Biology subjects

Kasparek, P.

Publications and source records attributed to Kasparek, P..

10 recordsLinked to original sources

bioRxiv2026

Open or closed? Exploring the conformational heterogeneity of human plasminogen across multiple resolution scales

Plasminogen (Plg), the zymogen of the fibrinolytic protease plasmin, is a multidomain, conformationally-rich protein that plays a crucial role in targeted thrombolysis for stroke and heart attack treatments. Yet, the conformational state that affects binding to Plg activators and fibrinolytic activity is rarely validated, contributing to poor reproducibility and failures in drug development. Here, we establish a structural biology workflow to characterize human Plg suspended in an aqueous solution, preserving it in a near-native state and eliminating the need for crystal growth. Two variants, cleavage-resistant Plg-RV (R561A) and catalytically inactive Plg-CAT (S741A), were expressed in mammalian cells. Both variants were correctly folded and stable (Tm {approx} 60.6{degrees}C) and, unlike commercial plasma-derived Plg, were resistant to staphylokinase-mediated activation. Small-angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry revealed substantial conformational heterogeneity. The recombinantly-produced Plg variants adopted a closed conformation, exhibiting a good fit to the closed structure determined by X-ray diffraction. Conversely, the plasma-derived Plg populated an extended, open-like state. Cryo-EM analysis of the Plg-RV variant yielded a 4.4 [A] resolution map, and a rigid-body-fitted model revealed the closed-state architecture. Our findings demonstrate that rigorous structural validation of Plg is essential for future functional studies and rational development of next-generation thrombolytic agents.

biochemistry↗

bioRxiv2026

The pseudoproteinase iRhom2 critically promotes acute lung inflammation

ADAM17 sheds cell surface molecules such as TNF-, IL-6R and L-selectin. This activity requires either iRhom1 or iRhom2 as adapter molecules. Since iRhom2 is predominantly expressed in leukocytes and upregulated in tissue cells during inflammation, it represents a potential anti-inflammatory target. We therefore investigated the effects of iRhom2 deficiency in mice using in vivo, ex vivo, and in vitro models of acute inflammation. In an in vivo model of LPS-induced lung inflammation, iRhom2 knockout mice showed reduced neutrophil recruitment into the bronchoalveolar space. Notably, the few recruited neutrophils remained L-selectin positive, whereas most neutrophils in wildtype mice were L-selectin negative, confirming that L-selectin shedding depends on the iRhom2/ADAM17 axis. Furthermore, it suggests that impaired shedding is associated with decreased neutrophil recruitment. Additionally, ADAM17-dependent release of TNF- and IL-6R into the alveolar space was diminished in the absence of iRhom2, accompanied by reduced expression of inflammatory mediators. In isolated perfused lungs challenged with LPS, iRhom2 deficiency similarly reduced inflammatory mediator production, indicating a role for iRhom2 in resident lung tissue cells during the initiation of inflammation. To specifically assess immune cell responses, we further examined macrophages, the sole resident immune cells in the lung. In vitro, LPS-stimulated bone marrow derived macrophages lacking iRhom2 showed decreased shedding of TNF- and IL-6R and reduced induction of secondary inflammatory mediators. Thus, targeting iRhom2 effectively suppresses ADAM17-mediated inflammatory responses in the lung, while preserving basal ADAM17 activity through iRhom1, offering a more selective therapeutic strategy with fewer side effects. HighlightsO_LIThe ADAM17 adapter molecule iRhom2 is required for the acute lung inflammation of mice in vivo including cytokine response and neutrophil recruitment. C_LIO_LIIn resident lung tissue cells iRhom2 promotes the LPS induced inflammatory response at the alveolar interface. C_LIO_LIIn macrophages iRhom2 is required for an effective ADAM17 dependent inflammatory response to LPS. C_LIO_LIThus, iRhom2 targeting can serve to suppress inflammatory activities of ADAM17 in the lung. C_LI Graphical AbstractSchematic overview depicting the role of the iRhom2-ADAM17 axis in mediating neutrophil infiltration and cytokine release during induced pulmonary inflammation, serving as a model for acute lung injury (ALI). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/730404v1_ufig1.gif" ALT="Figure 1"> View larger version (74K): org.highwire.dtl.DTLVardef@d7edc9org.highwire.dtl.DTLVardef@3c4654org.highwire.dtl.DTLVardef@12d36f8org.highwire.dtl.DTLVardef@173dc97_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

Fibrin Selective Alteplase with Improved Thrombolysis and Inhibition Resistance Engineered by Rational Design

