Biology subjects

Rau, C.

Publications and source records attributed to Rau, C..

10 recordsLinked to original sources

bioRxiv2025

Global Analyses of Genomic and Epigenomic Influences on Gene Expression Reveals Serpina3n as a Major Regulator of Cardiac Gene Expression in Response to Catecholamine Challenge During Heart Failure

Heart failure arises from maladaptive remodeling driven by genetic and epigenetic networks. Using a systems genetics framework, we mapped how DNA variants and CpG methylation shape cardiac transcriptomes during beta adrenergic stress in the Hybrid Mouse Diversity Panel, a cohort of over 100 fully inbred mouse strains. Expression QTLs (eQTLs), methylation QTLs (mQTLs) and methylation-driven eQTLs (emQTLs) were generated from over 13k expressed genes and 200k hypervariable CpGs in left ventricles. We discovered hundreds of regulatory "hotspots" that control large portions of the genome, including several that regulate over 10% of the transcriptome and/or methylome. Approximately 16% of these hotspots overlapped with prior GWAS or EWAS signals. We focus on a hotspot on chromosome 12 and identify the serpine peptidase inhibitor Serpina3n, as the most likely driver gene in this hotspot. Experimental knockdown of Serpina3n in neonatal rat ventricular cardiomyocytes blunted hypertrophy induced by a variety of hypertrophic signals, while altering predicted target expression and modulating the activity of Nppa and Nppb. Together, these findings position Serpina3n as a major regulator of stress-responsive cardiac gene programs, highlighting how integration of genetic and epigenetic signals can pinpoint key drivers of heart failure. Key HighlightsO_LICross-omics hotspot analysis: We identified 286 eQTL, mQTL, and emQTL hotspots in the Hybrid Mouse Diversity Panel, including several hotspots that regulate over 10% of the cardiac transcriptome. C_LIO_LIIntegration with prior GWAS/EWAS: [~]16% of hotspots overlapped with previously reported heart failure hotspots, strengthening their biological relevance. C_LIO_LIDiscovery of Serpina3n as heart failure regulator: A hotspot on chromosome 12 linked to Serpina3n controlled 4-6% of all gene expression and CpG methylation changes in response to isoproterenol. C_LIO_LIFunctional validation: siRNA knockdown of Serpina3n in cardiomyocytes significantly blunted hypertrophy induced by isoproterenol, angiotensin II, and phenylephrine. C_LIO_LIPathway insights: Genes regulated by the Serpina3n hotspot were enriched for mitochondrial function, dilated cardiomyopathy, and hypertrophic signaling pathways, highlighting a mechanistic link to heart failure progression. C_LI

genetics↗

bioRxiv2024

Novel Insights into Post-Myocardial Infarction Cardiac Remodeling through Algorithmic Detection of Cell-Type Composition Shifts

BackgroundRecent advances in single cell sequencing have led to an increased focus on the role of cell-type composition in phenotypic presentation and disease progression. Cell-type composition research in the heart is challenging due to large, frequently multinucleated cardiomyocytes that preclude most single cell approaches from obtaining accurate measurements of cell composition. Our in silico studies reveal that ignoring cell type composition when calculating differentially expressed genes (DEGs) can have significant consequences. For example, a relatively small change in cell abundance of only 10% can result in over 25% of DEGs being false positives. MethodsWe have implemented an algorithmic approach that uses snRNAseq datasets as a reference to accurately calculate cell type compositions from bulk RNAseq datasets through robust data cleaning, gene selection, and multi-sample cross-subject and cross-cell-type deconvolution. We applied our approach to cardiomyocyte-specific 1A adrenergic receptor (CM-1A-AR) knockout mice. 8-12 week-old mice (either WT or CM-1A-KO) were subjected to permanent left coronary artery (LCA) ligation or sham surgery (n=4 per group). Transcriptomes from the infarct border zones were collected 3 days later and analyzed using our algorithm to determine cell-type abundances, corrected differential expression calculations using DESeq2, and validated these findings using RNAscope. ResultsUncorrected DEGs for the CM-1A-KO X LCA interaction term featured many cell-type specific genes such as Timp4 (fibroblasts) and Aplnr (cardiomyocytes) and overall GO enrichment for terms pertaining to cardiomyocyte differentiation (P=3.1E-4). Using our algorithm, we observe a striking loss of cardiomyocytes and gain in fibroblasts in the 1A-KO + LCA mice that was not recapitulated in WT + LCA animals, although we did observe a similar increase in macrophage abundance in both conditions. This recapitulates prior results that showed a much more severe heart failure phenotype in CM-1A-KO + LCA mice. Following correction for cell-type, our DEGs now highlight a novel set of genes enriched for GO terms such as cardiac contraction (P=3.7E-5) and actin filament organization (P=6.3E-5). ConclusionsOur algorithm identifies and corrects for cell-type abundance in bulk RNAseq datasets opening new avenues for research on novel genes and pathways as well as an improved understanding of the role of cardiac cell types in cardiovascular disease.

