Biology subjects

Madl, T.

Publications and source records attributed to Madl, T..

At least 19 recordsLinked to original sources

bioRxiv2026

A metabolic perspective on eIF1A and eIF3B inhibition as a potential therapeutic strategy in psoriasis

Psoriasis is a chronic inflammatory skin disease marked by epidermal hyperplasia and distinct metabolic alterations. Here, we investigated the metabolic impact of targeting translation initiation factors by performing 1H NMR-based metabolomic profiling on polar skin extracts from imiquimod-induced (IMQ) and K5.TGF{beta}1 transgenic (TGF{beta}) mouse models treated with eIF1A or eIF3B siRNA. IMQ-treated skin demonstrated significant, human-like metabolic shifts, including depleted energy substrates (glucose, glycogen, 3-hydroxybutyrate) and elevated phospholipid/nucleotide markers, which correlated strongly with epidermal thickness. In contrast, TGF{beta} skin exhibited no broad baseline polar metabolome changes. eIF1A/eIF3B inhibition selectively attenuated IMQ-associated energy and phospholipid alterations without causing widespread metabolic disruption in TGF{beta} skin. Overall, eIF1A/eIF3B inhibition ameliorated psoriasis-like pathology and mitigated disease-associated metabolic demands in a context-dependent manner.

molecular biology↗

bioRxiv2026

A histidine switch controls the pH-responsive self-assembly of a helical protein filament

Self-assembling helical protein filaments underlie diverse biological processes, from signaling pathways to cell motility. Encoding tunable self-assembly into the sequences of filamentous proteins remains a major challenge. Here, we discovered that the caspase-9 CARD can natively self-assemble into helical filaments in a pH-regulated manner. We defined the determinants of filament assembly using an integrative structural, biophysical, and computational approach. Using NMR spectroscopy, we found that the protonation of a single histidine residue near an N-terminal helix dipole, H38, regulates the pH-dependent self-assembly process. Charge-altering mutations at this site tune thermodynamic stability and filament self-assembly across solution and pH conditions. We solved 3.3- and 3.5-[A] cryo-EM structures of the wild-type and H38R filaments, respectively, which show H38 positioned directly at a filament interface. Molecular dynamics simulations show that H38 functions as a molecular switch, whereby protonation rotates its positively charged side-chain toward solvent and away from the partial-positive charge at the N-terminal helix dipole. This reflects a fine balance between stabilizing intermolecular association and a destabilizing intramolecular electrostatic clash at the helix dipole. More broadly, across 350 helix-containing protein domains we identified electrostatic contributions to protein stability near helix dipoles by integrating AlphaFold2 predictions with deep mutational scanning data. Together, our results identify a native, pH-sensitive histidine switch that regulates a self-assembling helical protein filament. Our results establish a mechanism by which charge-altering mutations near helical N-termini can be engineered to control side-chain rotamers, protein stability, and self-assembly.

biophysics↗

bioRxiv2026

TDP-43 self-assembly is regulated by its disordered NLS-region

Cytosolic inclusions of the RNA-binding protein TDP-43 are a pathological hallmark of several neurodegenerative diseases, such as amyotrophic lateral sclerosis and frontotemporal dementia. Cellular or animal model systems often use TDP-43 mutated in its nuclear localization signal (NLS) to study its cytosolic mislocalization and aggregation. Here we show that the disordered NLS-region, in particular the basic amino acids, are crucial for self-assembly of full-length TDP-43 across size scales, ranging from small clusters to visible condensates and aggregates. Molecular dynamics simulations and NMR studies suggest that the NLS-region engages in inter-chain interactions with C-terminal aromatic residues as well as RRM1 and NTD interactions. We further demonstrate that a minimal NLS mutation (K82A) preserves TDP-43 condensation in vitro and in cells, while commonly used NLS mutations yield partially or strongly reduced self-assembly behaviors. Our data highlight TDP-43 K82A as ideal model system to study cytosolic TDP-43 aggregation in cell and animal models.

biochemistry↗

bioRxiv2026

Proteome-wide identification and modeling of interactions between transactivation domains and arginine-glycine-rich regions

