Biology subjects

Kraus, F.

Publications and source records attributed to Kraus, F..

10 recordsLinked to original sources

bioRxiv2026

Single-Cell proteomics discerns patient-specific subpopulations in pediatric B-cell acute lymphoblastic leukemia

B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer, representing ~30% of pediatric cancers and ~80-85% of pediatric ALL cases. Despite high remission rates, relapse remains a major challenge, often driven by therapy-resistant subpopulations, which are masked in bulk analysis, thus limiting our understanding of disease progression and optimal therapeutic intervention. Precision oncology enables proteome-level characterization of patient specific cancer samples and their subpopulations, essential for improving prognostic accuracy and individualized therapies. Single-cell proteomics by mass spectrometry (SCP-MS) enables quantification of hundreds to thousands of proteins at single cell level, uncovering cellular programs that may contribute to minimal residual disease (MRD) and relapse. Here, employing single-cell sorting of leukemic cells coupled with high-sensitivity SCP-MS, we profile individual leukemic blasts and normal immature B-cells from pediatric B-ALL bone marrow aspirates alongside age-matched controls. SCP-MS deconvoluted cellular heterogeneity and revealed subpopulations with variable leukemia-marker expression, highlighting its potential for early detection of relapse-prone phenotypes and personalized pediatric therapy.

cancer biology↗

bioRxiv2026

Cathepsin-dependent amyloid formation drives mechanical rupture of lysosomal membranes

Lysosomal membrane integrity is essential for cellular homeostasis, and its failure drives lysosomal storage disorders (LSD) and neurodegeneration. The dipeptide L-leucyl-L-leucine methyl ester (LLOMe) is widely used to model lysosomal damage, yet its mechanism remains poorly understood. The prevailing view holds that LLOMe polymerizes into membrane-permeabilizing peptide chains within the lysosomal lumen. Using cryo-electron tomography in cultured cells and primary neurons, we visualized the structural basis of LLOMe-induced lysosomal damage. We reveal that LLOMe forms amyloid structures within lysosomes that directly interact with and rupture the limiting membrane through mechanical stress. In vitro reconstitution confirms this amyloid-mediated mechanism. These findings establish a structural paradigm for lysosomal membrane disruption and provide insights into how disease-relevant protein aggregates, implicated in neurodegeneration and LSD, may compromise lysosomal integrity.

cell biology↗

bioRxiv2025

Proteome Landscapes Decode Organelle Vulnerabilities in cortical and dopaminergic-like induced neurons Across Lysosomal Storage Disorders

Lysosomes maintain cellular homeostasis by degrading proteins delivered via endocytosis and autophagy, and by recycling building blocks for organelle biogenesis. Lysosomal Storage Disorders (LSDs) comprise a group of diseases affecting diverse lysosomal functions. To facilitate molecular phenotyping across diverse LSD gene classes, we are developing a library of human embryonic stem cells engineered to lack individual LSD genes as a resource for the field. Here, we report our initial stem cell toolkit lacking one of 23 LSD genes, including the majority of genes associated with sphingolipidoses and neuronal ceroid lipofuscinoses, and its use in the generation of a proteomic resource for induced cortical-like and midbrain dopaminergic-like neurons In-depth abundance and correlation profiling across organelles and sub-organelle components revealed potential vulnerabilities that reflect distinct patterns of proteome alterations across both genotypes and neuronal cell types. We characterize alterations in the mitochondrial proteome associated with GBA1 and ASAH1 deficiency and identify synaptic and mitochondrial defects in ASAH1-/- induced neurons that correlate with defects in neuronal firing rates. Moreover, we developed an informatic pipeline for proteome-wide identification of individual protein interactions and protein complexes that may be disrupted as a result of LSD gene deficiency. Finally, we visualized structural alterations of ASAH1-deficient endolysosomes in situ using cryo-electron tomography, revealing swollen organelles that were largely devoid of dense internal membranes characteristic of wild-type cells, but containing numerous intralumenal vesicle compartments. This toolkit and associated proteomic landscapes provide a resource for defining molecular signatures associated with LSD gene dysfunction and organelle vulnerability.

cell biology↗

bioRxiv2025

Organoid-based modeling of platinum resistance identifies KRT17 as both a response mediator and biomarker for targeted therapy in ovarian cancer

Variable platinum responses drive high mortality in high-grade serous ovarian cancer (HGSOC), but to date, there is no molecular approach to define resistance levels for clinical decision-making. Here, we developed the organoid drug resistance assay (ODR-test) with patient-derived organoids from our ovarian cancer biobank and found that all HGSOC patients develop molecular resistance under exposure to carboplatin, although with varying clinical implications. Sustained phenotypic reprogramming and cellular plasticity under carboplatin pressure emerged as a conserved mechanism irrespective of the basal resistance level. Transcriptional and proteomic analyses revealed changes in cell adhesion and differentiation in post-platinum lines as adaptive responses that drive the increase in resistance. We identified Keratin 17 (KRT17) as a mediator of developing platinum resistance and validated its function by CRISPR/Cas9 and overexpression. Additionally, we found that KRT17 expression status (K-score) is a significant negative prognostic histopathological biomarker in a large cohort (N=384) of advanced HGSOC patients. In organoids, increased KRT17 levels enhanced sensitivity to PI3K/Akt inhibitors Alpelisib and Afuresertib, highlighting the potential of KRT17 as a stratification biomarker for targeted therapies.

