Biology subjects

Froehlich, F.

Publications and source records attributed to Froehlich, F..

At least 19 recordsLinked to original sources

bioRxiv2026

GEMOT: Towards Mechanistic World Models for Biology

Scientific discovery seeks mechanisms that explain observations and predict beyond the measurements that produced them. Whereas large language models (LLMs) encode knowledge implicitly, mechanistic world models organise it as a parsimonious set of explicit, modular, reusable mechanisms whose predictions can be scored against data. In biology, where measurements are sparse and noisy, mechanistic world modelling must discover latent states and governing equations jointly, yet the prior knowledge that could constrain this search is largely unstructured. We introduce gemot, an agentic framework for mechanistic world modelling, and evaluate it on 18 published biological problems spanning molecular biology, epidemiology, and immune-cell differentiation, with up to 1,755 training measurements, 65 observables, 170 experimental conditions, and 3 data modalities per problem. gemot is auditable by construction: a semantic layer records each hypothesis, and a Model Context Protocol layer separates hypothesis formulation from numerical evaluation, so hypothesis scoring cannot be fabricated. On every problem, autonomously constructed models match or exceed the reference models in fit and parsimony, and generalise where held-outs exist. We demonstrate that gemot can formulate novel, biologically plausible mechanistic hypotheses. This work will enable decoding of interventional biological data into competing mechanistic hypotheses and design experiments that distinguish between them, and may serve as a blueprint for mechanistic world modelling in other domains.

systems biology↗

bioRxiv2026

Cholesterol transport cycle of human ABCA2

Cholesterol is a key component of cellular membranes and is critical for brain function, particularly axon myelination. Among the 48 human ATP-binding cassette (ABC) transporters, ABCA2 exhibits the highest expression in the brain and is involved in cholesterol metabolism, primarily in oligodendrocytes. Notably, ABCA2 has been associated with myelin sheath integrity and maintenance, as well as Alzheimer's disease. Here, we report cryo-EM structures of human ABCA2 that reveal critical endogenous lipid-binding sites unique to ABCA2. Our five distinct conformations include a previously uncharacterized intermediate between the closed and apo states of ABCA subfamily transporters. Most importantly, we elucidated the cholesterol transport mechanism of ABCA2, which involves novel interdependent rotations of the exocytoplasmic domains (ECDs) and regulatory domains (RDs). Our structural findings provide a new perspective on ABCA transporter function and highlight the role of ABCA2 in facilitating efficient cholesterol recycling and transport in the brain.

molecular biology↗

bioRxiv2026

Deep Mechanistic Models reveal pathway-extrinsic drivers of mammary MAPK signalling heterogeneity

Cells sense and respond to their environment through signalling pathways, and the dynamics of these pathways shape cell fate even within genetically identical populations. Two largely separate computational traditions describe this behaviour: mechanistic differential-equation models and representation-learning methods. Mechanistic models encode pathway topology and kinetics but cannot easily represent variation arising outside the modelled pathway. Representation learning, instead, maps genome-wide measurements onto low-dimensional manifolds but offers no mechanistic account of how the resulting cell states execute their functions. Reconciling these views, explaining signalling heterogeneity in a manner that is at once data-driven and mechanistically interpretable, has remained difficult. Here we introduce deep mechanistic models (DMMs), which couple semi-supervised representation learning to an ordinary-differential-equation model of EGFR/MAPK signalling, trained end-to-end so that the learnt representation and mechanistic parametrisation inform each other. Applying DMMs to multiplexed signalling data from 63 breast cancer cell lines, we show that the models generalise to held-out cell lines and attribute most heterogeneity to pathway-extrinsic factors, namely baseline ERBB2 activation and a Ca{superscript 2}/p38 signalling axis, rather than to variation in core MAPK components. Where the models fail, the discrepancies pinpoint rare signalling-altering mutations and recurrent programmes, including a putative AMPK- BRAF MEK-inhibitor-resistance axis and a cytoskeletal programme. We further find that mechanistic integration of EGFR receptor levels reshapes the learnt representation, rendering a molecular and a systems-level account of the same data equivalent in predictive power. DMMs thus offer a general framework for fusing mechanism with learning, naturally extendable to further modalities such as imaging, and simultaneously turn model failure into a systematic route to discover and evaluate candidate biology.