Thrombolytic enzymes represent an important class of proteolytic biocatalysts for medical applications, yet currently used FDA-approved variants, including alteplase and tenecteplase, remain limited by suboptimal catalytic efficiency, off-target activity, and susceptibility to inhibition. These limitations reflect the complexity of enzyme function in physiological environments, where therapeutic performance depends on the simultaneous optimization of multiple catalytic and biophysical properties. Here, we introduce a multi-objective enzyme engineering strategy for the design of next-generation thrombolytic proteases, explicitly targeting multiple properties required for therapeutic performance. Our approach combines computer-aided design, evolutionary reconstruction, and literature-guided mutation selection to improve catalytic activity, fibrin selectivity, inhibition resistance, and functional lifetime within a single workflow. This framework is coupled with systematic biochemical characterization, in vitro evaluation of clot penetration and fibrinolytic activity, and in vivo validation of efficacy and safety. By addressing multiple performance parameters simultaneously, this strategy enables efficient navigation of trade-offs that typically limit enzyme optimization. Using this approach, we identify Brnoteplase as a lead variant with enhanced fibrin selectivity, improved resistance to inhibition, and superior clot penetration, resulting in increased effective catalytic lifetime and enabling bolus administration. In vivo studies demonstrate enhanced thrombolysis and recanalization with reduced hemorrhagic complications. These findings provide a broadly applicable framework for designing proteolytic biocatalysts suitable for complex biological environments.

biochemistry↗

bioRxiv2025

Claudin 1-mediated positioning of DC1 to mTECs is essential for antigen transfer-coupled DC1 maturation and maintenance of central tolerance

The mechanisms of central tolerance, which rely on the presentation of self-antigens by medullary thymic epithelial cells (mTECs) and DCs, prevent autoimmunity by eliminating self-reactive T-cells. While mTECs produce self-antigens in an autonomous manner, DCs acquire them from mTECs via cooperative antigen transfer (CAT). Our recent data showed that preferential pairing occurs between distinct subsets of mTECs and DCs in CAT, providing a rationale for the existence of molecular determinants which control such pairing and the outcome of central tolerance. Here, we compared the transcriptomes of CAT-experienced and -inexperienced DCs and identified Claudin 1 as a molecule involved in CAT-coupled type 1 DC (DC1) maturation. By mapping thymic DC1 heterogeneity, we identified their early and late maturation states. DC1-specific ablation of Claudin 1 led to a reduction in CAT-experienced late mature DC1s and hampered DC1 maturation. These phenotypes correlated with the displacement of DC1s from the vicinity of mTECs. This translated into impaired Treg selection and clonal deletion of TRA-specific T-cells manifested via a break in tolerance and symptoms of multi-organ autoimmunity. Collectively, our results identify thymic DC1-derived Claudin 1 as a regulator of immune tolerance. One Sentence SummaryThe expression of Claudin 1 on type 1 dendritic cells regulates their proximity to mTECs, which is required for effective antigen transfer coupled with DC1 maturation and establishment of T-cell tolerance.

immunology↗

bioRxiv2023

Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains

A key aspect of nutrient absorption is the exquisite division of labor across the length of the small intestine, with individual classes of micronutrients taken up at different positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum, and ileum. By examining fine-scale longitudinal segmentation of the mouse and human small intestines, we identified transcriptional signatures and upstream regulatory factors that define five domains of nutrient absorption, distinct from the three traditional sections. Spatially restricted expression programs were most prominent in nutrient-absorbing enterocytes but initially arose in intestinal stem cells residing in three regional populations. While a core signature was maintained across mice and humans with different diets and environments, domain properties were influenced by dietary changes. We established the functions of Ppar- and Cdx1 in patterning lipid metabolism in distal domains and generated a predictive model of additional transcription factors that direct domain identity. Molecular domain identity can be detected with machine learning, representing the first systematic method to computationally identify specific intestinal regions in mice. These findings provide a foundational framework for the identity and control of longitudinal zonation of absorption along the proximal:distal small intestinal axis.

genomics↗

bioRxiv2021

Comprehensive transcriptional profiling and mouse phenotyping reveals dispensable role for adipose tissue selective long noncoding RNA Gm15551

1Cold and nutrient activated brown adipose tissue (BAT) is capable of increasing systemic energy expenditure via uncoupled respiration and secretion of endocrine factors thereby protecting mice against diet-induced obesity and improving insulin response and glucose tolerance in men. Long non-coding RNAs (lncRNAs) have recently been identified as fine tuning regulators of cellular function. While certain lncRNAs have been functionally characterised in adipose tissue, their overall contribution in the activation of BAT remains elusive. We identified lncRNAs correlating to inter-scapular brown adipose tissue (iBAT) function in high fat diet (HFD) and cold stressed mice. We focused on Gm15551 which has an adipose tissue specific expression profile, is highly upregulated during adipogenesis and downregulated by {beta}-adrenergic activation in mature adipocytes. Albeit we performed comprehensive transcriptional and adipocyte physiology profiling in vitro and in vivo, we could not detect an effect of gain or loss of function of Gm15551.

