Biology subjects

Stadler, C.

Publications and source records attributed to Stadler, C..

9 recordsLinked to original sources

bioRxiv2026

An integrated protocol for multiplexed DNA FISH and protein detection in large tissue sections

Different omics types such as genomics and proteomics all contribute to deciphering biology. Applying these omics approaches in a spatial context helps reveal biology in situ at a single cell level. Here we present a protocol for the combined multiplexed detection of targeted genes using DNA FISH, and proteins using multiplexed immunofluorescence. The protocol is integrated on the commercial PhenoCycler platform and generates one single dataset with gene and protein readout at a single cell level in large tissue sections, allowing for a throughput of thousands to millions of cells. The workflow can be used for characterising malignant cells in large tumor areas based on genetic aberrations, while deciphering the cellular landscape and microenvironment from multiplexed protein detection using immunofluorescence.

cancer biology↗

bioRxiv2026

A workflow for combined detection of protein interactions and cell types for translational studies

Multiplexed imaging approaches of various molecular modalities in tissues are becoming increasingly adopted in discovery and translational studies. For clinical implementation, novel instrumentation, complex analysis workflows and high costs per sample are bottlenecks that hinders broader introduction in the clinical setting. Here, we demonstrate a cost efficient integrated workflow that combines multiplexed immunofluorescence of a handful of protein markers, with in situ proximity ligation assay, to detect direct protein interactions between neighboring cells. As a proof of concept case of relevance for clinical adaptation, we target the major immunotherapy signalling axis of programmed death receptor 1 (PD-1) and its ligand PD-L1, to demonstrate the interaction between immune cells in germinal centers of tonsil tissue and in a tertiary lymphoid structure in bladder cancer tissue, respectively, from a patient treated with immunotherapy.

cancer biology↗

bioRxiv2026

Brain Age in Conduct Disorder: A Mega-Analysis of the ENIGMA Antisocial Behavior Working Group

Conduct disorder (CD) is the leading global cause of mental health burden in children and adolescents and has recently been hypothesized to be a neurodevelopmental disorder. Although prior research has identified neuroanatomical differences associated with CD, it remains unclear whether these differences reflect atypical brain development. Here, we investigated the difference between an individuals brain age and chronological age as a proxy for variations in brain maturation. Using a pretrained model, we estimated brain age from structural neuroimaging data obtained from 1,119 youth with CD and 1,183 typically developing controls across 14 international cohorts participating in the ENIGMA-Antisocial Behavior Working Group. Youth with CD exhibited a statistically robust but small acceleration in brain age compared to typically developing youth (around 0.50 years), which was restricted to the adolescence-onset subtype of the disorder. Our large-scale, coordinated analysis provides the first evidence of accelerated neurodevelopment as a potential mechanism underlying CD.

neuroscience↗

bioRxiv2023

Hypothalamic representation of the imminence of predator threat detected by the vomeronasal organ in mice

Animals have the innate ability to select optimal defensive behaviors with appropriate intensity in response to predator threats within specific contexts. Such innate behavioral decisions are thought to be computed in the medial hypothalamic nuclei, which contain neural populations that directly control defensive behavioral outputs. The vomeronasal organ (VNO) serves as a primary sensory channel for detecting predator cues by relaying signals to the medial hypothalamic nuclei, particularly the ventromedial hypothalamus (VMH), via the medial amygdala (MeA) and bed nucleus of the stria terminalis (BNST). Here, we demonstrate that cat saliva contains predator cues that signal the imminence of predator threat and modulate the intensity of freezing behavior through the VNO in mice. Cat saliva activates neurons expressing the V2R-A4 subfamily of sensory receptors, suggesting that specific receptor groups are responsible for inducing the freezing behavior. The number of VNO neurons activated in response to saliva correlates with both the freshness of saliva and the intensity of freezing behavior. In contrast, the downstream neurons in the accessory olfactory bulb (AOB) and the defensive behavioral circuit are activated to a similar extent by fresh and old saliva. Strikingly, however, the number of VMH neurons activated by fresh, but not old, saliva positively correlates with the intensity of freezing behavior. Detailed analysis of the spatial distribution of neurons responding to fresh and old saliva, as well as the overlap of those activated within the same individual mice, revealed that fresh and old saliva predominantly activate distinct neuronal populations within the VMH. Collectively, this study suggests that there is an accessory olfactory circuit in mice that is specifically tuned to time-sensitive components of cat saliva, which optimizes their defensive behavior to maximize their chance of survival according to the imminence of threat.