Transcription factors (TFs) and RNA-binding proteins (RBPs) coordinate gene expression across transcriptional and post-transcriptional layers, yet the principles that govern their direct physical coupling, especially through intrinsically disordered regions, remain unclear. Here we combine proteome-scale interaction mapping, disordered-region annotation, coarse-grained simulations and sequence-based prediction to dissect a prevalent TF-RBP interface mediated by acidic/hydrophobic transactivation domains (TADs) and arginine-glycine-rich (RG/RGG) regions. Network analysis reveals a global enrichment of RBP partners among TF interactions and identifies TF and RBP hubs that bridge transcriptional regulation with RNA-centered pathways. Using a sequence grammar enriched in acidic and aromatic residues, we define 230 RG/RGG-binding TAD-like segments across 190 TFs and we map 1,008 compact RG/RGG regions across 823 RBPs based on proteome-wide motif spacing. Coarse-grained simulations (CALVADOS) of representative TAD-RGG pairs quantify interaction propensities and indicate that association is primarily driven by electrostatic complementarity and charge patterning, with sequence "stickiness" modulating interaction strength. Using a hybrid machine-learning model we predicted simulated interaction strengths from a compact, interpretable set of features and extrapolate these rules to the full combinatorial space, enabling systematic prioritization of candidate TF-RBP couplings. To validate these predictions experimentally, we used NMR titration experiments on a subset of TAD-RGG pairs spanning the predicted affinity range, which showed agreement between predicted affinities and NMR-derived dissociation constants. Together, our results support a predominantly electrostatic mode of association and establish a quantitative framework for identifying and prioritising TF-RBP partnerships, revealing how complementary sequence grammars within disordered regions couple transcriptional regulation to RNA processing and transport.

biophysics↗

bioRxiv2026

The sequence context of RG/RGG motifs determines condensate formation, transportin-1 binding and chaperoning

Intrinsically disordered arginine-glycine-rich (RG/RGG) regions are highly abundant in the eukaryotic proteome. Proteins containing these motifs participate in fundamental cellular processes, including nuclear import, transcriptional regulation, biomolecular condensate formation, and apoptosis. Mutations or dysfunction of RG/RGG proteins have been implicated in neurodegenerative diseases and cancer. Although some RG/RGG proteins have been shown to drive condensate formation, localize to membrane-less organelles, interact with nuclear import receptors, or undergo arginine methylation, these properties are not shared uniformly across the proteome. The considerable diversity in RG/RGG motif length and amino acid composition raises the question of which sequence features determine their functional behaviour. To address this, we conducted a systematic bioinformatics and experimental analysis, combining synthetic and natural peptides with studies on the RNA-binding protein FUS as a model system. Our results reveal that the sequence composition of RG/RGG motifs is a key determinant of their capacity for RNA-mediated condensate formation, stress granule recruitment, and transportin-1-mediated chaperoning and nuclear import. These findings provide new insight into the sequence grammar of disordered RG/RGG regions and how it encodes the multifunctionality of these proteins in cellular regulation.

molecular biology↗

bioRxiv2025

Presenilin-1 controls glucose metabolism and identity of pancreatic beta cells

AbstractPresenilin 1 is an endoplasmic reticulum protein, most known for its role in pathogenesis of familial Alzheimers Disease (AD). Presenilin 1 has been attributed roles in intracellular calcium homeostasis in the brain, as well as in the pancreatic beta cells, where it has been shown to be fundamental for glucose-induced insulin secretion. Functional similarity of presenilin 1 in regulation of intracellular calcium homeostasis in the brain and pancreas prompted us to investigate a prevalent assumption that associates AD and diabetes mellitus. By examining pancreatic islets from AD model mice, we have found deficits in initial phase of glucose-induced calcium signaling and insulin secretion. Furthermore, these transgenic mice showed a tendency towards reduced expression of mature beta cell markers, which was even more pronounced in islets and beta cell lines with a transient knock down of presenilin 1. We demonstrate here that presenilin 1 controls beta cell glycolysis by regulating sub-cellular calcium homeostasis and, in doing so, contributes to preservation of beta cell identity.