systems biology↗

bioRxiv2026

Nonlinear mixed-effect models and tailored parametrization schemes enables integration of single cell and bulk data

Experimental methods for characterizing single cells and cell populations have improved tremendously over the past decades. This progress has enabled the development of quantitative, mechanistic models for cellular processes based on either single cell or bulk data. However, coherent statistical frameworks for the model-based integration of different data types at the single-cell and population levels are still missing. In this work, we present a mathematical modeling approach for integrating single-cell time-lapse, single-cell snapshot, single-cell time-to-event and population-average data. Utilizing a formulation based on nonlinear mixed-effect modeling, we enable the description of multiple data types, with and without single-cell resolution, and we propose a tailored parameter estimation method. Furthermore, we propose a tailored parameter estimation scheme that facilitates the assessment of underlying process parameters. Our study demonstrates that the proposed approach can reliably integrate diverse data types, thereby improving parameter identifiability and prediction accuracy. Applying this framework of extrinsic apoptosis reveals that simultaneously considering multiple data types can be essential, particularly when experimental constraints limit data availability. The proposed approach is broadly applicable and may significantly advance our understanding of complex biological processes.

systems biology↗

bioRxiv2025

VPS13C/PARK23 initiates lipid transfer and membrane remodeling for efficient lysosomal repair

Perturbations in lysosome integrity are tightly linked to neurological disorders and ageing, but the underlying pathogenic mechanisms are incompletely understood. Using an unbiased proteomic approach, we here identified the bridge-like lipid transport protein VPS13C/PARK23 as a key component of a global early response pathway to lysosome damage. VPS13C readily binds lysosomes under mechanical or osmotic tension in anticipation of membrane lesions. The latter trigger a conformational change in the proteins C-terminus, involving its ATG2C domain acting as sensor of damage-induced lipid packing defects. We show that ER-lysosome contacts formed by VPS13C provide critical binding platforms for OSBP/ORPs to enable efficient ER wrapping of damaged lysosomes. A chemical approach to assess directional ER-to-lysosome lipid transport revealed that VPS13C is essential for large-scale lipid delivery to acutely damaged lysosomes to facilitate their repair. Our findings offer new mechanistic insights into how loss-of-function mutations in VPS13C may enhance the risk of Parkinsons disease.

cell biology↗

bioRxiv2024

Steric Repulsion Counteracts ER-to-Lipid Droplet Protein Movement

Lipid droplets (LDs) are uniquely shaped organelles consisting of a neutral lipid core surrounded by a phospholipid monolayer, continuous with the cytosolic leaflet of the endoplasmic reticulum (ER). The dynamics and function of LDs are closely tied to their proteome composition, which is subject to dynamic remodeling. Key proteins essential for LD biology relocate from the ER to LDs, yet the mechanisms governing their movement and accumulation in LDs remain poorly understood. Here, we developed an innovative ex vivo tool to quantify and classify ER proteins based on their affinity for LDs. We found a broad spectrum of ER-to-LD partitioning affinities. We identified steric hindrance as a key factor in regulating ER-to-LD protein transfer, where proteins with only slightly higher LD affinity can effectively displace those with lower affinity from the LD surface. Consistent with this model, we observed that differentiation of 3T3 pre-adipocytes into adipocytes involves extensive remodeling of ER proteins targeting LDs, with Plin1--a high-affinity LD protein--becoming predominantly recruited and excluding other ER proteins. These findings highlight lateral protein-protein exclusion as a fundamental mechanism in shaping the LD proteome, providing new insights into LD biogenesis and function.

