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Schaefer, M.

Publications and source records attributed to Schaefer, M..

At least 19 recordsLinked to original sources
bioRxiv2026

Near-future warming amplifies natural heatwave impacts and reorganizes freshwater communities

Future climate change may reshape ecological communities not only by increasing mean temperature, but also by altering the consequences of increasingly frequent heatwaves. Predicting these effects requires understanding how background warming interacts with short heatwaves in natural communities, where responses can arise through direct thermal stress and species interactions. We tested this using 32 outdoor freshwater mesocosms exposed to sustained near-future warming while capturing a documented natural heatwave. Warming raised temperature maxima that exceeded the thermal threshold of the pond snail, a main grazer in the community. Warmed communities showed lower grazer abundance, increased macrophyte and insect herbivore abundance, reduced phytoplankton biomass, and lower zooplankton density. Complementary assays showed that heatwave-level temperatures promoted macrophyte growth and reduced grazer survival, whereas reduced zooplankton performance mainly reflected indirect warming effects via food-web cascades. Thus, near-future warming can amplify natural heatwave impacts by exceeding consumer thermal thresholds and propagating through species interactions.

ecology↗
bioRxiv2026

CRISPR screens establish regulatory maps of immunosuppressive surface molecules in cancer

Cancer cells can evade immune surveillance by triggering inhibitory checkpoint responses in tumor-associated T cells through the expression of immunosuppressive surface molecules. While therapeutic blockade of such receptors has emerged as a pillar of cancer therapy, tumor cell-intrinsic mechanisms controlling their expression remain incompletely understood. Fluorescence-activated cell sorting (FACS)-based genetic screens can be used to decipher regulatory pathways, but conventional screening approaches are biased towards regulators that are dispensable for cancer cell proliferation and survival. Here, we used a tetracycline-inducible Cas9 system enabling fully time-controllable CRISPR-based mutagenesis to gain a more comprehensive and comparative survey of regulators controlling the expression of four major immunosuppressive surface molecules, PD-L1 (CD274), CD47, CD276 and HLA-E, as well as CD151, a candidate surface target associated with tumor growth and invasion. As a prominent hit, our screens identify the membrane-trafficking factor DNAJC13 as a regulator of PD-L1 and CD276. Among DNAJC13-controlled surface proteins, we identify other known and proposed immune-checkpoint molecules. Based on this function, suppression of DNAJC13 strongly increases the sensitivity of human cancer cells to T-cell attack in vitro and prolongs survival of mice bearing pancreatic tumors. Together, our study establishes regulatory maps of major immune-modulatory surface molecules and identifies DNAJC13 as a potential target for the coordinated inhibition of multiple immunosuppressive signals.

molecular biology↗
bioRxiv2026

Physiological re-replication during human stem cell differentiation

During defined developmental windows in Drosophila, controlled re-replication generates physiological gene amplification. Although gene amplification has also been observed during human stem cell differentiation, re-replication in human cells has largely been linked to tumor-associated genome instability. Here, we demonstrate that re-replication likewise operates as a physiological mechanism in human stem cells. Using Rerep-Seq and DNA fiber-combing, we identify distinct phases of re-replication during the differentiation of human myoblasts into myotubes and during the lineage commitment of mesenchymal stem cells toward adipogenic, osteogenic, chondrogenic, and neuronal fates. In all differentiation systems examined, re-replication occurred within defined temporal windows. FACS-isolated re-replicating cells exhibited elevated gene expression using RNA-Seq specifically within re-replicated genomic regions. Moreover, re-replicated DNA was detected as extranuclear DNA. These findings support a model in which cells that do not undergo re-replication, and thus avoid increased chromosomal instability, may nonetheless boost the expression of differentiation-relevant genes by acquiring re-replicated DNA released from neighboring re-replicating cells. We propose that human stem cells exploit an evolutionarily conserved re-replication mechanism to transiently increase gene copy number and thereby meet the heightened protein demands associated with differentiation.

genomics↗
bioRxiv2025

A unique mechanism explaining the outstanding performance of a newly discovered doxycycline riboswitch