bioinformatics↗

bioRxiv2023

Genome-wide association study and sequence similarity analysis for unilateral renal agenesis using heterogeneous stock rats undercovers the KIT gene and AHR, ATF3, GATA3, HNF1B, POU2F2, and TFCP2 transcription factors as potential candidates to explain incomplete penetrance

1Human unilateral renal agenesis is a congenital urinary tract malformation. Affected individuals have only one kidney, which is often an asymptomatic developmental defect. A total of 5,585 male and female HS rats were assessed for unilateral renal agenesis and genotyped for 3513,321 markers. The R package SAIGEgds was used for the association analysis. The adjusted p-value threshold for the association analysis determined by permutation was equal to 5.6 (-log10). Two additional datasets were used as validation tests. Population two included 1,577 rats genotyped for 7,425,889 markers and a case-control imbalance equal to 1:174; population three included 1,407 rats, genotyped for 254,932 markers and case-control ratio equal to 1:38. The python package GxTheta was used to perform a polygenic epistasis analysis for the analyzed HS rat population. A founder haplotype mosaic determination was performed using the R package QTL2. Associated regions were selected for further analysis, including long-read PacBio sequencing for founder individuals and a founder haplotype prediction test. A similarity analysis at a genomic level and for loci encoding transcription factors predicted to interact with selected sequences inside the associated loci were accomplished. A total of 1,181 polymorphisms were associated with URA. All associated polymorphisms were located on chromosome 14 between 32.9 and 36.6 Mb. The most significant polymorphism was chr14:36,411,266, a G/T transversion. The same associated region was identified in population three. Polygenic epistasis was determined as not predominant for the presentation of URA. Based on the haplotype mosaic probability estimation, cases display a higher probability of inheriting the ACI allele. The long-read sequencing analysis showed the presence of an Erv insertion inside the intron one of the KIT gene located inside the associated region. The Erv insertion comprises one Erv sequence and two Ltr sequences located downstream and upstream of the former. No Erv insertion was identified for the founder strain BN. For ACI and HSRA, only one Ltr sequence was identified. One hundred and seven genes encoding TFs that recognize binding sites on the Erv insertion were analyzed for sequence similarity against the reference HSRA. The TF similarity score analysis for the interaction genotype and phenotype showed significance after FDR correction for 20 TFs, including AHR, HNF1B, JUNB, RARG, and RXRA. A mechanism identifying URA as a threshold phenotype is suggested in HS rats. It implies the existence of a minimum threshold for the final number of nephrons and kidney associated structures required for stalling the apoptotic process of the metanephric rudiments. Animals exhibiting a quantitative cumulative defect would express URA, being this malformation identified as a phenotype with decreased penetrance in the assessed population of HS rats. All these processes are described as mediated by KIT and TFs able to interact with sequences of the Erv insertion.

genetics↗

bioRxiv2023

Evolution of compound eye morphology underlies differences in vision between closely related Drosophila species