biophysics↗

bioRxiv2023

Structure of the endosomal CORVET tethering complex

Cells depend on their endolysosomal system for nutrient uptake and downregulation of plasma membrane proteins. These processes rely on endosomal maturation, which requires multiple membrane fusion steps. Early endosome fusion is promoted by the Rab5 GTPase and its effector, the hexameric CORVET tethering complex, which is homologous to the lysosomal HOPS. How these related complexes recognize their specific target membranes remains entirely elusive. Here, we solved the structure of CORVET by cryo-electron microscopy and revealed its minimal requirements for membrane tethering. As expected, the core of CORVET and HOPS resembles each other. However, the function-defining subunits show marked structural differences. Notably, we discovered that unlike HOPS, CORVET depends not only on Rab5 but also on phosphatidylinositol-3-phosphate (PI3P) and membrane packaging defects for tethering, implying that an organelle-specific membrane code enables fusion. Our data suggest that both shape and membrane interactions of CORVET and HOPS are conserved in metazoans, thus providing a paradigm how tethering complexes function. One-Sentence SummaryUsing cryo-EM, we solved the structure of the CORVET tethering complex and explained how it promotes endosome fusion.

biochemistry↗

bioRxiv2023

Complex Sphingolipid Profiling and Identification of an Inositol Phosphorylceramide Synthase in Dictyostelium discoideum

Dictyostelium discoideum is a professional phagocyte frequently used as experimental model to study cellular processes underlying the recognition, engulfment and infection course of microbial pathogens. Sphingolipids are abundant components of the plasma membrane that bind cholesterol, control vital membrane properties, participate in signal transmission and serve as adhesion molecules in recognition processes relevant to immunity and infection. While the pathway of sphingolipid biosynthesis has been well characterized in plants, animals and fungi, the identity of sphingolipids produced in D. discoideum, an organism at the crossroads between uni- and multicellular life, is not known. Combining lipidomics with a bioinformatics-based cloning strategy for key sphingolipid biosynthetic enzymes, we show here that D. discoideum produces phosphoinositol-containing sphingolipids with predominantly phytoceramide backbones. Cell-free expression of candidate inositol-phosphorylceramide (IPC) synthases from D. discoideum in defined lipid environments enabled identification of an enzyme that selectively catalyses the transfer of phosphoinositol from phosphatidylinositol onto ceramide. The corresponding IPC synthase, DdIPCS1, is non-homologous to but shares multiple sequence motifs with yeast IPC and human sphingomyelin synthases and localizes to the Golgi apparatus as well as the contractile vacuole of D. discoideum. Collectively, these findings open up important opportunities for exploring a role of sphingolipids in phagocytosis and infection across major evolutionary boundaries.

cell biology↗

bioRxiv2023

Ferroptosis-Protective Membrane Domains in Quiescence

Quiescence is a common cellular state, required for stem-cell maintenance and microorganismal survival under stress conditions or starvation. However, the mechanisms promoting quiescence maintenance remain poorly known. Plasma membrane components segregate into distinct microdomains, yet the role of this compartmentalization in quiescence remains unexplored. Here, we show that Flavodoxin-like proteins (FLPs), ubiquinone reductases of the yeast eisosome membrane compartment, protect quiescent cells from lipid peroxidation and ferroptosis. Eisosomes and FLPs expand specifically in respiratory-active quiescent cells, and mutants lacking either show accelerated aging, defective quiescence maintenance, and accumulate peroxidized phospholipids with monounsaturated or polyunsaturated fatty acids (PUFA). FLPs are essential for the extra-mitochondrial regeneration of the lipophilic antioxidant ubiquinol. FLPs, alongside the Gpx1/2/3 glutathione peroxidases, prevent iron-driven, PUFA-dependent ferroptotic cell death. Our work is the first description of ferroptosis-protective mechanisms in yeast and introduces plasma membrane compartmentalization as an important factor for the long-term survival of quiescent cells.