cell biology↗

bioRxiv2025

Methanobrevibacter smithii associates with colorectal cancer through trophic control of the cancer bacteriome

The human gut is colonized by trillions of microbes that influence the health of their human host. Whereas many bacterial species have now been linked to a variety of different diseases, the involvement of Archaea in human disease remains elusive. Here we searched for gut archaeal signatures of disease by screening 19 cross-sectional clinical studies comprising more than 1,800 individuals. We found that associations between Archaea and medical disorders are common but highly variable and are dominated by a significant increase of Methanobrevibacter smithii in colorectal cancer (CRC) patients. Metabolic modelling and in vitro co-culture identified distinct mutualistic interactions of M. smithii with CRC-causing bacteria such as Fusobacterium nucleatum, including metabolic enhancement. Metabolomics further revealed archaeal-derived compounds with tumor-modulating properties. This provides the first mechanistic link between human gut archaeome and CRC and highlights its role in modulating health in humans through trophic control of the resident bacteriome.

microbiology↗

bioRxiv2025

A histidine switch regulates pH-dependent filament formation by the caspase-9 CARD

The caspase activation and recruitment domain (CARD) mediates protein-protein interactions in apoptotic and inflammatory signaling pathways. In humans, more than 30 proteins contain a CARD, several of which have been reported to polymerize into helical filaments. Here we found that the CARD from the apoptotic protease caspase-9 (C9CARD) self assembles into filaments in vitro at physiological pH and salt concentrations. The C9CARD more readily polymerizes under low-salt or mildly acidic conditions, suggesting a significant role for electrostatic interactions in mediating filament formation. Using NMR spectroscopy, we determined the pKa of the lone histidine residue, H38, which supports a role for histidine protonation in enhancing filament formation. Indeed, mutation of H38 to introduce a positive (H38R) or negative (H38D) charge, or to remove the pH-dependence of the side chain at this site altogether (H38N), dramatically alters the filament propensity of the domain. Using cryo-election microscopy, we determined 3.4- and 3.2-[A] structures of the wild-type and H38R C9CARD filaments, respectively, which provide new insights into the molecular basis of C9CARD polymerization and its pH dependence via H38.

biophysics↗

bioRxiv2024

Computational metabolic modeling unveils gut microbiomes role in metabolic shifts during murine cancer cachexia

Cancer cachexia is a multifactorial syndrome characterized by involuntary weight loss, muscle wasting, systemic inflammation, and metabolic alterations, affecting up to 87% of pancreatic and gastric cancer patients. Unlike simple starvation, cachexia is driven by metabolic disruption involving both host physiology and the gut microbiome. While microbiome changes in cachexia have been documented, a coherent understanding of how these changes translate into functional metabolic shifts remains elusive. In this study, we combined in vivo fecal and plasma metabolomic analyses with a novel computational microbiome simulation pipeline to identify cachexia-associated microbial metabolites. Using the murine MCA207 tumor line and its cachectic derivative CHX207, we differentiated microbiome changes driven by cachexia from those induced by tumor growth. Our computational tool, McMurGut, a murine-tailored extension of MICOM, enabled simulation of microbial metabolic interactions specific to the mouse microbiome, covering 91% of identified genera. We identified significant abundance changes in 35 microbial genera and corresponding shifts in metabolite production, including reductions in short-chain fatty acids (SCFAs) like acetate and butyrate, alongside increased production of galactose, formate, and propionate. Notably, decreases in SCFA production, particularly by genera such as Faecalibaculum and Dubosiella, correlated with exacerbated cachectic symptoms. Additionally, the elevated production of formate and galactose, primarily by Bacteroides and Lactobacillus, suggested altered fermentation pathways in cachexia, potentially linked to increased mucus degradation. Validation of our computational predictions via NMR metabolomics highlighted key congruencies between predicted and experimentally observed metabolites, supporting the role of microbiome-driven metabolic shifts in cachexia pathology. These findings provide crucial insights into the microbiomes involvement in cachexia and suggest future avenues for therapeutic interventions aimed at modulating microbial taxa and their metabolic outputs to improve patient outcomes.