cancer biology↗

bioRxiv2024

Neurophysiology of effortful listening: Decoupling motivational modulation from task demands

In demanding listening situations, a listeners motivational state may affect their cognitive investment. Here, we aim to delineate how domain-specific sensory processing, domain-general neural alpha power, and pupil size as a proxy for cognitive investment encode influences of motivational state under demanding listening. Participants performed an auditory gap-detection task while pupil size and the magnetoencephalogram (MEG) were simultaneously recorded. Task demand and a listeners motivational state were orthogonally manipulated through changes in gap duration and monetary-reward prospect, respectively. Whereas task difficulty impaired performance, reward prospect enhanced it. Pupil size reliably indicated the modulatory impact of an individuals motivational state. At the neural level, the motivational state did not affect auditory sensory processing directly but impacted attentional post-processing of an auditory event as reflected in the late evoked-response field and alpha power change. Both pre-gap pupil dilation and higher parietal alpha power predicted better performance at the single-trial level. The current data support a framework wherein the motivational state acts as an attentional top-down neural means of post-processing the auditory input in challenging listening situations. Significance StatementHow does an individuals motivational state affect cognitive investment during effortful listening? In this simultaneous pupillometry and MEG study, participants performed an auditory gap-detection task while their motivational state was manipulated through varying prospect of a monetary reward. The pupil size directly mirrored this motivational modulation of the listening demand. The individuals motivational state also enhanced top-down attentional post-processing of the auditory event but did neither change auditory sensory processing nor pre-gap parietal alpha power. These data suggest that a listeners motivational state acts as a late attentional top-down effect on auditory neural processes in challenging listening situations.

neuroscience↗

bioRxiv2024

Lysosomal storage disease proteo/lipidomic profiling using nMOST links ferritinophagy with mitochondrial iron deficiencies in cells lacking NPC2

Lysosomal storage diseases (LSDs) comprise [~]50 monogenic disorders marked by the buildup of cellular material in lysosomes, yet systematic global molecular phenotyping of proteins and lipids is lacking. We present a nanoflow-based multi-omic single-shot technology (nMOST) workflow that quantifies HeLa cell proteomes and lipidomes from over two dozen LSD mutants. Global cross-correlation analysis between lipids and proteins identified autophagy defects, notably the accumulation of ferritinophagy substrates and receptors, especially in NPC1-/- and NPC2-/- mutants, where lysosomes accumulate cholesterol. Autophagic and endocytic cargo delivery failures correlated with elevated lyso-phosphatidylcholine species and multi-lamellar structures visualized by cryo-electron tomography. Loss of mitochondrial cristae, MICOS- complex components, and OXPHOS components rich in iron-sulfur cluster proteins in NPC2-/- cells was largely alleviated when iron was provided through the transferrin system. This study reveals how lysosomal dysfunction affects mitochondrial homeostasis and underscores nMOST as a valuable discovery tool for identifying molecular phenotypes across LSDs.

cell biology↗

bioRxiv2023

Pupil-size sensitivity to listening demand depends on motivational state

Motivation plays a role when a listener needs to understand speech under acoustically demanding conditions. Previous work has demonstrated pupil-linked arousal being sensitive to both listening demands and motivational state during listening. It is less clear how motivational state affects the temporal evolution of the pupil size and its relation to subsequent behavior. We used an auditory gap-detection task (N=33) to study the joint impact of listening demand and motivational state on the pupil-size response and examine its temporal evolution. Task difficulty and a listeners motivational state were orthogonally manipulated through changes in gap duration and monetary-reward prospect. We show that participants performance decreased with task difficulty, but that reward prospect enhanced performance under hard listening conditions. Pupil size increased with both increased task difficulty and higher reward prospect, and this reward-prospect effect was largest under difficult listening conditions. Moreover, pupil-size time courses differed between detected and missed gaps, suggesting that the pupil response indicates upcoming behavior. Larger pre-gap pupil size was further associated with faster response times on a trial-by-trial within-participant level. Our results reiterate the utility of pupil size as an objective and temporally sensitive measure in audiology. However, such assessments of cognitive-resource recruitment need to consider the individuals motivational state. Significance statementThe literature is inconclusive to what degree pupil size may be representing the interaction of listening task demand and an individuals motivational state. Using an auditory gap-detection task, we manipulated both the degree of listening demand and a persons motivational state, and investigated the temporal evolution of the pupil-size response and its relation to behavior. We find that the pupil size represents the interaction of demand and motivational state. These results highlight the importance of considering a persons motivational state when using pupil size as a clinical measure. Pupil size appears as a key tool when assessing the impact of motivational state on the recruiting of cognitive resources.