cell biology↗

bioRxiv2022

Structure of the lysosomal membrane fusion machinery

Lysosomes are of central importance in cellular recycling, nutrient signaling 1,2 and endocytosis, and are tightly connected to autophagy 3 and the invasion of pathogenic bacteria and viruses 1,4. Lysosomal fusion events are fundamental to cell survival and require HOPS, a conserved heterohexameric tethering complex 5,6. HOPS recognizes and binds small membrane-associated GTPases on lysosomes and organelles, and assembles membrane bound SNAREs for fusion 7,8. Through tethering, HOPS brings membranes in close proximity to each other and significantly increases fusion efficacy by catalysing SNARE assembly. Consequently, different HOPS mutations are causative for severe diseases 6. Despite its fundamental cellular duties, it remained speculative how HOPS fulfils its function as high-resolution structural data were unavailable. Here, we used cryo-electron microscopy to reveal the structure of HOPS. In the complex, two central subunits form the backbone and an assembly hub for the functional domains. Two GTPase binding units extend to opposing ends, while the SNARE binding module points to the side, resulting in a triangular shape of the complex. Unlike previously reported, HOPS is surprisingly rigid and extensive flexibility is confined to its extremities. We show that HOPS complex variants with mutations proximal to the backbone can still tether membranes but fail to efficiently promote fusion indicating, that the observed integrity of HOPS is essential to its function. In our model, the core of HOPS acts as a counter bearing between the flexible GTPase binding domains. This positions the SNARE binding module exactly between the GTPase anchored membranes to promote fusion. Our structural and functional analysis reveals the link between the spectacular architecture of HOPS and its mechanism that couples membrane tethering and SNARE assembly, to catalyse lysosomal fusion.

biophysics↗

bioRxiv2022

Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance

BRAFV600E is prototypical of oncogenic mutations that can be targeted therapeutically and treatment of BRAF-mutant melanomas with RAF and MEK inhibitors results in rapid tumor regression. However, drug-induced rewiring causes BRAFV600E melanoma cells to rapidly acquire a drug-adapted state. In patients this is thought to promote acquisition or selection for resistance mutations and disease recurrence. In this paper we use an energy-based implementation of ordinary differential equations in combination with proteomic, transcriptomic and imaging data from melanoma cells, to model the precise mechanisms responsible for adaptive rewiring. We demonstrate the presence of two parallel MAPK (RAF-MEK-ERK kinase) reaction channels in BRAFV600E melanoma cells that are differentially sensitive to RAF and MEK inhibitors. This arises from differences in protein oligomerization and allosteric regulation induced by oncogenic mutations and drug binding. As a result, the RAS-regulated MAPK channel can be active under conditions in which the BRAFV600E-driven channel is fully inhibited. Causal tracing demonstrates that this provides a sufficient quantitative explanation for initial and acquired responses to multiple different RAF and MEK inhibitors individually and in combination. HighlightsO_LIA thermodynamic framework enables structure-based description of allosteric interactions in the EGFR and MAPK pathways C_LIO_LICausal decomposition of efficacy of targeted drugs elucidates rewiring of MAPK channels C_LIO_LIModel-based extrapolation from type I[1/2] RAF inhibitors to type II RAF inhibitors C_LIO_LIA unified mechanistic explanation for adaptive and genetic resistance across BRAF-cancers C_LI

systems biology↗

bioRxiv2021

LyTS: A Lysosome Localized Complex of TMEM192 and STK11IP

The degradative and signaling functions of lysosomes are dependent on numerous peripherally associated proteins. Targeting of lysosomes to sites of need is controlled by adaptors that link lysosomes to both dynein and kinesin motors. SKIP is one such adaptor that promotes microtubule plus-end-directed movement through its interaction with Arl8 on the lysosome surface and kinesin-1. Sequence homology between SKIP and STK11IP (also known as LIP1) led us to investigate a potential role for STK11IP at lysosomes. After first establishing that STK11IP localizes to lysosomes, we identified TMEM192, an abundant lysosomal integral membrane protein, as the major binding partner of STK11IP and demonstrated that STK11IP depends on TMEM192 for both its lysosome localization as well as its stability. Depletion studies furthermore support a role for these proteins in the control of lysosome homeostasis. Collectively, these new results define a lysosome localized complex of TMEM192 and STK11IP that we have named LyTS ("lights").

