Biology subjects

Spielmann, N.

Publications and source records attributed to Spielmann, N..

7 recordsLinked to original sources

bioRxiv2026

EchoVisuALL: From Echocardiography to Gene Discovery

Cardiovascular diseases are a major global health burden, demanding phenotyping frame-works that can match the scale and complexity of contemporary mouse genetics. Here, we introduce EchoVisuALL, an AI-enabled pipeline for automated high-throughput transthoracic echocardiography (TTE) coupling deep-learning-based left-ventricular segmentation with data reporting. Across 65,000 recordings from over 18,000 mice, including single-gene knockouts from the International Mouse Phenotyping Consortium, the framework quantified cardiac morphology and function with minimal operator dependency and high reliability, validated against an expert-curated gold standard dataset. By extracting quantitative parameters across the cardiac cycle, EchoVisuALL in combination with multi-dimensional clustering uncovered nonlinear phenotypic relationships and revealed 37 of 715 genes associated with significant cardiac abnormalities, encompassing well-known human disease genes as well as 12 previously unrecognized candidates, including Cep70, Acot12, Atp8b3, Eea1, Kctd2, and Tspan15. These genotype-phenotype associations are involved in myocardial energetics, membrane biology, and cardiac remodeling. We demonstrate the potential of EchoVisuALL to move beyond image segmentation by delivering a standardized, quantitative foundation for scalable downstream analyses, enabling the discovery of novel cardiac disease genes.

bioinformatics↗

bioRxiv2025

Rethinking ratio-based normalization: A guide towards model-based approaches in heart weight analysis

Heart weight is a critical parameter in cardiology and mouse research, reflecting structural and functional changes linked to cardiac size or hypertrophy and pathophysiological conditions. Normalizing heart weight (HW) to body weight (BW) or tibia length (TL) is a common practice; however, the validity of these ratios has been questioned due to non-proportional relationships between parameters, and this becomes particularly problematic when comparing distinct populations based on such normalized values. Using data from over 25,000 C57BL/6N wildtype mice provided by the International Mouse Phenotyping Consortium (IMPC), we investigated the limitations of ratio-based normalization when comparing different groups, aiming to propose a robust framework for HW analysis. Our findings reveal negligible to weak correlations between HW, BW, and TL across age and sex groups, undermining the validity of ratio-based methods. A modelling study using simulated data demonstrated that ratios could produce misleading results, including reversed or false group differences, when scaling assumptions are violated. Ratios yield accurate and interpretable results only when a truly proportional relationship exists between the variables--specifically, when the regression line passes through the origin--conditions under which ratio-based normalization aligns with outcomes obtained from more robust modelling approaches. These results underscore the superiority of linear models with covariate adjustment and allometric scaling for organ weight analysis, as they more accurately capture biologically relevant scaling relationships. By leveraging the IMPCs large-scale wildtype dataset, we establish the necessity of reassessing normalization practices in quantitative biology traits and propose that ratios should be avoided when comparing normalized values across distinct populations unless key mathematical assumptions are met. This study advances the analytical rigor in phenotyping research, enabling more accurate interpretations of organ mass and function across biological contexts.

physiology↗

bioRxiv2025

Establishing Comprehensive Transthoracic Echocardiography Reference Ranges for Mouse Models: Insights into the Impact of Anesthesia, Sex, and Age

Mouse models play a critical role in cardiology research, offering valuable insights into the molecular mechanisms, genetics, and potential treatments for cardiovascular diseases. However, the ability to transfer findings in mice between studies is limited by the absence of standardized protocols and valid reference values for the assessment of normal cardiac function in mice. This study aims to establish comprehensive transthoracic echocardiography (TTE) reference ranges for mice, particularly focusing on C57BL/6N wildtype controls. The study, which includes data from over 15,000 mice through the International Mouse Phenotyping Consortium (IMPC), highlights how variables such as sex, age, body weight, and anesthesia affect TTE parameters. The findings showed that anesthesia is the primary predictor of variability in cardiac function. Isoflurane and tribromoethanol anesthetized mice presented with modified cardiac function compared to conscious mice. Additionally, we observed minimal sex differences in cardiac morphology and function, except for small variations influenced by anesthesia. The effects of aging on cardiac function were modest, characterized by a decrease in heart rate and subtle changes in ventricular dimensions without evidence of pathological remodeling, likely attributable to disease-free cardiovascular aging. Validation of the reference ranges across multiple mouse strains showed that these values provide a reliable baseline for experiments involving cardiac function in mice. The data underscore the importance of using anesthesia-specific reference values when interpreting TTE results, ensuring robust comparisons in genetic and pharmacological studies. These reference ranges serve as quality assurance tools for future cardiac studies in mice, offering insights into typical TTE parameter values, supporting the detection of experimental perturbations, and contributing to more effective translation of findings from mouse to human.