neuroscience↗

bioRxiv2022

Neural alpha oscillations and pupil size differentially index cognitive demand under competing audio-visual task conditions

Cognitive demand is thought to modulate two often used, but rarely combined, measures: pupil size and neural alpha (8-12 Hz) oscillatory power. However, it is unclear whether these two measures capture cognitive demand in a similar way under complex audio-visual task conditions. Here we recorded pupil size and neural alpha power (using electroencephalography), while human participants of both sexes concurrently performed a visual multiple object-tracking task and an auditory gap-detection task. Difficulties of the two tasks were manipulated independent of each other. Participants performance decreased in accuracy and speed with increasing cognitive demand. Pupil size increased with increasing difficulty for both the auditory and the visual task. In contrast, alpha power showed diverging neural dynamics: Parietal alpha power decreased with increasing difficulty in the visual task, but not with increasing difficulty in the auditory task. Furthermore, independent of task difficulty, within-participant trial-by-trial fluctuations in pupil size were negatively correlated with alpha power. Difficulty-induced changes in pupil size and alpha power, however, did not correlate, which is consistent with their different cognitive-demand sensitivities. Overall, the current study demonstrates that the dynamics of the neurophysiological indices of cognitive demand and associated effort are multi-faceted and potentially modality-dependent under complex audio-visual task conditions. Significance StatementPupil size and oscillatory alpha power are associated with cognitive demand and effort, but their relative sensitivity under complex audio-visual task conditions is unclear as is the extent to which they share underlying mechanisms. Using an audio-visual dual-task paradigm, we show that pupil size increases with increasing cognitive demands for both audition and vision. In contrast, changes in oscillatory alpha power depend on the respective task demands: Parietal alpha power decreases with visual demand but not with auditory task demand. Hence, pupil size and alpha power show different sensitivity to cognitive demands, perhaps suggesting partly different underlying neural mechanisms.

neuroscience↗

bioRxiv2022

PARK15/FBXO7 is dispensable for PINK1/Parkin-dependent mitophagy in iNeuron and HeLa cell systems

The protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed-forward mechanism involving ubiquitin (Ub) phosphorylation (pUb), Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins to support recruitment of mitophagy receptors. The ubiquitin ligase substrate receptor FBXO7/PARK15 is mutated in an early-onset parkinsonian-pyramidal syndrome. Previous studies have proposed a role for FBXO7 in promoting Parkin-dependent mitophagy. Here, we systematically examine the involvement of FBXO7 in depolarization and mtUPR-dependent mitophagy in the well-established HeLa and induced-neurons cell systems. We find that FBXO7-/- cells have no demonstrable defect in: 1) kinetics of pUb accumulation, 2) pUb puncta on mitochondria by super-resolution imaging, 3) recruitment of Parkin and autophagy machinery to damaged mitochondria, 4) mitophagic flux, and 5) mitochondrial clearance as quantified by global proteomics. Moreover, global proteomics of neurogenesis in the absence of FBXO7 reveals no obvious alterations in mitochondria or other organelles. These results argue against a general role for FBXO7 in Parkin-dependent mitophagy and point to the need for additional studies to define how FBXO7 mutations promote parkinsonian-pyramidal syndrome.

cell biology↗

bioRxiv2020

Unilateral acoustic degradation delays attentional separation of competing speech

Hearing loss is often asymmetric, such that hearing thresholds differ substantially between the two ears. The extreme case of such asymmetric hearing is single-sided deafness. A unilateral cochlear implant (CI) on the more severely impaired ear is an effective treatment to restore hearing. The interactive effects of unilateral acoustic degradation and spatial attention to one sound source in multi-talker situations are at present unclear. Here, we simulated some features of listening with a unilateral CI in young, normal-hearing listeners (N = 22) who were presented with 8-band noise-vocoded speech to one ear and intact speech to the other ear. Neural responses were recorded in the electroencephalogram (EEG) to obtain the spectro-temporal response function (sTRF) to speech. Listeners made more mistakes when answering questions about vocoded (versus intact) attended speech. At the neural level, we asked how unilateral acoustic degradation would impact the attention-induced amplification of tracking target versus distracting speech. Interestingly, unilateral degradation did not per se reduce the attention-induced amplification but instead delayed it in time: Speech encoding accuracy, modelled on the basis of the sTRF, was significantly enhanced for attended versus ignored intact speech at earlier neural response latencies (<~250 ms). This attentional enhancement was not absent but delayed for vocoded speech. These findings suggest that attentional selection of unilateral, degraded speech is feasible, but induces delayed neural separation of competing speech, which might explain listening challenges experienced by unilateral CI users.

neuroscience↗