leads to epigenetic rewiring in a cell-intrinsic and cell type-specific manner. We envision that GoT-ChA will thus serve as a foundation for broad future explorations to uncover the critical link between mutated somatic genotypes and epigenetic alterations across clonal populations in malignant and non-malignant contexts.

cancer biology↗

bioRxiv2022

Proteogenomics refines the molecular classification of chronic lymphocytic leukemia

Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterized the proteome and transcriptome in-depth alongside genetic and ex-vivo drug response profiling in a clinically well annotated CLL discovery cohort (n= 68). Unsupervised clustering of the proteome data revealed six subgroups. Five of these proteomic groups were associated with genetic features, while one group was only detectable at the proteome level. This new group was characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). We developed classifiers to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n= 165, n= 169) and confirmed that ASB-CLL comprises about 20 % of CLL patients. The inferior overall survival observed in ASB-CLL was independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling. Single sentence summaryWe performed the largest proteogenomic analysis of CLL, linked proteomic profiles to clinical outcomes, and discovered a new poor outcome subgroup (ASB-CLL).

cancer biology↗

bioRxiv2021

Gut-derived bacterial flagellin induces beta-cell inflammation and dysfunction

ObjectiveHyperglycemia and type 2 diabetes (T2D) are caused by failure of pancreatic beta cells. The role of the gut microbiota in T2D has been studied but causal links remain enigmatic. DesignObese individuals with or without T2D were included from two independent Dutch cohorts. Human data was translated in vitro and in vivo by using pancreatic islets from C57BL6/J mice and by injecting flagellin into obese mice. ResultsFlagellin is part of the bacterial locomotor appendage flagellum, present on gut bacteria including Enterobacteriaceae, which we show to be more abundant in the gut of individuals with T2D. Subsequently, flagellin induces a pro-inflammatory response in pancreatic islets mediated by the Toll-like receptor (TLR)-5 expressed on resident islet macrophages. This inflammatory response associated with beta-cell dysfunction, characterized by reduced insulin gene expression, impaired proinsulin processing and stress-induced insulin hypersecretion in vitro and in vivo in mice. ConclusionWe postulate that increased systemically disseminated flagellin in T2D is a contributing factor to beta cell failure in time and represents a novel therapeutic target. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/463317v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@b719aeorg.highwire.dtl.DTLVardef@f72958org.highwire.dtl.DTLVardef@bb7af5org.highwire.dtl.DTLVardef@859c70_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2021

The genetic interaction of REVOLUTA and WRKY53 links plant development, senescence, and immune responses

In annual plants, tight coordination of successive developmental events is of primary importance to optimize performance under fluctuating environmental conditions. The recent finding of the genetic interaction of WRKY53, a key senescence-related gene with REVOLUTA, a master regulator of early leaf patterning, raises the question of how early and late developmental events are connected. Here, we investigated the developmental and metabolic consequences of an alteration of the REVOLUTA and WRKY53 gene expression, from seedling to fruiting. Our results show that REVOLUTA critically controls late developmental phases and reproduction while inversely WRKY53 determines vegetative growth at early developmental stages. We further show that these regulators of distinct developmental phases frequently, but not continuously, interact throughout ontogeny and demonstrated that their genetic interaction is mediated by the salicylic acid (SA). Moreover, we showed that REVOLUTA and WRKY53 are keys regulatory nodes of development and plant immunity thought their role in SA metabolic pathways, which also highlights the role of REV in pathogen defence. Together, our findings demonstrate how late and early developmental events are tightly intertwined by molecular hubs. These hubs interact with each other throughout ontogeny, and participate to the interplay between plant development and immunity.

plant biology↗

bioRxiv2021

The TIR-NBS-LRR protein CSA1 is required for autoimmune cell death in Arabidopsis pattern recognition co-receptor bak1 and bir3 mutants

The BRI1-associated kinase BAK1/SERK3 is a positive regulator of multiple leucine rich receptor kinase-mediated signaling pathways including pattern triggered immunity (PTI). Absence or overexpression of BAK1 leads to spontaneous cell death formation. BAK1-interacting receptors (BIR) constitutively interact with BAK1, and plants lacking or overexpressing BIR proteins phenocopy the cell death symptoms observed in bak1 knock outs or overexpressors. In the interactome of BIR3, the TIR-NBS-LRR protein CONSTITUTIVE SHADE-AVOIDANCE 1 (CSA1) was identified by mass spectrometry. CSA1 physically interacts with BIR proteins and can be detected in complexes with BAK1. Direct interaction was shown only for CSA1 with BIR proteins but not BAK1. Double mutant bak1 bir3 genotypes develop strong dwarfism and cell death symptoms that are dependent on EDS1 and salicylic acid. Loss of CSA1 blocks bak1 and bak1 bir3-mediated cell death formation thus demonstrating that CSA1 is causal for this type of cell death. We propose that CSA1 guards BIR proteins and initiates autoimmune cell death that is observed when BAK1 BIR complexes are impaired. Our findings reveal how cell death in the absence of BAK1 and BIR3 is executed and links BAK1, a common co-receptor of many pattern recognition receptors, to NLR proteins typically implicated in effector-triggered immunity.