molecular biology↗

bioRxiv2021

The production of 4,182 mouse lines identifies experimental and biological variables impacting Cas9-mediated mutant mouse line production

The International Mouse Phenotyping Consortium (IMPC) systematically produces and phenotypes mouse lines with presumptive null mutations to provide insight into gene function. The IMPC now uses the programmable RNA-guided nuclease Cas9 for its increased capacity and flexibility to efficiently generate null alleles in the C57BL/6N strain. In addition to being a valuable novel and accessible research resource, the production of 3,313 knockout mouse lines using comparable protocols provides a rich dataset to analyze experimental and biological variables affecting in vivo gene engineering with Cas9. Mouse line production has two critical steps - generation of founders with the desired allele and germline transmission (GLT) of that allele from founders to offspring. A systematic evaluation of the variables impacting success rates identified gene essentiality as the primary factor influencing successful production of null alleles. Collectively, our findings provide best practice recommendations for using Cas9 to generate alleles in mouse essential genes, many of which are orthologs of genes linked to human disease.

genetics↗

bioRxiv2020

DDI2 protease activity controls embryonic development and inflammation via TCF11/NRF1

DDI2 is an aspartic protease that cleaves polyubiquitinated substrates. Upon proteotoxic stress, DDI2 activates the ER-bound transcription factor TCF11/NRF1 (NFE2L1), a master regulator of proteostasis maintenance in mammalian cells, and ensures the expression of rescue factors including proteasome subunits. Here we describe the consequences of DDI2 ablation both in vivo and in cells. Knock-out of DDI2 in mice resulted in embryonic lethality at E12.5 with severe developmental failure. Molecular characterization of the embryos and surrogate DDI2 knock-out cell lines showed insufficient proteasome expression with proteotoxic stress, accumulation of high molecular weight ubiquitin conjugates, and induction of the unfolded protein and integrated stress responses. We also show that DDI2 KO-induced proteotoxic stress causes the cell-autonomous innate immune system to induce a type I interferon signature. These results indicate an important role for DDI2 in the proteostasis network of cells and tissues and in the maintenance of a balanced immune response. HighlightsO_LIDDI2-deficiency in mice causes severe developmental failure and embryonic lethality at mid-late gestation C_LIO_LIDDI2-deficiency causes severe proteotoxic stress and proteasome impairment C_LIO_LIDDI2-deficiency induces the UPR and ISR signaling pathways C_LIO_LIDDI2-deficient cells survive via STAT3-dependent interferon signaling C_LI

cell biology↗

bioRxiv2019

A resource of targeted mutant mouse lines for 5,061 genes

The International Mouse Phenotyping Consortium reports the generation of new mouse mutant strains for over 5,000 genes from targeted embryonic stem cells on the C57BL/6N genetic background. This includes 2,850 null alleles for which no equivalent mutant mouse line exists, 2,987 novel conditional-ready alleles, and 4,433 novel reporter alleles. This nearly triples the number of genes with reporter alleles and almost doubles the number of conditional alleles available to the scientific community. When combined with more than 30 years of community effort, the total mutant allele mouse resource covers more than half of the genome. The extensively validated collection is archived and distributed through public repositories, facilitating availability to the worldwide biomedical research community, and expanding our understanding of gene function and human disease.

genetics↗

bioRxiv2019

CRMP2 mediates Sema3F-dependent axon pruning and dendritic spine remodeling

Regulation of axon guidance and pruning of inappropriate synapses by class 3 semaphorins is key to development of neural circuits. Collapsin response mediator protein 2 (CRMP2) has been shown to regulate axon guidance by mediating Semaphorin 3A (Sema3A) signaling and its dysfunction has been linked to schizophrenia, however, nothing is known about its role in the synapse pruning. Here, using newly generated crmp2-/- mice we demonstrate that while CRMP2 has only a moderate effect on Sema3A-dependent axon guidance in vivo, it is essential for Sema3F-dependent axon pruning and dendritic spine remodeling. We first demonstrate that CRMP2 deficiency interferes with Sema3A signaling in compartmentalized neuron cultures and leads to a mild defect in axon guidance in peripheral nerves and corpus callosum. Strikingly, we show that crmp2-/- mice display more prominent defects in dendritic spine pruning and stereotyped axon pruning in hippocampus and visual cortex consistent with impaired Sema3F signaling and with autism spectrum disorder (ASD)-rather than schizophrenia-like phenotype. Indeed, we demonstrate that CRMP2 mediates Sema3F-induced axon retraction in primary neurons and that crmp2-/- mice display early postnatal behavioral changes linked to ASD. In conclusion, we demonstrate that CRMP2 is an essential mediator of Sema3F-dependent synapse pruning and its dysfunction in early postnatal stages shares histological and behavioral features of ASD.

neuroscience↗