Biology subjects

Seitz, C.

Publications and source records attributed to Seitz, C..

15 recordsLinked to original sources

bioRxiv2026

Fed-batch production of antiviral OP7 chimera defective interfering influenza A particles

Influenza A virus (IAV) defective interfering particles (DIPs) are regarded as promising broad-spectrum antivirals due to their high efficacy demonstrated in animal trials. Previously, an OP7 chimera DIP was generated that showed markedly enhanced antiviral efficacy compared to conventional IAV DIPs. In addition, a high-yield cell culture-based production process for OP7 chimera DIPs was established in perfusion mode. However, due to the technical complexity of this technology, we aimed to combine the advantages of perfusion in terms of yield with that of a simple and less complex batch process. In the present work, we established a fed-batch production process for OP7 chimera DIPs that allows a more straightforward implementation into existing production facilities. Using a feeding regime that was able to overcome the cell density effect, we achieved productive virus infection in stirred tank reactors until a cell density of 10E+6 cells/mL. Furthermore, we obtained a high virus titer of 3.8 log10(HAU/100 uL), corresponding to a 3.4-fold increase compared to a reference batch production. Moreover, the produced material demonstrated a significantly increased interfering bioactivity shown by an in vitro potency assay. Interestingly, this efficacy was similarly high as compared to OP7 chimera DIP material previously produced in perfusion mode, despite twofold lower virus titers. Finally, we demonstrate robustness of OP7 chimera DIP seed virus trains, which is significant step towards later pharmaceutical production. Further, corresponding GMP MDCK-PB2(sus) cell and OP7 chimera virus banks are now available for later biomanufacturing further use. In conclusion, the established fed-batch process offers a valid n additional option for pharmaceutical grade OP7 chimera DIP GMP manufacturing production under GMP conditions required for subsequent clinical testing and for later large-scale manufacturing.

bioengineering↗

bioRxiv2026

Advancing Neurological Liquid Biopsy via Six-Base Sequencing of Cerebrospinal Fluid Cell-Free DNA

Real-time molecular insights into the human brain are crucial for understanding neurological conditions and development of soluble biomarkers but challenged by the limited access to target tissue. Here we utilize 6-base sequencing to profile DNA modifications of cell-free DNA released from neural cells into cerebrospinal fluid. This strategy provides molecular, quantitative and qualitative insights into the ongoing neurodegenerative biology, which paves the way for liquid biopsy approaches to study neurological conditions.

neuroscience↗

bioRxiv2026

Uncertainty-aware localization microscopy by variational diffusion

Fast extraction of physically relevant information from images using deep neural networks has led to significant advances in fluorescence microscopy and its application to the study of biological systems. For example, the application of deep networks for kernel density (KD) estimation in single-molecule localization microscopy (SMLM) has accelerated super-resolution imaging of densely labeled structures in the cell. However, localization of fluorescent molecules in dense images is a difficult inverse problem with potentially multiple solutions. To model a probability distribution of solutions to this problem, we propose a generative modeling framework for KD estimation in SMLM based on a conditional variational diffusion model (CVDM). In this framework, CVDM is trained to perform localization tasks on low-resolution measurements by modeling a distribution of high-resolution KD estimates. This approach allows us to probe the structure of the distribution on KD estimates and express uncertainty, which is not currently offered by existing deep models for localization microscopy. We demonstrate that this model permits high-fidelity super-resolution, enables the uncertainty estimation of regressed KD estimates, and has important implications for image restoration in single-molecule and super resolution microscopy.

bioinformatics↗

bioRxiv2026

Counting fluorescent emitters with a single photon avalanche diode array

For decades, the photon counting histogram (PCH) was used as the sole method to quantify fluorophore numbers in a diffraction-limited focal volume. This technique combines spatial excitation profiles, and the distribution of photon counts to register the photon emission statistics of individual fluorophores. However, this approach has not yet been transferred to widefield fluorescent imaging due to the lack of fast and single photon sensitive camera sensors which can capture the photon emission statistics of a single fluorophore. Here, we explore avenues towards quantitative analysis of the active fluorophore number by leveraging recent advancements in single photon avalanche diode (SPAD) array technology. Binary exposures of a SPAD array can be synchronized with picosecond laser pulses to measure the PCH in a widefield setting. Then, by modeling the statistical relationship between the active fluorophore number and the PCH in a region of interest following a laser pulse, we can perform Bayesian inference of this number. The model is demonstrated experimentally by counting quantum dots and various numbers of fluorescent dye molecules bound to DNA origamis. We find that this method has several important applications in widefield microscopy, including enhanced localization microscopy and constrained fitting of multiple unresolvable fluorescent emitters.