genetics↗

bioRxiv2023

Comparative phenotyping of mice reveals canonical and noncanonical physiological functions of TRα and TRβ

Thyroid hormone (TH) effects are mediated through TH receptors (TRs) TR1, TR{beta}1, and TR{beta}2. The TRs bind to thyroid hormone responsive elements on the DNA and regulate expression of TH target genes as ligand dependent transcription factors (canonical signaling). In addition, the TRs and {beta} mediate activation of signaling pathways, e.g. the PI3K/AKT and MAPK/ERK pathways (noncanonical signaling). Whether such DNA-binding independent TR action contributes to the spectrum of physiological TH effects is largely unknown. The aim of this study was to attribute physiological effects to the two TR isoforms and {beta} and their canonical and noncanonical signaling. We conducted multi-parameter phenotyping in male and female TR knockout mice (TRKO, TR{beta}KO), mice with disrupted canonical signaling due to a mutation in the TR DNA-binding domain (TRGS, TR{beta}GS) and their respective wild-type littermates. Perturbations in senses, especially hearing (mainly TR{beta} with a lesser impact of TR), visual acuity and retinal thickness (TR and TR{beta}), in muscle metabolism (TR) and in heart rate (TR) highlighted the role of canonical TR action. Strikingly, selective abrogation of canonical TR action often had little to no phenotypic consequence, suggesting that noncanonical TR action sufficed to maintain the wild-type phenotype for specific effects. For instance, macrocytic anemia, reduced retinal vascularization or increased anxiety related behavior were only observed in TRKO, but not TRGS mice. Noncanonical TR action increased the efficiency of energy utilization and prevented hyperphagia observed in TRKO mice. In summary, by examining the phenotypes of TR and TR{beta} knockout models alongside their DNA-binding-deficient GS mutants and wildtype counterparts, we could establish that the independent noncanonical actions of TR and TR{beta} play a crucial role in modulating sensory, behavioral, and metabolic functions. This comparison underscores the significance of the TRs in orchestrating a spectrum of physiological processes beyond their traditional genomic pathways.

physiology↗

bioRxiv2023

Canonical and noncanonical contribution of thyroid hormone receptor isoforms alpha and beta to cardiac hypertrophy and heart rate in male mice

BackgroundStimulation of ventricular hypertrophy and heart rate are two major cardiac effects of thyroid hormone (TH). Aim of this study was to determine in vivo which TH receptor (TR), or {beta}, and which mode of TR action, canonical gene expression or DNA-binding independent noncanonical action, mediate these effects. Material and methodsWe compared global TR and TR{beta} knockout mice (TRKO; TR{beta}KO) with WT mice to determine the TR isoform responsible for T3 effects. The relevance of TR DNA- binding was studied in mice with a mutation in the DNA-binding domain that selectively abrogates DNA binding and canonical TR action (TRGS; TR{beta}GS). Hearts were studied with echocardiography at baseline and after seven weeks T3-treatment. Gene expression was measured with real-time PCR. Heart rate was recorded with radiotelemetry transmitters for seven weeks in untreated, hypothyroid and T3-treated mice. ResultsT3 induced ventricular hypertrophy in WT and TR{beta}KO mice, but not in TRKO mice. Hypertrophy was also induced in TRGS mice. Thus, hypertrophy is mostly mediated by noncanonical TR action. Similarly, repression of Mhy7 occurred in WT and TRGS mice. Basal heart rate was largely dependent on canonical TR action. But responsiveness to hypothyroidism and T3-treatment as well as expression of pacemaker gene Hcn2 were still preserved in TRKO mice, demonstrating that TR{beta} could compensate for absence of TR. ConclusionT3-induced cardiac hypertrophy could be attributed to noncanonical TR action, whereas heart rate regulation was mediated by canonical TR action. TR{beta} could substitute for canonical, but not noncanonical TR action.