cell biology↗

bioRxiv2021

A yeast lysosomal biogenesis map uncovers the cargo spectrum of lysosomal protein targeting pathways

The lysosome is the major catabolic organelle and a key metabolic signaling center of the cell. Mutations in lysosomal proteins can have catastrophic effects, causing neurodegeneration, cancer, and age-related diseases. The vacuole is the lysosomal analog of Saccharomyces cerevisiae that harbors many conserved proteins. Vacuolar proteins reach their destination via the endosomal vacuolar protein sorting (VPS) pathway, via the alkaline phosphatase (ALP or AP-3) pathway, and via the cytosol-to-vacuole transport (CVT) pathway. While these pathways have been extensively studied, a systematic understanding of the cargo spectrum of each pathway is completely lacking. Here we combine quantitative proteomics of purified vacuoles with mutant analyses to generate the lysosomal biogenesis map. This dataset harbors information on the cargo-receptor relationship of virtually all vacuolar proteins. We map binding motifs of Vps10 and the AP-3 complex and identify a novel cargo of the CVT pathway under nutrient-rich conditions. Our data uncover how organelle purification and quantitative proteomics can uncover fundamental insights into organelle biogenesis.

cell biology↗

bioRxiv2021

Fides: Reliable Trust-Region Optimization for Parameter Estimation of Ordinary Differential Equation Models

Ordinary differential equation (ODE) models are widely used to describe biochemical processes, since they effectively represent mass action kinetics. Optimization-based calibration of ODE models on experimental data can be challenging, even for low-dimensional problems. However, reliable model calibration is a prerequisite for uncertainty analysis, model comparison, and biological interpretation. Multiple hypotheses have been advanced to explain why optimization based calibration of biochemical models is challenging, but there are few comprehensive studies that test these hypotheses, likely because tools for performing such studies are also lacking. We implemented an established trust-region method as a modular Python framework (fides) to enable systematic comparison of different approaches to ODE model calibration involving various Hessian approximation schemes. We evaluated fides on a set of benchmark problems for which real experimental data are available. Unexpectedly, we observed high variability in optimizer performance among different implementations of the same algorithm. Overall, fides performed most reliably and efficiently. Our investigation of possible sources of poor optimizer performance identified drawbacks in the widely used Gauss-Newton, BFGS and SR1 Hessian approximations. We address these drawbacks by proposing a novel hybrid Hessian approximation scheme that enhances optimizer performance and outperforms existing hybrid approaches. We expect fides to be broadly useful for ODE constrained optimization problems and to enable future methods development. Availabilityfides is published under the permissive BSD-3-Clause license with source code publicly available at https://github.com/fides-dev/fides. Citeable releases are archived on Zenodo. Code to reproduce results presented in this manuscript is available at https://github.com/fides-dev/fides-benchmark.

systems biology↗

bioRxiv2020

Combination Treatment Optimization Using aPan-Cancer Pathway Model

The design of efficient combination therapies is a difficult key challenge in the treatment of complex diseases such as cancers. The large heterogeneity of cancers and the large number of available drugs renders exhaustive in vivo or even in vitro investigation of possible treatments impractical. In recent years, sophisti-cated mechanistic, ordinary differential equation-based pathways models that can predict treatment responses at a molecular level have been developed. However, surprisingly little effort has been put into leveraging these models to find novel therapies. In this paper we use for the first time, to our knowledge, a large-scale state-of-the-art pan-cancer signaling pathway model to identify potentially novel combination therapies to treat individual cancer cell lines from various tissues (e.g., minimizing proliferation while keeping dosage low to avoid adverse side effects) and populations of cancer cell lines (e.g., minimizing the maximum or average proliferation across the cell lines while keeping dosage low). We also show how our method can be used to optimize the mixtures and dosages used in sequential treatment plans--that is, optimized sequences of potentially different drug combinations--providing additional benefits. In order to solve the treatment optimization problems, we combine the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) algorithm with a significantly more scalable sampling scheme for truncated Gaussian distributions, based on a Hamiltonian Monte-Carlo method. These optimization techniques are independent of the signaling pathway model, and can thus be used for other signaling pathway models also, provided that a suitable predictive model is available.