biophysics↗

bioRxiv2025

AID facilitates TET2 demethylation of Irf4 for plasma cell fate in germinal center B cells

Activation-induced cytidine deaminase (AID) is essential for B cell affinity maturation. We investigated why AID deficiency gives rise to giant germinal centers (GC) using the AIDR112H mouse model that is devoid of AID activity. The increased GC response was associated with accumulation of GC B cells in the light zone in immunized AIDR112H mice. AIDR112H GC B cells had reduced capacity to up-regulate IRF4 to initiate plasma cell differentiation, leading to accumulation of a transitional GC population with reduced GL7 expression. Genetic introduction of a high affinity B cell receptor (BCR) was unable to restore plasma cell differentiation of AIDR112H B cells while ectopic expression of catalytic active AID rescued plasma cell generation. AIDR112H impaired recruitment of AID to the Irf4 promoter/enhancer and disrupted the interaction with Ten-eleven Translocation 2 (TET2). Consequently, DNA demethylation at the Irf4 promoter/enhancer was reduced in AIDR112H GC B cells and impeded high Irf4 expression for transition into plasma cells. This data reveals a B cell-intrinsic mechanism that governs the plasma cell fate decision through epigenetic remodeling mediated by AID in cooperation with TET2. Key messagesO_LIAID deficiency leads to accumulation of a transitional (t)GC population of B cells with low expression of GL7 and failure to up-regulate IRF4 C_LIO_LIAID deamination activity is needed to promote up-regulation of IRF4 for plasma cell differentiation. C_LIO_LICo-operation between TET2 and AID facilitates demethylation of the Irf4 enhancer/promoter. C_LI

immunology↗

bioRxiv2025

Cysteine-Engineered CAR-T Cells to Counter Antigen Escape in B Cell Lymphoma

Chimeric Antigen Receptor (CAR-) T cell therapy represents a paradigm shift in immunotherapy of hematological cancers. However, selective pressure on cancer cells often leads to suppression of target antigens, eventually causing cancer relapse1,2. This so-called antigen escape renders CAR-T cells ineffective, posing a significant clinical challenge2-5. Therefore, identifying alternative targets less susceptible to antigen escape is crucial. Here, we describe a novel type of CAR-T cells utilizing cysteine-engineered antibody fragments that target altered redox states on the surface of B cell lymphoma (BCL)6. We demonstrate that cysteine-engineered CAR-T cells exhibit specific cytotoxicity in vitro against various BCL subtypes, including antigen escape models. Additionally, we show that cysteine engineering, achieved through single amino acid substitution in the state-of-the-art anti-CD19-CAR, enables co-targeting of both CD19-positive and -negative BCL. Our findings introduce a novel class of bifunctional CAR-T cells that target conventional antigens and altered redox states simultaneously, potentially reducing the risk of antigen escape. Abnormal redox states occur in several cancers, including breast and leukemia7-12, indicating a broad therapeutic scope.

cancer biology↗

bioRxiv2024

BRD4 phosphorylation regulates the structure of chromatin nanodomains

The interplay between chromatin structure and phase-separating proteins is an emerging topic in cell biology with implications for understanding disease states. Here, we investigate the functional relationship between bromodomain protein 4 (BRD4) and chromatin architecture. By combining molecular dynamics simulations with live-cell imaging, we demonstrate that BRD4, when mutated at specific N-terminus sites, significantly impacts nucleosome nanodomain (NN) organization and dynamics. Our findings reveal that enhanced chromatin binding activity of BRD4 condenses NNs, while both loss or gain of BRD4 chromatin binding reduced diffusion of single nucleosomes, suggesting a role for BRD4 in the regulation of nanoscale chromatin architecture and the chromatin microenvironment. These observations shed light on the nuanced regulation of chromatin structure by BRD4, offering insights into its role in maintaining the nuclear architecture and transcriptional activity.