neuroscience↗

bioRxiv2023

N-terminal proteoforms may engage in different protein complexes

Alternative translation initiation and alternative splicing may give rise to N-terminal proteoforms, proteins that differ at their N-terminus compared to their canonical counterparts. Such proteoforms can have altered localizations, stabilities and functions. While proteoforms generated from splice variants can be engaged in different protein complexes, it remained to be studied to what extent this applies to N-terminal proteoforms. To address this, we mapped the interactomes of several pairs of N-terminal proteoforms and their canonical counterparts. First, we generated a catalogue of N-terminal proteoforms found in the HEK293T cellular cytosol from which 22 pairs were selected for interactome profiling. Additionally, we provide evidence for the expression of several N-terminal proteoforms, identified in our catalogue, across different human tissues as well as tissue-specific expression, highlighting their biological relevance. Protein-protein interaction profiling revealed that the overlap of the interactomes for both proteoforms is generally high, showing their functional relation. We also showed that N-terminal proteoforms can be engaged in new interactions and/or lose several interactions compared to their canonical counterpart, thus further expanding the functional diversity of proteomes.

systems biology↗

bioRxiv2022

Action initiation and punishment learning differ from childhood to adolescence while reward learning remains stable

Theoretical and empirical accounts suggest that adolescence is associated with heightened reward learning and impulsivity. Experimental tasks and computational models that can dissociate reward learning from the tendency to initiate actions impulsively (action initiation bias) are thus critical to characterise the mechanisms that drive developmental differences. However, existing work has rarely quantified both learning ability and action initiation, or it has tested small samples. Here, using computational modelling of a learning task collected from a large sample (N=742, 9-18 years, 11 countries), we tested differences in reward and punishment learning and action initiation from childhood to adolescence. Computational modelling revealed that whilst punishment learning rates increased with age, reward learning remained stable. In parallel, action initiation biases decreased with age. Results were similar when considering pubertal stage instead of chronological age. We conclude that heightened reward responsivity in adolescence can reflect differences in action initiation rather than enhanced reward learning.

neuroscience↗

bioRxiv2022

Subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing

The COVID-19 pandemic has resulted in millions of deaths and affected socioeconomic structure worldwide and the search for new antivirals and treatments are still ongoing. In the search for new drug target and to increase our understanding of the disease, we used large scale immunofluorescence to explore the host cell response to SARS-CoV-2 infection. Among the 602 host proteins studied in this host response screen, changes in abundance and subcellular localization were observed for 97 proteins, with 45 proteins showing increased abundance and 10 reduced abundances. 20 proteins displayed changed localization upon infection and an additional 22 proteins displayed altered abundance and localization, together contributing to diverse reshuffling of the host cell protein landscape. We then selected existing and approved small-molecule drugs (n =123) against our identified host response proteins and identified 3 compounds - elesclomol, crizotinib and rimcazole, that significantly reduced antiviral activity. Our study introduces a novel, targeted and systematic approach based on host protein profiling, to identify new targets for drug repurposing. The dataset of [~]75,000 immunofluorescence images from this study are published as a resource available for further studies.

cell biology↗

bioRxiv2020

A sample preparation protocol for high throughput immunofluorescence of suspension cells

Imaging is a powerful approach for studying protein expression and has the advantage over other methodologies in providing spatial information in situ at single cell level. Using immunofluorescence and confocal microscopy, detailed information of subcellular distribution of proteins can be obtained. While adherent cells of different tissue origin are relatively easy to prepare for imaging applications, nonadherent cells from hematopoietic origin, present a challenge due to their poor attachment to surfaces and subsequent loss of a substantial fraction of the cells. Still, these cell types represent an important part of the human proteome and express genes that are not expressed in adherent cell types. In the era of cell mapping efforts, overcoming the challenge with suspension cells for imaging applications would enable systematic profiling of hematopoietic cells. In this work, we successfully established an immunofluorescence protocol for preparation of suspension cell lines and peripheral blood mononucleated cells (PBMC) and human platelets. The protocol is based on a multi-well plate format with automated sample preparation, allowing for robust high throughput imaging applications. In combination with confocal microscopy, the protocol enables systematic exploration of protein localization to all major subcellular structures.

cell biology↗

bioRxiv2018

The human secretome - the proteins secreted from human cells

The proteins secreted by human tissues (the secretome) are important for the basic understanding of human biology, but also for identification of potential targets for future diagnosis and therapy. Here, we present an annotation of all predicted secreted proteins (n=2,623) with information about their spatial distribution in the human body. A high-throughput mammalian cell factory was established to create a resource of recombinant full-length proteins. This resource was used for phenotypic assays involving {beta}-cell dedifferentiation and for development of targeted proteomics assays. A comparison between host cells, including omics analysis, shows that many of the proteins that failed to be generated in CHO cells could be rescued in human HEK293 cells. In conclusion, the human secretome has been mapped and characterized to facilitate further exploration of the human secretome.

molecular biology↗