microbiology↗

bioRxiv2024

Expanding the cultivable human archaeome: Methanobrevibacter intestini sp. nov. and strain Methanobrevibacter smithii GRAZ-2 from human feces

Two mesophilic, hydrogenotrophic methanogens, WWM1085 and M. smithii GRAZ-2 were isolated from human fecal samples. WWM1085 was isolated from an individual in the USA, and represents a novel species with in the genus Methanobrevibacter. M. smithii GRAZ-2 (= DSM 116045) was retrieved from fecal samples of a European, healthy female and represents a novel strain within this genus. Both Methanobrevibacter representatives form non-flagellated, short rods with variable morphologies and the capacity to form filaments. Both isolates showed the typical fluorescence of F420 and methane production. Compared to M. smithii GRAZ-2, WWM1085 did not accumulate formate when grown on H2 and CO2. The optimal growth conditions were at 37{degrees}C, and pH 7. Full genome sequencing revealed a genomic difference of WWM1085 to the type strain of M. smithii PS (type strain; DSM 861), with 93.55% ANI and major differences in the sequence of its mcrA gene (3.3% difference in nucleotide sequence). Differences in the 16S rRNA gene were very minor and thus distinction based on this sequence might not be possible. M. smithii GRAZ-2 was identified as a novel strain within the Methanobrevibacter genus (ANI 99.04 % to M. smithii PS). Due to the major differences of WWM1085 and M. smithii type strain PS in phenotypic, genomic and metabolic features, we propose M. intestini sp. nov. as a novel species with WWM1085 as the type strain (DSM 116060T = CECT 30992).

microbiology↗

bioRxiv2023

IGF2BP1 phosphorylation regulates ribonucleoprotein condensate formation by impairing low-affinity protein and RNA interactions

The insulin-like growth factor 2 mRNA binding protein (IGF2BP1) is a conserved RNA-binding protein that regulates RNA stability, localization, and translation. IGF2BP1 is part of various ribonucleoprotein (RNP) condensates regulating RNA outputs. However, the mechanism that regulates its assembly into condensates remains unknown. Here we found, using proteomics, that IGF2BP1 phosphorylation at S181 in a disordered linker is regulated in a stress-dependent manner. Phosphomimetic mutations in two disordered linkers, S181E and Y396E, modulated RNP condensate formation by IGF2BP1 without impacting its binding affinity for RNA. Intriguingly, the S181E mutant, which lies in linker 1, impaired IGF2BP1 condensate formation in vitro and in cells, whereas a Y396E mutant in the second linker increased condensate size and dynamics. Structural approaches showed that the first linker binds RNAs nonspecifically through its RGG/RG motif, an interaction weakened in the S181E mutant. Notably, linker 2 interacts with IGF2BP1s folded domains and these interactions were partially impaired in the Y396E mutant. Our data reveal how phosphorylation modulates low affinity interaction networks in disordered linkers to regulate RNP condensate formation.

biochemistry↗

bioRxiv2023

Fecal microbiota transplantation (FMT) from healthy and bipolar donors elicits distinct emotional behaviors and gut-brain metabolite profiles in mice

Bipolar disorder (BD) is a chronic mood disorder characterized by recurrent episodes of depression and (hypo-) mania. The gut microbiome is a potential avenue through which metabolic signaling, inflammatory pathways, environmental factors, and genetics influence BD pathogenesis via the gut-brain axis. Fecal microbiota transplantation (FMT) is a powerful translational tool for investigating the connections between the gut microbiome and BD, and there is evidence FMT can transfer affective symptoms of BD from humans to mice. In this study, we compared the behavior, gut-brain metabolomic profiles, and inflammatory marker expression in two groups of adult female C57BL/6J mice, one receiving FMT from a human donor with BD in a mixed episode ( HAM-D = 20, YMRS = 14) and another receiving FMT from a mentally healthy weight and age-matched control donor without BD (HAM-D and YMRS = 0). Here, we demonstrate that mice receiving FMT from individuals with BD had an increased abundance of Bacteroidota and decreased abundances of Parabacteroides merdae and Akkermansia muciniphila associated with altered levels of fecal metabolites, short-chain fatty acids, and related gut hormone expression relative to mice receiving control donor FMT. BD mice also exhibited differential regulation of several metabolites and inflammatory markers in the amygdala, with glycine being the most prominently affected. Furthermore, BD mice displayed increased anxiety-like behavior and decreased sociability, indicating that aspects of the behavioral phenotype of BD are transferable from humans to mice via FMT. Taken together, these findings implicate gut-brain signaling in the physiological and behavioral changes observed in our BD-FMT mouse model.