biophysics↗

bioRxiv2024

Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase

Discovered in the 1920s, cytochrome bd is a terminal oxidase that has received renewed attention as a drug target since its atomic structure was first solved in 2016. Only found in prokaryotes, we study it here as a drug target for Mycobacterium tuberculosis (Mtb). Most previous drug discovery efforts towards cytochrome bd have involved analogs of the canonical substrate quinone, known as Aurachin D. Here we report six new cytochrome bd inhibitor scaffolds determined from a computational screen totaling over one million molecules and confirmed on target activity through in vitro testing. These scaffolds provide new avenues for lead optimization towards Mtb therapeutics.

biochemistry↗

bioRxiv2024

Somatic gene delivery for flexible in vivo modeling of high-risk sarcoma

A particular challenge hampering therapeutic advancements for high-risk sarcoma patients is the broad spectrum of molecularly distinct sarcoma entities and the corresponding lack of suitable model systems to recapitulate and study these diseases. To overcome this predicament, we developed a novel genetically-controlled, yet versatile mouse modeling platform allowing delivery of different genetic lesions by electroporation (EPO) of the thigh muscle wildtype mice. This optimized sarcoma EPO-GEMM (EPO-based genetically engineered mouse model) platform allowed the generation of ten biologically distinct sarcoma entities, including Synovial Sarcoma (SS), fusion-positive and fusion-negative Rhabdomyosarcoma (RMS), Alveolar Soft Part Sarcoma (ASPS), Undifferentiated Pleomorphic Sarcoma (UPS) and Infantile Fibrosarcoma (IFS). Comprehensive molecular profiling and cross-species analyses confirmed faithful recapitulation of the human disease, including the expression of relevant immunotherapy targets. Syngeneic allografting enabled reliable preservation and scalability of Sarcoma-EPO-GEMMs for treatment trials, such as B7-H3-directed CAR-T cell therapy in an immunocompetent background.

cancer biology↗

bioRxiv2023

Forward Genetic Stomatal CO2 Response Screen in Grass Brachypodium distachyon Reveals Central Function of a MAP Kinase in Early Stomatal CO2 Signal Transduction

Plants respond to increased CO2 concentrations through rapid stomatal closure which can contribute to increased water use efficiency. Grasses display faster stomatal responses than eudicots due to dumbbell-shaped guard cells flanked by subsidiary cells working in opposition. However, forward genetic screening for stomatal CO2 signal transduction mutants in grasses has not been reported. The grass model Brachypodium distachyon is closely related to agronomically important cereal crops, sharing largely collinear genomes. To gain insights into CO2 control mechanisms of stomatal movements in grasses, we developed a forward genetics screen with an EMS-mutagenized Brachypodium distachyon M5 generation population using infrared imaging to identify plants with altered canopy leaf temperature at elevated CO2. Among isolated mutants, a "chill1" mutant exhibited cooler leaf temperatures than wildtype Bd21-3 parent control plants after exposure to increased [CO2]. chill1 plants showed strongly impaired high CO2-induced stomatal closure, despite retaining a robust abscisic acid-induced stomatal closing response. Through bulked segregant whole-genome-sequencing analyses followed by analyses of further backcrossed F4 generation plants and generation and characterization of CRISPR-cas9 mutants, chill1 was mapped to a protein kinase, BdMPK5. The chill1 mutation impaired BdMPK5 protein-mediated CO2/HCO3- sensing in vitro. Furthermore, AlphaFold2-directed structural modeling suggests that the identified BdMPK5-D90N chill1 mutant residue is located at the interface with the HT1 Raf-like kinase. BdMPK5 is a key signaling component involved in CO2-induced stomatal movements, potentially functioning as a component of the CO2 sensor in grasses.

plant biology↗

bioRxiv2023

Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics

All protein simulations are conducted with varying degrees of simplifications, oftentimes with unknown ramifications on how these simplifications affect the interpretability of the results. In this work we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: 1) Glycosylated neuraminidase in a whole virion (i.e. crowded membrane) environment 2) Glycosylated neuraminidase in its own lipid bilayer 3) Unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large scale conformational change while making the protein structure more compact. Understanding these effects informs what factors one must consider while attempting to recapture the desired level of physical accuracy. TOC figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=50 SRC="FIGDIR/small/556910v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@ec7a9org.highwire.dtl.DTLVardef@563495org.highwire.dtl.DTLVardef@1965cd7org.highwire.dtl.DTLVardef@a9659d_HPS_FORMAT_FIGEXP M_FIG TOC. Schematic of the three systems used here. (A) 2009-H1N1-ungly is the unglycosylated, single protein NA system. (B) 2009-H1N1-gly is the glycosylated, single protein NA system. (C) 2009-H1N1-vir is the NA in the virion context. C_FIG

biophysics↗

bioRxiv2022

Breathing and Tilting: Mesoscale simulations illuminate influenza glycoprotein vulnerabilities

Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investigate the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. The flexibility of HA and NA highlights antigenically relevant conformational states, as well as facilitates the characterization of a novel monoclonal antibody, derived from human convalescent plasma, that binds to the underside of the NA head. Our work provides previously unappreciated views on the dynamics of HA and NA, advancing the understanding of their interplay and suggesting possible strategies for the design of future vaccines and antivirals against influenza. One-Sentence SummaryIn situ dynamics of influenza glycoproteins expose antigenically relevant states and a new site of vulnerability in neuraminidase.

biophysics↗

bioRxiv2022

Architecture and self-assembly of the jumbo bacteriophage nuclear shell

Bacteria encode myriad defenses that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR/Cas systems. In response, one family of large bacteriophage employs a nucleus-like compartment to protect their replicating genomes by excluding host defense factors. However, the principle composition and structure of this compartment remain unknown. Here, we find that the bacteriophage nuclear shell assembles primarily from one protein, termed chimallin. Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin cooperatively self-assembles as a flexible sheet into closed micron-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.

biophysics↗

bioRxiv2020

Multiscale simulations examining glycan shield effects on drug binding to influenza neuraminidase

Influenza neuraminidase is an important drug target. Glycans are present on neuraminidase, and are generally considered to inhibit antibody binding via their glycan shield. In this work we studied the effect of glycans on the binding kinetics of antiviral drugs to the influenza neuraminidase. We created all-atom in silico systems of influenza neuraminidase with experimentally-derived glycoprofiles consisting of four systems with different glycan conformations and one system without glycans. Using Brownian dynamics simulations, we observe a two- to eight-fold decrease in the rate of ligand binding to the primary binding site of neuraminidase due to the presence of glycans. These glycans are capable of covering much of the surface area of neuraminidase, and the ligand binding inhibition is derived from glycans sterically occluding the primary binding site on a neighboring monomer. Our work also indicates that drugs preferentially bind to the primary binding site (i.e. the active site) over the secondary binding site, and we propose a binding mechanism illustrating this. These results help illuminate the complex interplay between glycans and ligand binding on the influenza membrane protein neuraminidase. Statement of SignificanceThe influenza glycoprotein neuraminidase is the target for three FDA-approved influenza drugs in the US. However, drug resistance and low drug effectiveness merits further drug development towards neuraminidase, which is hindered by our limited understanding of glycan effects on ligand binding. Generally, drug developers do not include glycans in their development pipelines. Here, we show that even though glycans can reduce drug binding towards neuraminidase, we recommend future drug development work to focus on strong binders with a long lifetime. Furthermore, we examine the binding competition between the primary and secondary binding sites on neuraminidase, leading us to propose a new, to the best of our knowledge, multivalent binding mechanism.

biophysics↗

bioRxiv2017

Modified hCFTR mRNA restores normal lung function in a mouse model of cystic fibrosis

Being a classic monogenic disease, gene therapy has always been a promising therapeutic approach for Cystic Fibrosis (CF). However, numerous trials using DNA or viral vectors encoding the correct protein resulted in a general low efficacy. In the last years, chemically modified messenger RNA (cmRNA) has been proven to be a highly potent, pulmonary effective drug. We thus explored the expression of human (h)CFTR encoded by hCFTR cmRNA in vitro, analyzed by flow cytometry and Western Blot and its function with a YFP assay. Very similar effects could be observed in vivo when hCFTR cmRNA was assembled with Chitosan-coated PLGA to nanoparticles (NPs) and intratracheally (i.t.) or intravenously (i.v) injected, the latter one as an alternative administration route to circumvent the clogged airways of CF patients. This significantly improved lung function, which suggests that hCFTR cmRNA-NPs are a promising therapeutic option for CF patients independent of their CFTR genotype.

genetics↗