Synthetic riboswitches offer a versatile and protein-independent solution for conditional gene regulation. They consist of a regulatory domain and an aptamer domain that binds a specific ligand, with their performance largely depending on the ability of the aptamer to control the regulatory domain. Expanding the range of synthetic riboswitches therefore requires the discovery and characterization of new regulatory aptamers. In the present study, we identified a doxycycline-binding aptamer with outstanding regulatory properties in both yeast and human cells which are based on a unique structural dynamic upon ligand binding. Single-molecule force spectroscopy revealed that doxycycline binding strongly stabilizes an intermediate aptamer conformation offering mechanistic insights into its function. The identification of the aptamer through a combination of parallel SELEX and subsequent in vivo screening in yeast, also provided valuable insights into selection dynamics and the first proof for the effectiveness of RNA Capture-SELEX in aptamer selection. Together, the presented data deepen our understanding of regulatory aptamer selection and functionality while adding a high-performing doxycycline-responsive aptamer to the synthetic biology toolbox.

molecular biology↗
bioRxiv2025

Engineering human protein switches for functional control of CARs and transcription factors via oral drug administration

While CAR T cells have revolutionized the treatment of certain hematologic malignancies, they can cause severe toxicities, which are expected to be exacerbated with next-generation CAR Ts engineered for improved proliferation, persistence, and efficacy. Therefore, regulatory systems are urgently needed to be able to control these living drugs directly in patients. Here, we engineered a molecular switch, in which the interaction of two human proteins is efficiently induced with the orally available and non-toxic drug A1120. We demonstrate the versatility of this switch by regulating CAR signaling and transcriptional activity in human T cells in vitro and in vivo. Both systems were tightly controlled in the absence of the drug but strongly activated upon administration of the small molecule. Since this switch enables the regulation of diverse systems including CARs and transcription factors, we anticipate that it represents an important step towards next-generation cellular therapies with improved safety and efficacy.

synthetic biology↗
bioRxiv2025

Maladaptive aphid-induced transgenerational plasticity is overcome in nature

Inherited stress responses are widely assumed to be adaptive for plants by preparing offspring for renewed attack. To date, it remains unclear whether and under which conditions these responses may benefit the attacker rather than the host. Studying the interaction between the aphid Rhopalosiphum nymphaeae and its native host, the aquatic duckweed Spirodela polyrhiza, we show that aphids can either benefit or suffer from inherited stress responses, depending on metabolite identity and ecological context. In multigenerational clonal plant lineages maintained indoors, ancestral aphid herbivory increased aphid reproduction and reduced plant fitness under renewed attack, indicating that the net effect of inherited stress responses can favor the herbivore. However, not all inherited responses benefited the aphid: using genetic and chemical manipulations, we found that transgenerational priming of jasmonate enhanced aphid performance, whereas transgenerational priming of tyramine reduced it. Notably, tyramine--but not jasmonates--accumulated to higher levels across generations also in large mesocosms outdoors, albeit only within and not across growing seasons. Together, our results reveal that inherited responses of hosts can favor the attackers and highlight ecological context and life-cycle transitions as key determinants of the persistence, duration, and ecological consequences of inherited stress responses.

ecology↗
bioRxiv2025

A Phosphoinositide Interacting Protein Coordinates Stress Precursor Activities

Samd14 is crucial for cell signaling and survival in mouse models of acute anemia. Samd14 has an N-terminal actin capping protein (CP) and a C-terminal sterile alpha motif (SAM) to coordinate stem cell factor/Kit and erythropoietin receptor signaling pathways during terminal differentiation of red blood cell precursors. Here we present new findings that Samd14 expression is needed to maintain balanced autophagy in red blood cell precursors following acute anemia. Autophagy gene signatures and protein levels are markedly altered within the context of acute anemia when red blood cell precursors accelerate the process of erythropoiesis. Samd14 interacted via its SAM domain with phosphatidylinositol 3-phosphate (PI3P) which is an integral component of endosomal and autophagic membranes. We tested PI3Ps role in red blood cell differentiation using a small molecule inhibitor of the Class III PI 3-kinase VPS34, which is the sole kinase responsible for PI3P genesis. SAR405 treatment blocked red blood cell formation. In the absence of Samd14, higher doses of VPS34 inhibition were required to block erythroid differentiation. Given the critical roles of autophagy in normal differentiation, Samd14s stress-dependent activation and roles in autophagy suggest that this mechanism is needed to maintain progenitor levels and balance the production of healthy, mature red blood cells. Key Points- Autophagy genes/proteins are deregulated in red blood cell progenitors after hemolysis-induced acute anemia. - The anemia-activated Samd14 protein interacts with the PI3P lipid moiety which is integral to endosomal and autophagic membrane functions. - VPS34 inhibition blocks terminal erythroid maturation in a Samd14-dependent manner.