Insects have evolved complex visual systems and display an astonishing range of adaptations for diverse ecological niches. Differences in eye size within and between Drosophila species provide the opportunity to study the impact of eye structure on vision. Here we further explored differences in D. mauritiana and its sibling species D. simulans and confirmed that D. mauritiana have rapidly evolved larger eyes as a result of more and wider ommatidia than D. simulans since their recent common ancestor. The functional impact of eye size, and specifically ommatidia size, is often only estimated based on the rigid surface morphology of the compound eye. Therefore, we used 3D synchrotron radiation tomography to measure optical parameters in 3D, predict optical capacity, and compare the modelled vision to in vivo optomotor responses. Our optical models predicted higher contrast sensitivity for D. mauritiana, which we verified by presenting sinusoidal gratings to tethered flies in a flight arena. Similarly, we confirmed the higher spatial acuity predicted for Drosophila simulans with smaller ommatidia and found evidence for higher temporal resolution.

evolutionary biology↗

bioRxiv2022

"Same same but different"Exploring evolutionary and ecological causes of eye diversification in bumblebees

Bees rely heavily on vision during most of their interaction with the environment, but so far, visual abilities have not been included into functional investigations of these crucial pollinators. This is probably due to the lack of comprehensive and phylogenetically-controlled quantification of visual traits across species. In the present study, we used high-throughput micro-CT tools to quantify, compare and understand the diversity of visual traits of compound eyes in bumblebees. Visual systems of bumblebees were far from identical, with variations across sizes, castes and species. While phylogenetic proximity poorly supported interspecific variations, these were better explained by two ecological factors: social parasitism and habitat. The eye parameter - a metric that measures the relative investment of a compound eye into resolution or sensitivity - was lower in queens of social parasitic species than of non-parasitic species. Workers of species associated with forested habitat had distinct visual traits, including a higher eye parameter, than those of species living in open landscapes. These diverse visual traits are likely to provide selective advantages to bumblebees given their specific ecological requirements. We thus propose that social parasitism and forest habitat are drivers of the diversification of compound eyes in bumblebees. Finally, we discuss how the present study can inspire trait-based approaches in ecology and conservation biology.

neuroscience↗

bioRxiv2022

Cardiomyocyte ploidy is dynamic during postnatal development and varies across genetic backgrounds

Somatic polyploidization, an adaptation by which cells increase their DNA content to support cell and organ growth, is observed in many mammalian cell types, including cardiomyocytes. Although polyploidization is beneficial in many contexts, progression to a polyploid state is often accompanied by a loss of proliferative capacity. Recent work suggests that heterogeneity in cardiomyocyte ploidy is highly influenced by genetic diversity. However, the developmental course by which cardiomyocytes reach their final ploidy state has only been investigated in select genetic backgrounds. Here, we assessed cardiomyocyte number, cell cycle activity, and ploidy dynamics across two divergent inbred mouse strains; C57Bl/6J and A/J. Both strains are born and reach adulthood with a comparable number of cardiomyocytes, however the end composition of ploidy classes and developmental progression to reach the final state and number differ substantially. In addition to corroborating previous findings that identified Tnni3k as a mediator of cardiomyocyte ploidy, we also uncover a novel role for Runx1 and Tnni3k in ploidy dynamics and cardiomyocyte cytokinesis. These data provide novel insight into the developmental path to cardiomyocyte ploidy states and challenge the paradigm that polyploidization and hypertrophy are the only mechanisms for growth in the mouse heart after the first week of life.

developmental biology↗

bioRxiv2022

Allometric scaling of a superposition eye optimises sensitivity and acuity in large and small hawkmoths

