Biology subjects

Heymann, T.

Publications and source records attributed to Heymann, T..

7 recordsLinked to original sources

bioRxiv2026

Scanning DIA on the ZenoTOF 8600 system enables ultra-sensitive and quantitative proteomics from single cells to post-translational modifications in a compact platform

Mass spectrometry-based proteomics increasingly demands platforms that combine quantitative rigor with the discovery capabilities of accurate mass systems. Here we present the ZenoTOF 8600 system, a compact mass spectrometry system that integrates enhanced ion capture and transmission optics with an optical detection system, Zeno trap-enhanced MS/MS, electron-activated dissociation, and scanning quadrupole data-independent acquisition (ZT Scan DIA). We show that ZT Scan DIA outperforms conventional variable-window DIA (Zeno SWATH DIA) in both identifications and quantitative reproducibility, and demonstrate the platforms versatility across proteomics applications: thousands of protein groups from bulk samples at up to 500 samples per day, single-cell proteomics yielding up to 4,700 proteins, accurate ratio recovery in mixed-species quantitative benchmarks, low-attomole targeted quantitation, and detection of disease-relevant phosphorylation in a Parkinsons disease cellular model using complementary CID and EAD fragmentation. The instruments compact footprint makes it attractive for settings where both analytical breadth and operational robustness are required.

biophysics↗

bioRxiv2025

A Solid-Phase Extraction Capture (SPEC) workflow in nanoliter volumes for fast, robust and ultrasensitive proteomics

Sample preparation remains a critical bottleneck in mass spectrometry (MS)-based proteomics, particularly for limited sample amounts where surface adsorption and dilution cause substantial losses. Here, we present Solid-Phase Extraction Capture (SPEC), a workflow that confines protein processing to nanoliter volumes within ion-exchange or C18 matrix inside a pipette tip. This achieves near-complete proteolysis within 5 minutes instead of hours and maintains full compatibility with strong detergents without cleanup steps, enabling effective lysis of challenging samples. From 200 ng FFPE tissue, SPEC achieves proteome depth and reproducibility exceeding conventional bulk protocols using 100 {micro}g, critical when sample is irreplaceable. The modular two-tip configuration enables on-tip chemical modifications for mTRAQ labeling and fractionation, while integration with enrichment workflows yields 2-fold improved glycopeptide identifications from plasma and 3-fold enhanced ubiquitin remnant identification at low amounts. SPEC enables nanoPhos for cell-type resolved tissue phosphoproteomics and provides a universal platform for proteomics sample preparation.

systems biology↗

bioRxiv2025

nanoPhos enables ultra-sensitive and cell-type resolved spatialphosphoproteomics

Mass spectrometry (MS)-based phosphoproteomics has transformed our understanding of cell signaling, yet current workflows face limitations in sensitivity and spatial resolution at sub-microgram inputs. Here, we present nanoPhos, a robust method that extends phosphoproteomics to nanogram scale, making it compatible with cell-type-resolved spatial analysis. It employs loss-less solid phase extraction capture (SPEC) for sample preparation, followed by automated phosphopeptide enrichment using Fe(III)-NTA cartridges. nanoPhos identifies over 57,000 unique phosphorylation sites from 1 {micro}g cell lysate and over 4,000 from only 10 ng, a hundred-fold improvement from recent protocols. Combined with Deep Visual Proteomics (DVP), it enables region- and cell-type resolved phosphoproteomics of mouse brain tissue with spatial fidelity and a depth of 13,000 phosphosites from only 1000 cell shapes. This establishes nanoPhos as a versatile and ultra-sensitive platform that extends DVP to post-translational modifications and opens up for cell-type-specific signaling analysis in intact tissue.

systems biology↗

bioRxiv2025

DCHS1 Modulates Forebrain Proportions in Modern Humans via a Glycosylation Change

Comparative anatomical studies of primates and extinct hominins, including Neanderthals, show that the modern human brain is characterised by a disproportionately enlarged neocortex relative to the striatum. To explore the molecular basis of this difference, we screened for missense mutations that are unique to modern humans and occur at high frequency and that alter post-translational sites. One such mutation was identified in DCHS1, a protocadherin family gene, and it was found to disrupt an N-glycosylation site in modern humans. Using CRISPR/Cas9-editing we introduced into human-induced pluripotent stem cells (hiPSCs) this ancestral DCHS1 variant present in Neanderthals and other primates, representing the ancestral state before the modern human-specific substitution. Leveraging hiPSCs-derived neural organoids, we observed an expansion of striatal progenitors at the expense of the neocortex, mirroring the anatomical distribution seen in non-human primates. We further identify the ephrin receptor EPHA4 as a binding partner of DCHS1 and show that modern human-specific alterations in DCHS1 modulate EPHA4-ephrin signalling, contributing to a gradual shift in the neocortex-to-striatum ratio - a hallmark of brain organisation in our species.