molecular biology↗
bioRxiv2025

The olfactory bulb reflects structural plasticity within a genetically stable olfactory network

The olfactory bulb (OB), the first central relay of the olfactory pathway, plays a critical role in odor perception and exhibits remarkable structural plasticity shaped by environmental influences. This raises a fundamental question about the extent to which the structure of the OB is genetically determined. While both OB volume and function have been implicated in a range of neurodegenerative and neuropsychiatric disorders, such as Parkinsons disease, schizophrenia, and depression, all of which involve known genetic risk factors, the heritability of the OB structure remains poorly understood. Here, we investigated the heritability of OB volume and the broader olfactory network architecture in a large sample of healthy young adults (n = 941; aged 22-35 years), including monozygotic and dizygotic twin pairs. Using a deep learning-based segmentation model, we first automatically segmented OB volumes and then employed a support vector machine framework to classify zygosity based on within-pair morphological similarity. The OB volume alone showed weak classification performance in distinguishing between monozygotic and dizygotic twins, suggesting limited heritability. However, integrating OB volume with morphometric features from olfactory-associated brain regions, including the hippocampus, parahippocampal gyrus, entorhinal cortex, and medial orbitofrontal cortices, substantially improved classification performance. This effect was specific to the olfactory network, underscoring the distributed nature of genetic influence in this system. These findings suggest that the OB, despite being a highly plastic and environmentally responsive structure, is embedded within a genetically coordinated neural network.

neuroscience↗
bioRxiv2025

Molecularly informed analysis of histopathology images using natural language

Histopathology refers to the microscopic examination of diseased tissues and routinely guides treatment decisions for cancer and other diseases. Currently, this analysis focuses on morphological features but rarely considers gene expression information, which can add an important molecular dimension. Here, we introduce SpotWhisperer, an AI method that links histopathological images to spatial gene expression profiles and their text annotations, enabling molecularly grounded histopathology analysis through natural language. Our method outperforms pathology vision-language models on a newly curated benchmark dataset, dedicated to spatially resolved H&E annotation. Integrated into a web interface, SpotWhisperer enables interactive exploration of cell types and disease mechanisms using free-text queries with access to inferred spatial gene expression profiles. In summary, SpotWhisperer analyzes cost-effective pathology images with spatial gene expression and natural-language AI, demonstrating a path for routine integration of microscopic molecular information into histopathology.

bioinformatics↗
bioRxiv2025

Copper resistance predicts heritable transgenerational fitness variation in the clonal duckweed Spirodela polyrhiza

Transgenerational plasticity in the absence of genetic change can alter organismal fitness, yet we know little about the genetic basis of transgenerational fitness effects. Here, we explored whether transgenerational fitness effects can be predicted by the rate of vegetative reproduction, plant resistance and defence. Thereto, we exposed monoclonal, singledescendant lineages from 56 globally distributed genotypes of the clonal duckweed Spirodela polyrhiza to five generations of copper excess, followed by five generations without stress, and then measured plant fitness and phenotypes in both environments. Previous copper excess reduced fitness variation within each genotype and elicited heritable and reproducible fitness effects that depended on both the genotype and environment: genotypes that benefited from previous stress under recurring conditions suffered when the stress was absent, and vice versa. These transgenerational fitness effects were predicted best by copper resistance, explaining 30% of the intraspecific variation: the more susceptible a genotype, the more its offspring suffered from ancestral stress in the absence of recurrent stress; however, these offspring became more resistant to copper excess, likely by protecting the photosystem II. Together, these findings show that transgenerational fitness effects are heritable and variable and likely controlled by genes that regulate plant reproduction and defence.

evolutionary biology↗
bioRxiv2025

Caffeine-regulated molecular switches for functional control of CAR T cells in vivo

The limited controllability of CAR T cells in patients represents a key challenge of this highly potent immunotherapy. A molecular ON-switch, which can be regulated with a non-toxic and readily available small molecule drug, would represent a major advance towards controllable CAR T therapeutics. For that purpose, we engineered caffeine-responsive heterodimeric ON-switches (CaffSwitches) and demonstrate their high caffeine-dependency and virtually absent leakiness. When incorporating these CaffSwitches into CARs, the resulting CaffCARs were efficiently activated by caffeine concentrations achieved in human plasma after drinking one cup of coffee. Moreover, CaffCAR T cells also showed efficient tumor clearance in an in vivo mouse model, which was completely abolished in the absence of caffeine. This tight control was even observed with c-Jun overexpressing CaffCAR T cells, despite their massive expansion. Together, we anticipate that these novel CaffSwitches will be valuable tools for the development of safe and efficient next generation CAR T cells.