Animals vary widely in body size across and within species. This has consequences in large and small individuals for the function of organs and body parts. How these scale in relation to body size reveals evolutionary investment strategies, often resulting in trade-offs between functions. Eyes exemplify these trade-offs, as they are limited by their absolute size in two key performance features: sensitivity and spatial acuity. Previous studies of the 3D structure of apposition compound eyes, which are ideal models for allometric studies due to their size polymorphism, revealed that allometric scaling improves both local resolution and visual sensitivity in larger bumblebees (Taylor et al., 2019). Here, we build on the established methods and results to investigate allometric scaling in superposition compound eyes - the second prominent eye type in insects - for the first time. Our research highlights a surprising strategy to cope with the challenge of trading off sensitivity and spatial resolution in small eyes, as we show that the eyes of the hummingbird hawkmoth retain an optimal balance of these performance measures across all body sizes.

neuroscience↗

bioRxiv2021

Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron micro-tomography and volume electron microscopy

Attributing in vivo neurophysiology to the brains ultrastructure requires a large field of view containing contextual anatomy. Electron microscopy (EM) is the gold standard technique to identify ultrastructure, yet acquiring volumes containing full mammalian neural circuits is challenging and time consuming using EM. Here, we show that synchrotron X-ray computed tomography (SXRT) provides rapid imaging of EM-prepared tissue volumes of several cubic millimetres. Resolution was sufficient for distinguishing cell bodies as well as for tracing apical dendrites in olfactory bulb and hippocampus, for up to 350 m. Correlating EM with SXRT allowed us to associate dendritic spines on pyramidal cell apical dendrites in the stratum radiatum to their corresponding soma locations. Superficial pyramidal neurons had larger spine apparatus density compared to deeper ones, implying differential synaptic plasticity for superficial and deeper cells. Finally, we show that X-ray tomography and volume EM can be reliably correlated to prior in vivo imaging. Thus, combining functional measurements with multiscale X-ray microscopy and volume EM establishes a correlative workflow that enables functional and structural investigation of subcellular features in the context of cellular morphologies, tissues and ultimately whole organs.

neuroscience↗

bioRxiv2018

Using micro-CT techniques to explore the role of sex and hair in the functional morphology of bumblebee (Bombus terrestris) ocelli

Many insects have triplets of camera type eyes, called ocelli, whose function remains unclear for most species. Here, we investigate the ocelli of the bumblebee, Bombus terrestris, using reconstructed 3D data from X-ray micro computed-tomography scans combined with computational ray-tracing simulations. This method enables us, not only to predict the visual fields of the ocelli, but to explore for the first time the effect that hair has on them as well as the difference between worker female and male ocelli.\n\nWe find that bumblebee ocellar fields of view are directed forward and dorsally, incorporating the horizon as well as the sky. There is substantial binocular overlap between the median and lateral ocelli, but no overlap between the two lateral ocelli. Hairs in both workers and males occlude the ocellar field of view, mostly laterally in the worker median ocellus and dorsally in the lateral ocelli. There is little to no sexual dimorphism in the ocellar visual field, suggesting that in B. terrestris they confer no advantage to mating strategies.\n\nWe compare our results with published observations for the visual fields of compound eyes in the same species as well as with the ocellar vision of other bee and insect species.

physiology↗

bioRxiv2018

Bumblebee visual allometry results in locally improved resolution and globally improved sensitivity

The quality of visual information that is available to an animal is limited by the size of its eyes. Differences in eye size can be observed even between closely related individuals but we understand little about how this affects visual quality. Insects are good models for exploring the effects of size on visual systems because many species exhibit size polymorphism, which modifies both the size and shape of their eyes. Previous work in this area has been limited, however, due to the challenge of determining the 3D structure of eyes. To address this, we have developed a novel method based on x-ray tomography to measure the 3D structure of insect eyes and calculate their visual capabilities. We investigated visual allometry in the bumblebee Bombus terrestris and found that size affects specific aspects of visual quality including binocular overlap, optical sensitivity across the field of view, and visual resolution in the dorsofrontal visual field. This holistic study on eye allometry reveals that differential scaling between different eye areas provides substantial flexibility for larger bumblebees to have improved visual capabilities.

neuroscience↗