Biology subjects

Stroustrup, N.

Publications and source records attributed to Stroustrup, N..

10 recordsLinked to original sources

bioRxiv2026

Declines in mRNA synthesis set the rate of organismal aging

The abundance of mRNA sets a ceiling on a cells capacity to produce protein and carry out its functions. Here, we describe a pathological decline in absolute mRNA abundance that occurs in most cell types during invertebrate and mammalian aging, caused by decreases in mRNA synthesis capacity. In C. elegans, decreases in mRNA abundance are tightly coupled to declines in RNA Polymerase II (Pol II) protein abundance. Measuring Pol II abundance dynamics in vivo, we find that individuals enter adulthood with a four-fold excess of Pol II, whose kinetic equilibration towards its homeostatic set point drives reductions in mRNA abundance and, in turn, organismal aging. Briefly accelerating Pol II declines produces permanent, dose-dependent reductions in healthspan and lifespan, whereas deceleration extends both. Although disrupted cellular homeostasis is conventionally seen as a consequence of aging, our results reveal how an out-of-equilibrium state established during development provides a driving force for aging.

systems biology↗

bioRxiv2026

In vivo functional classification of PTEN variants reveals context-dependent oncogenicity and interindividual variability

Gene variants, secondary mutations, and stochastic individual variability complicate cancer diagnosis, prognosis, and treatments. Here, we systematically assess the functional impact of PTEN cancer-related missense mutations in mammalian cell lines, yeast, and Caenorhabditis elegans. While cell-based assays revealed alterations in lipid phosphatase activity, CRISPR-based engineering of orthologous mutations in C. elegans enabled classification of variants based on organismal phenotypes and transcriptional profiles, providing a rapid framework to predict oncogenic potential. We further show that secondary mutations, such as gain-of-function of cdc-25.1/CDC25A, can enhance the phenotypic impact of specific daf-18/PTEN variants, revealing context-dependent oncogenicity. Finally, single-worm transcriptomic analyses uncovered substantial interindividual variability among isogenic animals with identical cdc-25.1 and daf-18 mutations, linking transcriptional states to divergent phenotypic outcomes. Together, our results establish C. elegans as a powerful in vivo platform to integrate genetic, functional, and transcriptional information for the interpretation of cancer-associated variants.

cancer biology↗

bioRxiv2025

STOMP-seq: early multiplexing for high-throughput Smart-seq2 RNA-sequencing.

RNA-sequencing provides high-dimensional, quantitative measurements of the states of cells, tissues, organs, and whole organisms. Plate-based RNA-seq protocols allow for a wider range of experimental designs than droplet sequencing methods, but are less scalable due to the practical challenges of plate-based liquid handling. Here, we present STOMP-seq, a method that extends SMART RNA-seq protocols, like Smart-seq2 and Smart-seq3, to include sample-identifying barcodes on the 5 end of each amplified transcript. These barcodes allow samples to be pooled immediately after reverse transcription, enabling a 12-fold multiplexing strategy that reduces liquid handling complexity and enzyme costs several-fold. Suitable for both manual and robotic library preparation approaches, STOMP-seq reduces protocol execution times four-fold while improving library complexity and coverage. Together, these advantages combine to make possible new large-scale experimental designs, in particular population-scale sequencing projects like the multi-generational study of gene-expression heritability presented here. STOMP-seq offers a "drop-in" replacement for Smart-seq2 and Smart-seq3, removing practical barriers that currently limit the quality and scope of plate-based transcriptomic data. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/645277v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@83f1b4org.highwire.dtl.DTLVardef@717012org.highwire.dtl.DTLVardef@174e34forg.highwire.dtl.DTLVardef@f790b3_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

Intergenerational control of ribosomes under dietary restriction

Cells adjust their proteome to their environment. Most prominently, ribosome expression scales near linearly with the cellular growth rate to provide sufficient translational capacity while preventing metabolically wasteful ribosomal excess. In microbes, such proteome adjustments can passively perpetuate through symmetric cell division. However, in animals, a passive propagation is hindered by the separation between soma and germline. This separation raises the crucial question whether the proteome of animals is reset at every generation or can be propagated from parent to offspring despite this barrier. We addressed this question by exploring the intergenerational effects of dietary restriction in C. elegans, combining proteomics and live imaging. While most proteins showed no intergenerational regulation, ribosomal proteins remained reduced in offspring after maternal dietary restriction. When offspring of dietarily restricted mothers were raised under improved dietary conditions, this reduced ribosome content delayed their growth until normal ribosomal protein levels were restored. Soma-specific maternal inhibition of mTORC1 signalling replicated these effects, while other growth-reducing perturbations, such as reduced insulin signalling or maternal ribosome depletion, did not impact offspring ribosomes. Thus, mTORC1 signalling bridges across the soma-germline divide to regulate ribosome levels of the next generation, likely priming the offspring for the anticipated demand in protein synthesis.

physiology↗

bioRxiv2024

Engineering the auxin-inducible degron system for tunable in vivo control of organismal physiology

The physiological mechanisms governing health and disease exhibit complex interactions between multiple genes and gene products. To study the dynamics of living systems, researchers need experimental methods capable of producing calibrated, quantitative perturbations in vivo -- perturbations that cannot be obtained using classical genetics, RNAi interference, or small molecule drugs. Recently, an auxin-inducible degron (AID) system has been developed to allow targeted degradation of proteins using small-molecule activators, providing spatiotemporal control of protein abundance. However, a better understanding of the biochemical activities of AID system components in their physiological context is needed to design quantitative interventions. Here, we apply engineering approaches to characterize and understand the performance of several AID technologies and then improve this performance in the multicellular animal Caenorhabditis elegans. We 1) develop new technologies that allow for a careful calibration of AID activity for specific purposes; 2) develop new TIR1 enzyme constructs with improved performance over existing constructs; 3) develop an approach to simultaneously and independently degrade target proteins in distinct tissues; and finally, 4) develop an approach for pan-organismal protein degradation by re-engineering the TIR1 enzyme. Taken together, these advances enable new quantitative experimental approaches to study the cellular and systems dynamics of animals.