systems biology↗

bioRxiv2020

Phosphorylation of the GARP Subunit Vps53 by Snf1 Leads to the Formation of a Golgi-Mitochondria Contact Site (GoMiCS) in Yeast

The canonical function of the Golgi-associated retrograde protein (GARP) complex is the tethering of transport carriers. GARP belongs to the complexes associated with tethering containing helical rods (CATCHR) family and is a hetero-tetrameric complex consisting of the subunits Vps51, Vps52, Vps53 and Vps54. How the activity of GARP is regulated and if it possesses other functions besides tethering remains largely unknown. Here we identify the GARP subunit Vps53 as a novel regulatory target of the S. cerevisiae AMP kinase (AMPK) homolog Snf1. We find that Vps53 is both an in vivo and in vitro target of Snf1 and show that phosphorylation depends on the nature and quantity of the available carbon source. Phosphorylation of Vps53 does not affect the canonical trafficking pathway, but results in altered mitochondrial dynamics and the formation of a previously unknown contact site between the Golgi apparatus and mitochondria, termed GoMiCS. Our results provide an example of a subunit of a CATCHR complex with a constitutive function in membrane trafficking and an inducible role in organelle contact site formation. We anticipate our results to be the starting point for the characterization of this novel contact site.

cell biology↗

bioRxiv2020

Multiple roles for the ESCRT machinery in maintaining plasma membrane homeostasis

The endosomal sorting complexes required for transport (ESCRT) execute evolutionary conserved membrane remodeling processes. Here we used budding yeast to explore how the ESCRT machinery contributes to plasma membrane (PM) homeostasis. In response to reduced membrane tension and inhibition of the target of rapamycin complex 2 (TORC2), ESCRT-III/Vps4 assemblies form at the PM and help to maintain membrane integrity. Conversely, the growth of ESCRT mutants strongly depends on TORC2-mediated homeostatic regulation of sphingolipid (SL) metabolism. This is caused by calcineurin phosphatase activity which causes Orm2 to accumulate at the endoplasmic reticulum (ER) in ESCRT mutants. Orm2 is a repressor of SL biosynthesis and its accumulation provokes increased membrane stress. This necessitates TORC2 signaling through its downstream kinase Ypk1 to control Orm2 protein levels and prevent a detrimental imbalance of SL metabolism. Our findings reveal new aspects of antagonistic calcineurin/TORC2 signaling for the regulation of SL biosynthesis and the maintenance of PM homeostasis, and suggest that the ESCRT machinery contributes directly and indirectly to these processes.

cell biology↗

bioRxiv2019

Sporadic ERK pulses drive non-genetic resistance in drug-adapted BRAFV600E melanoma cells

Anti-cancer drugs commonly target signal transduction proteins activated by mutation. In patients with BRAFV600E melanoma, small molecule RAF and MEK kinase inhibitors cause dramatic but often transient tumor regression. Emerging evidence suggests that cancer cells adapting by non-genetic mechanisms constitute a reservoir for the development of drug-resistant tumors. Here, we show that few hours after exposure to RAF/MEK inhibitors, BRAFV600E melanomas undergo adaptive changes involving disruption of negative feedback and sporadic pulsatile reactivation of the MAPK pathway, so that MAPK activity is transiently high enough in some cells to drive proliferation. Quantitative proteomics and computational modeling show that pulsatile MAPK reactivation is possible due to the co-existence in cells of two MAPK cascades: one driven by BRAFV600E that is drug-sensitive and a second driven by receptors that is drug-resistant. Paradoxically, this may account both for the frequent emergence of drug resistance and for the tolerability of RAF/MEK therapy in patients.

cancer biology↗