microbiology↗

bioRxiv2023

Hexokinase 1 forms rings that constrict mitochondria during energy stress

Metabolic enzymes can adapt during energy stress, but the precise mechanisms and consequences of these adaptations remain understudied. Here, we discovered that hexokinase 1 (HK1), a key glycolytic enzyme, clusters into ring-like structures around mitochondria during energy stress. These HK1-rings constrict mitochondria at contact sites with the endoplasmic reticulum (ER) and prevent mitochondrial fission by displacing the dynamin-related protein 1 (Drp1) from mitochondrial constriction sites. Mechanistically, we identified that the lack of ATP and glucose-6-phosphate (G6P) promotes the clustering of HK1. Moreover, we found several mutations that are critical for the formation of HK1-rings. Utilizing these mutations, we could show that HK1-rings keep mitochondria connected and rewire cellular metabolism during energy stress. Our findings highlight that HK1 is a robust energy stress sensor that regulates the shape, connectivity and metabolic activity of mitochondria. Thus, the formation of HK1-rings may affect mitochondrial function in energy stress-related pathologies.

cell biology↗

bioRxiv2022

Increased glycolysis and functional mitochondria fuel acinar-ductal metaplasia in the pancreas

Reprogramming of the cellular metabolism is a hallmark of pancreatic cancer, yet it remains unclear at what stage during carcinogenesis it occurs. Here, we investigated the metabolic requirements for acinar-to-ductal metaplasia (ADM), the first step in pancreatic carcinogenesis. We detected increased glycolytic marker expression in human ADM suggesting that a metabolic switch occurs during ADM formation. We report that this switch was similarly required for ADM formation in different oncogenic mouse models (KRAS, PI3K, and MEK1) and in ligand-induced ADM in mouse wild-type acini. In addition, we show that a functional electron transport chain (ETC), but not mitochondrial ATP production, was essential to ADM formation. We conclude that the ETC provides NAD+ for the de novo synthesis of serine from glycolysis intermediates. Our findings demonstrate that metabolic programming is essential for the initiation of pancreatic carcinogenesis and thus identifies potential targets for metabolic intervention.

cancer biology↗

bioRxiv2021

Fasting reverses drug-resistance in hepatocellular carcinoma through p53-dependent metabolic synergism

Cancer cells voraciously consume nutrients to support their growth, exposing a metabolic vulnerability that can be therapeutically exploited. Here we show in hepatocellular carcinoma (HCC) cells, xenografts, and in patient-derived HCC organoids that fasting can synergistically sensitize resistant HCC to sorafenib. Mechanistically, sorafenib acts non-canonically as an inhibitor of mitochondrial respiration, causing resistant cells to depend on glycolysis for survival. Fasting, through reduction in glucose and impeded AKT/mTOR-signaling, prevents this Warburg shift. Regulating glucose transporter and pro-apoptotic protein expression, p53 is necessary and sufficient for the sorafenib-sensitizing effect of fasting. p53 is also crucial for fasting-mediated improvement of sorafenib efficacy in an orthotopic HCC mouse model. Together, our data suggest intermittent fasting and sorafenib as rational combination therapy for HCC with intact p53 signaling. As HCC therapy is currently severely limited by resistance, these results should instigate clinical studies aimed at improving therapy response in advanced-stage, and possibly even early-stage, HCC. HIGHLIGHTSO_LIFasting sensitizes resistant HCC xenografts and patient-derived organoids to sorafenib C_LIO_LISorafenib-mediated Warburg shift is prevented by glucose limitation upon fasting C_LIO_LIFasting synergistically improves sorafenib efficacy in non-resistant models C_LIO_LIp53 is required for synergism by regulating glucose uptake and apoptosis C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/430545v2_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1c0bf9org.highwire.dtl.DTLVardef@15638b4org.highwire.dtl.DTLVardef@1a4b322org.highwire.dtl.DTLVardef@1ec863a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