physiology↗

bioRxiv2023

TRPS1 maintains luminal progenitors in the mammary gland by repressing SRF/MRTF activity

The transcription factor TRPS1 is a context-dependent oncogene in breast cancer [1] [2] [3] [4] [5]. In the mammary gland, TRPS1 activity is restricted to the luminal population and is critical during puberty and pregnancy [2]. Its function in the resting state remains however unclear. To evaluate whether it could be a target for cancer therapy, we investigated TRPS1 function in the healthy adult mammary gland using a conditional ubiquitous depletion mouse model where long-term depletion does not affect fitness. We show that TRPS1 activity is essential to maintain a functional luminal progenitor compartment. This requires the repression of both YAP/TAZ and SRF/MRTF activities, TRPS1 represses SRF/MRTF activity indirectly by modulating RhoA activity. Our work uncovers a hitherto undisclosed function of TRPS1 in luminal progenitors intrinsically linked to mechanotransduction in the mammary gland. It also provides new insights into the oncogenic functions of TRPS1 as luminal progenitors are likely the cells of origin of many breast cancers. Significance statementThe transcription factor TRPS1 is a context-dependent oncogene in breast cancer. It is unclear how TRPS1 contributes to cancer development and whether it could be a target for therapy. Here we established a mouse model mimicking the systemic effect of TRPS1 drug targeting. With this model, we can show that TRPS1 depletion does not impact the fitness of the animals and that the role of TRPS1 is to maintain a functional luminal progenitor pool in the mammary gland. Mechanistically, TRPS1 represses a mechano-transduction program preventing their commitment to an alveolar fate. Because there is growing evidence that breast cancer originates from the expansion of altered luminal progenitors, our work provides valuable insights into the understanding of breast cancer initiation.

cell biology↗

bioRxiv2022

Deep Phenotyping and Lifetime Trajectories Reveal Limited Effects of Longevity Regulators on the Aging Process in C57BL/6J Mice

Current concepts regarding the biology of aging are based on studies aimed at identifying factors regulating natural lifespan. However, lifespan as a sole proxy measure for aging can be of limited value because it may be restricted by specific sets of pathologies, rather than by general physiological decline. Here, we employed large-scale phenotyping to analyze hundreds of phenotypes and thousands of molecular markers across tissues and organ systems in a single study of aging male C57BL/6J mice. For each phenotype, we established lifetime profiles to determine when age-dependent phenotypic change is first detectable relative to the young adult baseline. We examined central genetic and environmental lifespan regulators (putative anti-aging interventions, PAAIs; the following PAAIs were examined: mTOR loss-of-function, loss-of-function in growth hormone signaling, dietary restriction) for a possible countering of the signs and symptoms of aging. Importantly, in our study design, we included young treated groups of animals, subjected to PAAIs prior to the onset of detectable age-dependent phenotypic change. In parallel to our studies in mice, we assessed genetic variants for their effects on age-sensitive phenotypes in humans. We observed that, surprisingly, many PAAI effects influenced phenotypes long before the onset of detectable age-dependent changes, rather than altering the rate at which these phenotypes developed with age. Accordingly, this subset of PAAI effects does not reflect a targeting of age-dependent phenotypic change. Overall, our findings suggest that comprehensive phenotyping, including the controls built in our study, is critical for the investigation of PAAIs as it facilitates the proper interpretation of the mechanistic mode by which PAAIs influence biological aging. HighlightsO_LIPhenotyping at scale defines lifetime trajectories of age-dependent changes in C57BL/6J mice C_LIO_LICentral genetic and environmental lifespan regulators (putative anti-aging interventions; PAAIs) influence age-sensitive phenotypes (ASPs) often long before the appearance of age-dependent changes in these ASPs C_LIO_LICorresponding genetic variants in humans also have age-independent effects C_LIO_LIMany PAAI effects shift the baseline of ASPs rather than slowing their rate of change C_LI

physiology↗