synthetic biology↗
bioRxiv2025

Basophils activate splenic B cells and Dendritic cells via IL-13 signaling in acute Traumatic Brain Injury

Peripheral consequences following traumatic brain injury (TBI) are characterized by both systemic inflammatory responses and autonomic dysregulation, with almost all peripheral organs affected. One of the main immune regulatory organs, the spleen, shows high interaction with the brain which is controlled by both circulating mediators as well as autonomic fibers targeting splenic immune cells. The brain-spleen axis does not function as a one-way street, it also shows reciprocal effects where the spleen affects neuroinflammatory and cognitive functions post injury. To date, systemic and splenic inflammatory responses are measured by cells or mediators located in circulation. Nevertheless, most of the signaling and inflammation post injury takes place in the organs. Therefore, we set out to investigate the early signaling landscape in the spleen following TBI, using phospho-proteomic signaling approaches and immunofluorescence stainings to investigate novel molecular and cellular players. Based on the signaling signature, we found a rapid influx of basophil granulocytes towards the spleen, which are recruited via CXCL1 expressed by B-cells and dendritic cells. The basophils activate B cells and dendritic cells (DCs) via the IL-13/IL-13Ra1 signaling pathway to enhance protein translation through the long non-coding RNA NORAD. The early recruitment of basophils and subsequent activation of B cells and DCs, is short lived and sets at 3dpi. Interestingly, the rapid recruitment of basophils is inhibited by ethanol intoxication in TBI. In conclusion, basophils recruitment to the spleen may serve as an early mediator of systemic inflammatory responses to TBI with potential implications for research on biomarkers and therapeutic targets.

neuroscience↗
bioRxiv2024

Multimodal learning of transcriptomes and text enables interactive single-cell RNA-seq data exploration with natural-language chats

Single-cell RNA-seq characterizes biological samples at unprecedented scale and detail, but data interpretation remains challenging. Here we introduce CellWhisperer, a multimodal machine learning model and software that connects transcriptomes and text for interactive single-cell RNA-seq data analysis. CellWhisperer enables the chat-based interrogation of transcriptome data in English language. To train our model, we created an AI-curated dataset with over a million pairs of RNA-seq profiles and matched textual annotations across a broad range of human biology, and we established a multimodal embedding of matched transcriptomes and text using contrastive learning. Our model enables free-text search and annotation of transcriptome datasets by cell types, states, and other properties in a zero-shot manner and without the need for reference datasets. Moreover, Cell-Whisperer answers questions about cells and genes in natural-language chats, using a biologically fluent large language model that we fine-tuned to analyze bulk and single-cell transcriptome data across various biological applications. We integrated CellWhisperer with the widely used CELLxGENE browser, allowing users to in-teractively explore RNA-seq data through an integrated graphical and chat interface. Our method demonstrates a new way of working with transcriptome data, leveraging the power of natural language for single-cell data analysis and establishing an important building block for future AI-based bioinformatics research assistants.

bioinformatics↗
bioRxiv2024

Terrestrial herbivory drives adaptive evolution in an aquatic community via indirect effects

Indirect ecological effects, which occur when the impact of one species on another is mediated by a third species or the shared environment, are ubiquitous in nature. Given the complexity of natural systems, indirect ecological effects were thought to be important in driving eco-evolutionary processes across community boundaries. However, we know remarkably little about such effects. Here we show that indirect effects of terrestrial insect (aphids) herbivory on macrophytes (duckweed) drives adaptive evolution of water fleas (Daphnia) in large outdoor aquatic mesocosms. Aphid herbivory reduced macrophyte growth and increased the abundance of phytoplankton, which in turn increased the abundance of Daphnia. Whole genome pool sequencing and phenotypic assays revealed an impact on the genetic compositions of the Daphnia populations and transplant experiments indicated that these evolutionary changes were adaptive. Furthermore, these changes in the aquatic community altered the interactions of the aphids and the macrophytes. These results demonstrate that indirect ecological effects can shape eco-evolutionary interactions between different communities.