Global analysis of protein arginine methylation

Quantitative information about the levels and dynamics of post-translational modifications (PTMs) is critical for an understanding of cellular functions. Protein arginine methylation (ArgMet) is an important subclass of PTMs and is involved in a plethora of (patho)physiological processes. However, due to the lack of methods for global analysis of ArgMet, the link between ArgMet levels, dynamics and (patho)physiology remains largely unknown. We utilized the high sensitivity and robustness of Nuclear Magnetic Resonance (NMR) spectroscopy to develop a general method for the quantification of global protein ArgMet. Our NMR-based approach enables the detection of protein ArgMet in purified proteins, cells, organoids, and mouse tissues. We demonstrate that the process of ArgMet is a highly prevalent PTM and can be modulated by small-molecule inhibitors and metabolites and changes in cancer and during ageing. Thus, our approach enables to address a wide range of biological questions related to ArgMet in health and disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/428036v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@37a0f1org.highwire.dtl.DTLVardef@273ebdorg.highwire.dtl.DTLVardef@87fcd6org.highwire.dtl.DTLVardef@1e84c07_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2020

N-acetylaspartate improves cell survival when glucose is limiting

N-acetylasparate (NAA), previously considered a brain-specific metabolite, is found in several cancers. However, whether it plays a role in tumor growth or survival is not fully understood. We provide evidence that NAA prevents cell death in low-glucose conditions via sustaining intracellular UDP-N-acetylglucosamine (UDP-GlcNac) levels, suppressing endoplasmic reticulum (ER) stress, and enabling continued protein synthesis. NAA production is critical for in vivo tumor growth where lower glucose levels are present than those in cell culture. Furthermore, the breakdown of NAA leads to ER stress and cell death, suggesting that the role of NAA in low-glucose is independent of its catabolism to produce aspartate or acetate. Together, these data suggest NAA can support the growth of some tumors by helping them cope with glucose limitations in vivo. HighlightsEndogenous N-acetylaspartate (NAA) production boosts tumor growth NAA supports cell survival in low glucose via suppressing ER stress Breaking down NAA limits tumor growth and induces ER stress in vivo The role of NAA to rescue low glucose is independent of donating acetate or aspartate In briefCancer cells need N-acetylaspartate to avoid ER stress and cell death when glucose availability is low.

cancer biology↗

bioRxiv2019

Human Milk Oligosaccharides modulate the risk for preterm birth in a microbiome dependent and independent manner

BackgroundPreterm birth is one of the leading causes of neonatal mortality. The causes for spontaneous preterm birth (PTB) are multifactorial and remain often unknown. In this study, we tested the hypothesis that human milk oligosaccharides (HMOs) in blood and urine modulate the maternal urinary and vaginal microbiome and influence the risk for PTB. We analyzed the vaginal and urinary microbiome of a cross-sectional cohort of women with and without preterm labor and correlated our findings with measurements of metabolites and HMOs in urine and blood.\n\nResultsWe identified several microbial signatures associated with short cervix, PTB and/or preterm contractions such as Lactobacillus jensenii, L. gasseri, Ureaplasma sp. and Gardnerella sp.. Additionally, we observed associations between sialylated HMOs, in particular 3-sialyllactose, with PTB, short cervix and increased inflammation and confirmed an influence of HMOs on the microbiome profile.\n\nConclusionsIdentifying serum and urinary HMOs and several key microorganisms associated with PTB, our findings point at two distinct processes modulating the risk for PTB. One process seems to be driven by sterile inflammation, characterized by increased concentrations of sialylated HMOs in serum. Another process might be microbiome-mediated, potentially driven by secretor-active HMOs in urine. Our results support current efforts to improve diagnostics and therapeutic strategies.

microbiology↗