Biology subjects

Schmid, T.

Publications and source records attributed to Schmid, T..

11 recordsLinked to original sources

bioRxiv2026

Enhanced IGFL1 translation in response to IL-1β is controlled by distinct 3UTR elements

Translation is a crucial regulatory mechanism involved in several diseases, including cancer, where pro-inflammatory conditions within the microenvironment have been shown to modulate the translation of specific mRNAs. In the present study, we focused on the regulation of insulin growth factor-like family member 1 (IGFL1) in MCF7 breast cancer cells in response to pro-inflammatory IL-1{beta} and observed an induction of both transcription and translation. We characterized the 3 untranslated region as regulatory hub for the post-transcriptional regulation and identified a distinct G-rich region to confer the IL-1{beta}-dependent translational increase. Our study therefore provides new insights into the translation regulation of IGFL1 in the context of an inflammatory tumor microenvironment.

molecular biology↗

bioRxiv2025

An Integrated In Vitro Platform and Biophysical Modeling Approach for Studying Synaptic Transmission in Isolated Neuronal Pairs

Studying synaptic transmission and plasticity is facilitated in experimental systems that isolate individual neuronal connections. We developed an integrated platform combining polydimethylsiloxane (PDMS) microstructures with high-density microelectrode arrays to isolate and record single neuronal pairs from human induced pluripotent stem cell (hiPSC)-derived neurons. The system maintained hundreds of parallel neuronal pairs for over 100 days, demonstrating functional synapses through pharmacological validation and long-term potentiation studies. We coupled this platform with a biophysical Hodgkin-Huxley model and simulation-based inference to extract mechanistic parameters from electrophysiological data. The analysis of long-term potentiation stimulation using a biophysical model revealed (-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) AMPA and (N-methyl-D-aspartate) NMDA receptor-specific alterations, providing quantitative insights into synaptic plasticity mechanisms. This integrated approach represents the first system combining isolated synaptic pairs, long-term stability, and mechanistic modeling, offering unprecedented opportunities for studying human synaptic function and plasticity.

neuroscience↗

bioRxiv2024

Hypoxia impedes differentiation of cranial neural crest cells into derivatives relevant for craniofacial development

Orofacial clefts are the second-most prevalent congenital malformation. Risk factors are multifactorial and include genetic components but also environmental factors. One environmental factor is hypoxia during pregnancy, caused for instance by tobacco smoking, medication or living at high altitudes. Knowledge about the molecular link between hypoxia and orofacial clefts is at large. We here show that hypoxia has only modest effects on proliferating cranial neural crest cells, but dramatically influences their differentiation potential. We detected massive perturbations in their differentiation to chondrocytes, osteoblasts and smooth muscle cells. The transcriptional induction of the majority of regulated genes during each of these processes was grossly impaired by hypoxic conditions, as evidenced by genome-wide transcriptomic analyses. Bioinformatic analyses pointed to cytoskeletal organization and amino acid metabolism as two main processes compromised during all three differentiation pathways, and several orofacial cleft risk genes were among the genes with impaired induction during hypoxia. Our analyses reveal a drastic influence of hypoxia on the differentiation potential of cranial neural crest cells as a possible source for the occurrence of orofacial clefts.

genomics↗

bioRxiv2023

A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match

MicroRNAs (miRNAs) are critical post-transcriptional regulators in many biological processes. They act by guiding RNA-induced silencing complexes to miRNA response elements (MREs) in target mRNAs, inducing translational inhibition and/or mRNA degradation. Functional MREs are expected to predominantly occur in the 3 untranslated region and involve perfect base-pairing of the miRNA seed. Here, we generate a high-resolution map of miR-181a/b-1 (miR-181) MREs to define the targeting rules of miR-181 in developing murine T-cells. By combining a multi-omics approach with computational high-resolution analyses, we uncover novel miR-181 targets and demonstrate that miR-181 acts predominantly through RNA destabilization. Importantly, we discover an alternative seed match and identify a distinct set of targets with repeat elements in the coding sequence which are targeted by miR-181 and mediate translational inhibition. In conclusion, deep profiling of MREs in primary cells is critical to expand physiologically relevant targetomes and establish context-dependent miRNA targeting rules. Key Points* Deep profiling identifies novel targets of miR-181 associated with global gene regulation. * miR-181 MREs in repeat elements in the coding sequence act through translational inhibition. * High-resolution analysis reveals an alternative seed match in functional MREs.

immunology↗

bioRxiv2023

Boosting class II HLA epitope presentation to T cells with endoplasmic reticulum transmembrane domain fusion proteins