evolutionary biology↗
bioRxiv2024

Genome-Wide Association Study of Metabolic Traits in the Duckweed Spirodela polyrhiza

The exceptionally high growth rate and high contents of flavonoids make the giant duckweed Spirodela polyrhiza (L.) Schleid. (Arales: Lemnaceae) an ideal organism for food production and metabolic engineering. To facilitate this, identification of the genetic basis underlying growth and metabolic traits is essential. Here, we characterized the genetics underpinning the growth and contents of 42 metabolites in S. polyrhiza using a genome-wide association (GWA) approach. We found that biomass positively correlates with contents of many free amino acids, including L-Glutamine, L-Tryptophane and L-Serine, but negatively correlates with many specialized metabolites, such as flavonoids. GWA analysis showed that several candidate genes were simultaneously associated with several metabolic traits, qualifying them as targets for growth manipulation and metabolic engineering. Together, this study provides insights into the metabolic diversity of S. polyrhiza and its underlying genetic architecture, paving the way for industrial applications of this plant via targeted breeding or genetic engineering.

plant biology↗
bioRxiv2024

Ideal efficacy photoswitches for TRPC4/5 channels harness high potency for spatiotemporally-resolved control of TRPC function in live tissues

Directly probing the endogenous biological roles of target proteins with high spatial and temporal resolution, as non-invasively and reproducibly as possible, is a shared conceptual goal for research across many fields, as well as for targeted therapies. Here we describe the rational conceptual design and test-case practical implementation of a photopharmacological paradigm to empower high-performance photomodulation studies in vivo. TRPC4/5 ion channels are involved in many spatiotemporally resolved circuits, from pain and anxiety, to reproductive signaling, digestion, and obesity. To unpick their biology requires spatiotemporally precise tools, which were lacking. We developed "ideal efficacy photoswitch" ligands to control their diverse functions in situ. These E{leftrightarrows}Z-photoswitchable ligands bias TRPC[4]/5 channel activity with exquisite photocontrol, from strong agonism under 360 nm, to low agonism at 385 nm, to strong antagonism at 410-460 nm. Cryo-EM structures of both TRPC4 and TRPC5 with both Z-agonists and E-antagonists support the rationale for efficacy switching through competitive E/Z isomer binding. Crucially, since the E/Z ratio is exclusively determined by the light wavelength applied, their channel photocontrol is exclusively wavelength-dependent, yet drug-concentration-independent: so is reproducible from cell culture to >millimetre-depth tissues. Indeed, we were able to photocontrol both direct and downstream TRPC4/5 biology in cell lines or primary cells in culture, from calcium flux, to primary neuron excitability and adrenaline release; and even in tissues, photoswitching small intestine motility and peristalsis. The TRPC4/5 ligands we develop will thus unlock a range of high-precision investigations in TRP biology. More broadly, we propose that the success of this efficacy photoswitch program, from concept to tissue level translation, is mainly a consequence of how biology has evolved proteins for efficacy control. We therefore foresee that a variety of functionally responsive protein targets, not only sensory and signaling ion channels and receptors, will be amenable to similarly high-performance photocontrol even in vivo, if a new generation of reagent development adopts this paradigm of ideal efficacy photoswitching. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/602451v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1f8e527org.highwire.dtl.DTLVardef@18c72d0org.highwire.dtl.DTLVardef@1c5d648org.highwire.dtl.DTLVardef@177203d_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗
bioRxiv2024

The Respiratory-Pupillary Phase Effect: Pupils size is smallest around inhalation onset and largest during exhalation

The prevailing view in the study of animal and human pupillary function has been that pupils dilate and are largest during inhalation and constrict and are smallest during exhalation. However, this notion has recently been challenged. Here, we systematically address this question by conducting a study encompassing three experiments (two resting tasks and one visual perception task), with the latter two being pre-registered. Collectively, across nasal and oral breathing, resting, and task conditions, our experiments consistently and robustly demonstrate that pupil size is smallest around inhalation onset and largest around peak exhalation. This phenomenon, which we term the Respiratory-Pupillary Phase Effect (RPPE), directly contradicts the long-held notion that pupils are largest during inhalation and smallest during exhalation. Notably, the dilation and constriction processes overlap with both phases. The observed consistency and significance of the RPPE across various conditions underscore the need for further investigation into its underlying mechanisms and potential impact on human behavior.

physiology↗