systems biology↗

bioRxiv2024

Selective autophagy of ribosomes balances a tradeoff between starvation survival and growth resumption

Animals facing fluctuating food availability must balance survival during starvation with rapid resumption of growth when encountering food. We investigated how proteome turnover and remodelling through autophagy influences this trade-off in C. elegans L1 larvae by combining live imaging and proteomics. Starvation triggered an autophagy-dependent, disproportionate loss of ribosomal and other growth-related proteins. Residual ribosomal protein abundance at the end of starvation predicted the rate of growth recovery of individual animals during post-starvation feeding, linking proteome-scale changes to organism-scale life-history. Hyperactivation of the mTORC1 regulator RAGA-1 preserved ribosomal proteins, accelerated recovery after short starvation, but reduced survival under prolonged starvation. These findings identify autophagy-dependent ribosomal protein decline as a central component of starvation-induced proteome remodelling and reveal its role in balancing the trade-off between starvation endurance and recovery speed in a multicellular animal.

physiology↗

bioRxiv2023

An mTOR/RNA pol I axis shapes chromatin architecture in response to fasting

Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom. Yet, how it impacts on 3D genome organization is unknown. Here, we show that fasting induces a reversible and large-scale spatial reorganization of chromatin in C. elegans. This fasting-induced 3D genome reorganization requires inhibition of the nutrient-sensing mTOR pathway, a major regulator of ribosome biogenesis. Remarkably, loss of transcription by RNA Pol I, but not RNA Pol II nor Pol III, induces a similar 3D genome reorganization in fed animals, and prevents the restoration of the fed-state architecture upon restoring nutrients to fasted animals. Our work documents the first large-scale chromatin reorganization triggered by fasting and reveals that mTOR and RNA Pol I shape genome architecture in response to nutrients.

cell biology↗

bioRxiv2022

Neuronal temperature perception induces specific defenses that enable C. elegans to cope with the enhanced reactivity of hydrogen peroxide at high temperature

Hydrogen peroxide is the most common reactive chemical that organisms face on the microbial battlefield. The rate with which hydrogen peroxide damages biomolecules required for life increases with temperature, yet little is known about how organisms cope with this temperature-dependent threat. Here, we show that Caenorhabditis elegans nematodes use temperature information perceived by sensory neurons to cope with the temperature-dependent threat of hydrogen peroxide produced by the pathogenic bacterium Enterococcus faecium. These nematodes preemptively induce the expression of specific hydrogen peroxide defenses in response to perception of high temperature by a pair of sensory neurons. These neurons communicate temperature information to target tissues expressing those defenses via an insulin/IGF1 hormone. This strategy, which we call "enhancer sensing," is the first example of a multicellular organism inducing their defenses to a chemical when they sense an inherent enhancer of the reactivity of that chemical.

neuroscience↗

bioRxiv2021

A Hierarchical Process Model Links Behavioral Aging and Lifespan in C. elegans

Individuals who remain vigorous longer tend to live longer, supporting the design of predictive behavioral biomarkers of aging. In C. elegans, the timing of age-associated vigorous movement cessation (VMC) and lifespan correlate strongly between individuals. However, many genetic and pharmaceutical interventions that alter aging produce disproportional effects on VMC and lifespan, appearing to "uncouple" the rate of behavioral aging and lifespan. To study the causal structure underlying such uncoupling, we developed a high-throughput, automated imaging platform to quantify behavioral aging and lifespan at an unprecedented scale. Our method reveals an inverse correlation between each individuals vigorous movement span and their remaining lifespan. Robust across many lifespan-altering interventions including a new RNA-polymerase II auxin-inducible degron system, our data shows that individual C. elegans experience at least two distinct but coupled physical declines--one governing VMC and the other governing lifespan. Through simulations and modeling, we clarify the causal relationship between these two "biological ages" and highlight a crucial but often untested assumption in conventional aging biomarker research: predictive biomarkers may not always report on the same biological age as that which determines long-term health outcomes.

systems biology↗

bioRxiv2018

Transcriptomics-based screening identifies pharmacological inhibition of Hsp90 as a means to defer aging

Aging is a major risk factor for human morbidity and mortality. Thus, the identification of compounds that defer aging, also known as geroprotectors, could greatly improve our health and promote a longer life. Here we screened for geroprotectors, employing the power of human transcriptomics to predict biological age. We used age-stratified human tissue transcriptomes to generate machine-learning-based classifiers capable of distinguishing transcriptomes from young versus old individuals. Then we applied these classifiers to transcriptomes induced by 1300 different compounds in human cell lines and ranked these compounds by their ability to induce a youthful transcriptional state. Besides known geroprotectors, several new candidate compounds emerged from this ranking. Testing these in the model organism C. elegans, we identified two Hsp90 inhibitors, Monorden and Tanespimycin, which substantially extended the animals lifespan and improved their health. Hsp90 inhibition specifically induces the expression of heat shock proteins, known to improve protein homeostasis. Consistently, Monorden treatment improved the survival of C. elegans under proteotoxic stress, and its lifespan benefits were fully dependent on the master regulator of the cytosolic unfolded protein response, the transcription factor HSF-1. Taken together, we present an innovative transcriptomics-based screening approach to discover aging-preventive compounds and highlight Hsp90 inhibitors as powerful geroprotectors that could be of great value, to target the aging process in humans.

cell biology↗