plant biology↗

bioRxiv2020

Plasmacytoid dendritic cell expansion defines a distinct subset of RUNX1 mutated acute myeloid leukemia

Plasmacytoid dendritic cells (pDC) are the principal natural type I interferon producing dendritic cells. Neoplastic expansion of pDCs and pDC precursors leads to blastic plasmacytoid dendritic cell neoplasm (BPDCN) and clonal expansion of mature pDCs has been described in chronic myelomonocytic leukemia (CMML). The role of pDC expansion in acute myeloid leukemia (AML) is poorly studied. Here we characterize AML patients with pDC expansion (pDC-AML), which we observe in approximately 5% of AML. pDC-AML often possess crosslineage antigen expression and have adverse risk stratification with poor outcome. RUNX1 mutations are the most common somatic alterations in pDC-AML (>70%) and are much more common than in AML without PDC expansion. We demonstrate that pDCs are clonally related to, and originate from, leukemic blasts in pDC-AML. We further demonstrate that leukemic blasts from RUNX1-mutated AML upregulate a pDC transcriptional program, poising the cells towards pDC differentiation and expansion. Finally, tagraxofusp, a targeted therapy directed to CD123, reduces leukemic burden and eliminates pDCs in a patient-derived xenograft model. In conclusion, pDC-AML is characterized by a high frequency of RUNX1 mutations and increased expression of a pDC transcriptional program. CD123 targeting represents a potential treatment approach for pDC-AML.Competing Interest StatementConflict-of-interest disclosure: W.X. has received research support from Stemline Therapeutics. S.F.C. is a consultant for Imago Biosciences and has received honoraria from DAVA Oncology. A.D.G. served on advisory boards or as a consultant for Abbvie, Aptose, Celgene, Daiichi Sanyko, Genentech, received research funding from Abbvie, ADC Therapeutics, Aprea, AROG, Daiichi Sanyko, Pfizer, received Honoraria from Dava Oncology. R.K.R has received consulting fees from: Constellation, Incyte, Celgene, Promedior, CTI, Jazz Pharmaceuticals, Blueprint, Stemline, and research funding from Incyte, Constellation, and Stemline Therapeutics. M.S.T has received research funding from AbbVie, Cellerant, Orsenix, ADC Therapeutics, Biosight, Glycomimetics, Rafael Pharmaceuticals and Amgen. He also served on advisory Boards for AbbVie, BioLineRx, Daiichi-Sankyo, Orsenix, KAHR, Rigel, Nohla, Delta Fly Pharma, Tetraphase, Oncolyze, Jazz Pharma, Roche, Biosight and Novartis. He received royalties from UpToDate. R.L.L. is on the supervisory board of Qiagen and is a scientific advisor to Loxo (until 2019), Auron, Ajax, Mission Bio, Imago, C4 Therapeutics and Isoplexis, which each include an equity interest. He receives research support from and consulted for Celgene and Roche, he has received research support from Prelude Therapeutics, and he has consulted for Incyte, Novartis and Janssen. He has received honoraria from Lilly and Amgen for invited lectures and from Gilead for grant reviews.View Full Text

pathology↗

bioRxiv2019

AtDAT1 is a key enzyme of D-amino acid stimulated ethylene production in Arabidopsis thaliana

D-enantiomers of proteinogenic amino acids (D-AAs) are found ubiquitously, but the knowledge about their metabolism and functions in plants is scarce. A long forgotten phenomenon in this regard is the D-AA-stimulated ethylene production in plants. As a starting point to investigate this effect the Arabidopsis accession Landsberg erecta (Ler) got into focus as it was found defective in metabolizing D-AAs. Combining genetics and molecular biology of T-DNA lines and natural variants together with biochemical and physiological approaches we could identify AtDAT1 as a major D-AA transaminase in Arabidopsis. Atdat1 loss-of-function mutants and Arabidopsis accessions with defective AtDAT1 alleles were not able to produce D-Ala, D-Glu and L-Met, the metabolites of D-Met, anymore. This result corroborates the biochemical characterization of AtDAT1, which showed highest activity using D-Met as substrate. Germination of seedlings in light and dark led to enhanced growth inhibition of atdat1 mutants on D-Met. Ethylene measurements revealed an enhanced D-AA stimulated ethylene production in these mutants. According to initial working models of this phenomenon D-Met is preferentially malonylated instead of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). This decrease of ACC degradation should then lead to the increase of ethylene production. We could observe in our studies a reciprocal relation of malonylated methionine and ACC upon D-Met application and even significantly more malonyl-methionine in atdat1 mutants. Unexpectedly, the malonyl-ACC levels did not differ between mutants and wild type in these experiments. With AtDAT1, the first central enzyme of plant D-AA metabolism was characterized biochemically and physiologically. The specific effects of D-Met on ACC metabolization, ethylene production and plant development of dat1 mutants unraveled the impact of AtDAT1 on these processes, but they are not in full accordance to previous working models. Instead, our results imply the influence of additional candidate factors or processes on D-AA-stimulated ethylene production which await to be uncovered.

plant biology↗