Antigen processing and presentation are crucial for T-cell receptor engagement and potent adaptive immune responses. While establishing an antigen presentation system to identify TCR-epitope pairs from large libraries of genetically templated, ectopically expressed antigens, we observed a longitudinal suppression of antigen processing in B cells, which we call antigen processing attenuation (APA). Beyond its potential role in regulating B cell-enforced peripheral tolerance, APA represents a bottleneck to sustained antigen presentation in screening and vaccination approaches. To overcome APA we screened several pathways which might enhance processing. Notably, we identified several sequences derived from transmembrane domains (TM) of endoplasmic reticulum-resident proteins which promote sustained minigene-encoded antigen presentation. In particular, the first TM domain of SYT6, a protein associated with synaptic vesicles, greatly enhances processing and ameliorates APA. These findings suggest a new entry point into antigen processing pathways, enabling the discovery of novel immune epitopes and improving T-cell based immunization strategies.

molecular biology↗

bioRxiv2023

T-FINDER: A highly sensitive, pan-HLA platform for functional T cell receptor and ligand discovery

Effective, unbiased, high-throughput methods to functionally identify both class II and class I HLA-presented T cell epitopes and their cognate T cell receptors (TCRs) are essential for and prerequisite to diagnostic and therapeutic applications, yet remain underdeveloped. Addressing this bottleneck, we established T-FINDER (T cell Functional Identification and (Neo)-antigen Discovery of Epitopes and Receptors), a platform that rapidly deconvolutes CD4 and CD8 TCR reactivities to targets physiologically processed and presented by an individuals unmanipulated, complete HLA haplotype. By using a highly sensitive TCR signaling reporter capable of detecting even low-affinity TCR:ligand interactions, T-FINDER not only robustly identifies unknown peptide:HLA ligands from complex antigen libraries, but also rapidly screens and functionally validates the specificity of complex TCR libraries against known or predicted targets. To demonstrate its pan-HLA presentation capacity, we apply the platform to multiple TCR-based applications, including glioma, celiac disease, and rheumatoid arthritis, providing unique biological insights and showcasing T-FINDERs potency and versatility.

immunology↗

bioRxiv2022

The Tip60/Ep400 chromatin remodeling complex impacts basic metabolic and cellular functions in cranial neural crest-derived tissue during early orofacial development

The cranial neural crest plays a fundamental role in orofacial development and morphogenesis. Accordingly, mutations with impact on the cranial neural crest and its development lead to orofacial malformations such as cleft lip and palate. As a pluripotent and dynamic cell population, the cranial neural crest undergoes vast transcriptional and epigenomic alterations throughout the formation of facial structures pointing to an essential role of factors regulating chromatin state or transcription levels. Using CRISPR/Cas9-guided genome editing and conditional mutagenesis in the mouse, we here show that inactivation of Kat5 and Ep400 as the two essential enzymatic subunits of the Tip60/Ep400 chromatin remodeling complexes severely affects carbohydrate and amino acid metabolism in cranial neural crest cells. The resulting decrease in protein synthesis, proliferation and survival leads to a drastic reduction of cranial neural crest cells early in fetal development and a loss of most facial structures in the absence of either protein. Following heterozygous loss of Kat5 in neural crest cells palatogenesis was impaired. These findings point to a decisive role of the Tip60/Ep400 chromatin remodeling complex in facial morphogenesis and lead us to conclude that the orofacial clefting observed in patients with heterozygous KAT5 missense mutations is at least in part due to disturbances in the cranial neural crest.

developmental biology↗

bioRxiv2019

Advances in Spiral fMRI: A High-resolution Study with Single-shot Acquisition

Spiral fMRI has been put forward as a viable alternative to rectilinear echo-planar imaging, in particular due to its enhanced average k-space speed and thus high acquisition efficiency. This renders spirals attractive for contemporary fMRI applications that require high spatiotemporal resolution, such as laminar or columnar fMRI. However, in practice, spiral fMRI is typically hampered by its reduced robustness and ensuing blurring artifacts, which arise from imperfections in both static and dynamic magnetic fields. Recently, these limitations have been overcome by the concerted application of an expanded signal model that accounts for such field imperfections, and its inversion by iterative image reconstruction. In the challenging ultra-high field environment of 7 Tesla, where field inhomogeneity effects are aggravated, both multi-shot and single-shot 2D spiral imaging at sub-millimeter resolution was demonstrated with high depiction quality and anatomical congruency. In this work, we further these advances towards a time series application of spiral readouts, namely, single-shot spiral BOLD fMRI at 0.8 mm in-plane resolution. We demonstrate that high-resolution spiral fMRI at 7 T is not only feasible, but delivers both excellent image quality, BOLD sensitivity, and spatial specificity of the activation maps, with little artifactual blurring. Furthermore, we show the versatility of the approach with a combined in/out spiral readout at a more typical resolution (1.5 mm), where the high acquisition efficiency allows to acquire two images per shot for improved sensitivity by echo combination. HighlightsO_LIThis work reports the first fMRI study at 7T with high-resolution spiral readout gradient waveforms. C_LIO_LIWe achieve spiral fMRI with sub-millimeter resolution (0.8 mm, FOV 230 mm), acquired in a single shot (36 slices in 3.3 s). C_LIO_LISpiral images exhibit intrinsic geometric congruency to anatomical scans, and spatially specific activation patterns. C_LIO_LIImage reconstruction rests on a signal model expanded by measured trajectories and static field maps, inverted by cg-SENSE. C_LIO_LIWe assess generalizability of the approach for spiral in/out readouts, providing two images per shot (1.5 mm resolution). C_LI

neuroscience↗

bioRxiv2018

uORF-Tools - Workflow for the determination of translation-regulatory upstream open reading frames

Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5 untranslated region) preceding the main open reading frame (ORF), which indicates the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of functional uORFs, which contribute to the translational regulation of their associated main ORFs. The workflow is available as free and open Snakemake workflow. Furthermore, we provide a comprehensive human uORF annotation file, which can be used within the pipeline, thus reducing the runtime. (Availability: https://github.com/anibunny12/uORF-Tools)

bioinformatics↗

bioRxiv2017

Hydrogen peroxide formation by Nox4 limits malignant transformation

Reactive oxygen species (ROS) can cause cellular damage and are thought to promote cancer-development. Nevertheless, under physiological conditions, all cells constantly produce ROS, either as chemical by-products or for signaling purpose. During differentiation cells induce the NADPH oxidase Nox4, which constitutively produces low amounts of H2O2. We infer that this constitutive H2O2 is unlikely to be carcinogenic and may rather maintain basal activity of cellular surveillance systems.\n\nUtilizing two different murine tumor models we demonstrate that Nox4 prevents malignant transformation and facilitated the recognition of DNA-damage. Upon DNA-damage repair is initiated as consequence of phosphorylation of H2AX ({gamma}H2AX). Repair only occurs if nuclear activity of the {gamma}H2AX-dephosphorylating phosphatase PP2A is kept sufficiently low, a task fulfilled by Nox4: Nox4 continuously oxidizes AKT, and once oxidized AKT captures PP2A in the cytosol. Absence of Nox4 facilitates nuclear PP2A translocation and dephosphorylation of {gamma}H2AX. Simultaneously the proportion of active, phosphorylated AKT is increased. Thus, DNA-damage is not recognized and the increase in AKT activity promotes proliferation. The combination of both events resulted in genomic instability and tumor initiation.\n\nWith the identification of the first cancer-protective source of reactive oxygen species, Nox4, the paradigm of reactive-oxygen species-induced initiation of malignancies should be revised.\n\nSignificanceThe stereotype of ROS produced by NADPH oxidases as cause of malignant diseases persists generalized since decades. We demonstrate that the NADPH oxidase Nox4, as constitutive source of ROS, prevents malignant transformation and that its pharmacological inhibition as currently aspired by several companies will potentially increase the risk of malignant cell transformation and eventually tumor formation.\n\nPrecisBy oxidizing AKT and keeping PP2A in the cytosol, the NADPH oxidase Nox4 allows proper DNA damage repair and averts cancer development.

cancer biology↗

bioRxiv2017

Genetical genomics reveals Ras/MAPK modifier loci

The oncogenic Ras/MAPK pathway is evolutionary conserved across metazoans and is essential for many cellular functions. Mutant screens in the model nematode Caenorhabditis elegans have been invaluable for elucidating Ras/MAPK pathway characteristics and identification of the genes involved. Almost all of these screens have been conducted in a single genetic background. However, phenotypic traits of induced mutations can vary widely depending on the genetic background. At the moment, we lack insight into how different genetic backgrounds modulate Ras/MAPK-signaling and which genetic modifiers are involved.\n\nWe previously introduced a gain-of-function mutation in the Ras/MAPK pathway gene let-60 in over 200 recombinant inbred lines (mutant introgressed RILs: miRILs) and detected genetic modifiers affecting this pathway by studying variation in vulval development. In the present study, we investigate how gene expression regulation is affected by the let-60 gain-of-function mutation and the genetic background by mapping eQTL using 33 miRILs. We found that the majority ([~]73%) of the 1516 detected cis-eQTL are not specific for the let-60 mutation, whereas most ([~]76%) of the 898 detected trans-eQTL are associated with the let-60 mutation. We detected 6 eQTL trans-bands that were specific for the interaction between the genetic background and the mutation. One of these eQTL hotspots co-localizes with the previously identified polymorphic Ras/MAPK modifier amx-2. Comparing gene expression profiles between transgenic lines expressing either the N2 or the CB4856 alleles of amx-2 showed the involvement of amx-2 in 79% of the trans-eQTLs for genes mapping to this trans-band.\n\nTogether, our results have revealed hidden loci affecting Ras/MAPK signaling using sensitized backgrounds in C. elegans. These loci harbor putative polymorphic modifier genes that would not have been detected using mutant screens in single genetic backgrounds.

genetics↗