neuroscience↗

bioRxiv2024

Acute and early stress axis modulation in joint disease permanently reduces pain and emotional comorbidities

Chronic pain affects 20-30% of the population and imposes a significant socio-economic burden as it is often accompanied by substantial emotional comorbidities such as anxiety and depression. Yet, the mechanisms underlying the interactions between the sensory and emotional aspects of chronic pain remain poorly understood. Here, we investigated the role of FKBP51, a regulator of the stress response, in mediating both sensory and emotional symptoms of chronic pain. Inhibition of FKBP51, via genetic deletion or pharmacological blockade, in persistent joint pain reduced fast-onset sensory, functional and activity-related symptoms, as well as late anxio-depressive comorbidities. FKBP51 inhibition after the establishment of the hypersensitive state provided only temporary symptoms relief, while acute inhibition at disease onset protected from the full development of sensory and anxio-depressive symptoms for up to 6 months. Our results also indicated that early pain symptoms could predict the late sensory and emotional outcomes of chronic pain. RNA sequencing of spinal cord tissue revealed that late FKBP51 inhibition transiently altered nociceptive genes associated with mechanical hypersensitivity. In contrast, early inhibition persistently downregulated the Naaa gene, a key regulator of the transition to chronic pain, and reorganized spinal cilia. Our results indicate that early FKBP51 inhibition after injury can persistently reduce chronic pain and prevent the onset of associated emotional comorbidities by modulating critical spinal neurobiological pathways that play pivotal roles in the transition to chronic pain. Significance statementOur study reveals that early inhibition of FKBP51, a modulator in the stress axis, at the onset of joint damage provides sustained pain relief and significantly delays or prevents emotional comorbidities in a sex-dependent manner. In contrast, FKBP51 inhibition initiated after chronic pain is established results in only temporary symptoms improvement. These findings highlight a critical therapeutic window during which timely intervention can prevent the transition from acute to chronic pain. By establishing a predictive link between early therapeutic response and long-term outcomes, this work has important clinical implications for proactive and personalized chronic pain management.

neuroscience↗

bioRxiv2024

AlphaDIA enables End-to-End Transfer Learning for Feature-Free Proteomics

Mass spectrometry (MS)-based proteomics continues to evolve rapidly, opening more and more application areas. The scale of data generated on novel instrumentation and acquisition strategies pose a challenge to bioinformatic analysis. Search engines need to make optimal use of the data for biological discoveries while remaining statistically rigorous, transparent and performant. Here we present alphaDIA, a modular open-source search framework for data independent acquisition (DIA) proteomics. We developed a feature-free identification algorithm particularly suited for detecting patterns in data produced by sensitive time-of-flight instruments. It naturally adapts to novel, more eTicient scan modes that are not yet accessible to previous algorithms. Rigorous benchmarking demonstrates competitive identification and quantification performance. While supporting empirical spectral libraries, we propose a new search strategy named end-to-end transfer learning using fully predicted libraries. This entails continuously optimizing a deep neural network for predicting machine and experiment specific properties, enabling the generic DIA analysis of any post-translational modification (PTM). AlphaDIA provides a high performance and accessible framework running locally or in the cloud, opening DIA analysis to the community.

bioinformatics↗

bioRxiv2023

Involvement of FKBP5, but not of stress, in alcohol memory reconsolidation

Relapse is a fundamental challenge in drug addiction, often evoked by exposure to drug-associated cues. Upon retrieval, memories become temporarily labile before re-stabilizing in a process termed reconsolidation. Therefore, targeting the reconsolidation process offers a therapeutic approach for relapse prevention via the disruption of the drug-cue memories. We recently demonstrated that retrieval of contextual alcohol memories increased the expression of the mRNA encoding for FK506 binding protein 51 (FKBP51), a regulator of the hypothalamic-pituitary-adrenal (HPA) axis. Here, we explored the role of the HPA axis, and FKBP5/FKBP51 in particular, in the reconsolidation of alcohol memories. We found that the FKBP51 inhibitor SAFit2 given before alcohol-memory retrieval using contextual cues prevented the extinction of alcohol place preference behavior in female mice, suggesting that this protein may play a role in cognitive flexibility in a sex-dependent manner. Conversely, the retrieval of alcohol memories using an odor-taste cue did not affect Fkbp5 expression in rats with a history of chronic alcohol consumption, suggesting that FKBP5 may play a differential role in different alcohol-associated memories. In addition, we provide evidence for HPA axis activation following alcohol memory retrieval, by showing that exposure to an alcohol-associated context led to elevated corticosterone secretion. However, we found that the reconsolidation process was unaffected by HPA axis-related manipulations, namely stress exposure, and administration of corticosterone or the glucocorticoid receptors inhibitor, mifepristone. Our results suggest that although FKBP5 can affect cognitive flexibility, and thereby impact the reconsolidation of alcohol memories, this effect is not likely mediated by HPA axis-related mechanisms.

neuroscience↗