Biology subjects

Cook, A. C.

Publications and source records attributed to Cook, A. C..

5 recordsLinked to original sources

bioRxiv2026

BigHeart: Mapping connectivity in the adult human heart at the micron scale

The human heart depends on coordinated muscular, electrical, vascular, lymphatic, and neural systems, but their three-dimensional relationships remain unresolved at microscopic resolution across an intact adult organ. Using hierarchical phase-contrast tomography, we generated a continuous three-dimensional structural reference of a whole adult human heart at 8.01 micrometer isotropic voxel size, without sectioning or staining. Organ-wide imaging revealed hierarchical myocardial architecture, and quantitative orientation analysis identified regional differences in myocardial cell aggregate organization. The atrioventricular conduction axis was traced into a distinct subendocardial Purkinje network interfacing with working myocardium. Integrated segmentation showed that coronary vessels, lymphatic collectors, and autonomic nerves occupy shared epicardial corridors. This publicly accessible dataset integrates cardiac systems within a common spatial framework for anatomy, computational modeling, and future molecular atlases.

physiology↗

bioRxiv2026

Revisiting the Structure of the Ventricular Myocardium in Tetralogy of Fallot Using Hierarchical Phase Contrast Tomography and Structure Tensor Analysis

BACKGROUNDIn tetralogy of Fallot (ToF), changes in right ventricular function (as assessed by strain or TAPSE) reflect altered myocardial structure. Direct three-dimensional anatomical evidence supporting these changes remains limited. The objective of this study was to non-destructively characterize myocardial architecture in pediatric ToF hearts using Hierarchical Phase-Contrast Tomography (HiP-CT) and structure tensor analysis. METHODSTwenty ToF and control pediatric hearts were imaged at the European Synchrotron, ESRF. Myocyte orientation was assessed through structure tensor analysis and distributed high-performance computing. A region-specific framework was developed for analysis of the right ventricle. The predominant direction of myocardial aggregates (their helical angle) was compared across ventricular regions. RESULTSSignificant differences in orientation were found in all ToF segments vs controls (left ventricle, right ventricular inlet, right ventricular outflow tract, septum; p < 0.001). Myocytes in the ToF right ventricular inlet were more circumferential overall, with regional heterogeneity. Contrary to traditional models, no discrete middle layer was found in the ToF right ventricle; instead, a shift towards more circumferentially orientated myocytes and disrupted septal and outflow components was observed. Right ventricular contribution to the septum was greater in ToF (47.3% vs 34.0%; p = 0.0026), with extension of ventricular insertion points disrupting septal architecture. There were more longitudinally oriented myocytes in the ToF right ventricular outflow tract, consistent with hypertrophied septoparietal trabeculations. Left ventricular structure in ToF demonstrated a greater proportion of circumferentially oriented myocytes compared to controls. CONCLUSIONSWe reveal profound alterations in ToF myocardial organization which broadly align with clinical observations and provide the first open-access HiP-CT congenital heart disease data as a basis for future computational modelling. Clinical PerspectiveWhole-heart HiP-CT demonstrates a loss of normal LV-RV distinction in the ToF myocardium, alongside extensive septal disarray. These findings provide a structural substrate for RV dysfunction, ventricular-ventricular interaction, and arrhythmogenesis in ToF, challenging traditional layer-based models of ventricular myocardium. Understanding myocardial organization as a continuous, developmentally patterned three-dimensional structure is essential for accurate interpretation of ventricular mechanics and disease progression. Although HiP-CT imaging is not applicable in vivo, the structural phenotypes identified in this study generate testable hypotheses for clinical imaging. Future work should focus on correlating ex-vivo measures with in-vivo imaging markers derived from cardiac magnetic resonance, including strain, TAPSE, and assessment of ventricular interactions. Investigating myocardial phenotype across the life-course, from fetal life to adulthood, paired with multi-omics mapped to these three-dimensional datasets, may help elucidate mechanisms underlying myocardial remodeling in ToF and support the development of novel therapeutic approaches.

physiology↗

bioRxiv2025

The Heterogeneous Nature of Atrioventricular Conduction Tissues in Tetralogy of Fallot demonstrated by Hierarchical Phase-contrast Tomography - redefining the anatomic substrate

ObjectivesPostoperative arrhythmias are frequent after Tetralogy of Fallot (ToF) repair, yet anatomic substrate and preventive strategies remain poorly defined. Using hierarchical phase-contrast tomography (HiP-CT) the atrioventricular conduction system in pediatric ToF specimens was investigated non-destructively and in 3D. MethodsEighteen whole-heart specimens (11 ToF, 7 controls) were imaged at the European Synchrotron, ESRF. Segmentation and 3D renderings demonstrated gross morphology. Morphology, size, depth and course of the non-branching bundle and right bundle branch (RBB) were quantified using custom computational pipelines. Segmentations were visualized in VheaRts, a Unity3D-based XR platform. ResultsThe ToF conduction system was more draped than in controls, bilaterally spanning the septum, resembling early embryonic architecture. The RBB was variable in origin, course and morphologic structure with significantly smaller indexed cross-sectional area in native ToF versus controls (0.05 {+/-} 0.20 vs 0.50 {+/-} 0.20 mm{superscript 2}, p = 0.005). One anomalous fasciculo-ventricular connection and six dead-end tracts were found. Regions at surgical risk included the posterior-inferior margin of the ventricular septal defect (VSD) and the septal crest along its nadir. The superior margin of the VSD at its intersection with the aortic root was free of conduction tissue. The HiP-CT to VR pipeline enabled interactive 3D visualization of conduction pathways relative to key structures. ConclusionsThis first pediatric cardiac HiP-CT series reveals a broader anomalous conduction complex in ToF, including variable RBB origin and hypoplasia, providing insight into preoperative vulnerability, arrhythmia, and surgical risk. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/692356v1_fig7.gif" ALT="Figure 7"> View larger version (50K): org.highwire.dtl.DTLVardef@1b39e89org.highwire.dtl.DTLVardef@16d49c2org.highwire.dtl.DTLVardef@5884borg.highwire.dtl.DTLVardef@136fc24_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 7:C_FLOATNO Graphical Abstract C_FIG

developmental biology↗

bioRxiv2023

Multidimensional Analysis of the Adult Human Heart in Health and Disease using Hierarchical Phase-Contrast Tomography (HiP-CT)

Cardiovascular diseases (CVDs) are a leading cause of death worldwide. Current clinical imaging modalities provide resolution adequate for diagnosis but are unable to provide detail of structural changes in the heart, across length-scales, necessary for understanding underlying pathophysiology of disease. Hierarchical Phase-Contrast Tomography (HiP-CT), using new (4th) generation synchrotron sources, potentially overcomes this limitation, allowing micron resolution imaging of intact adult organs with unprecedented detail. In this proof of principle study (n=2), we show the utility of HiP-CT to image whole adult human hearts ex-vivo: one control without known cardiac disease and one with multiple known cardiopulmonary pathologies. The resulting multiscale imaging was able to demonstrate exemplars of anatomy in each cardiac segment along with novel findings in the cardiac conduction system, from gross (20 um/voxel) to cellular scale (2.2 um/voxel), non-destructively, thereby bridging the gap between macroscopic and microscopic investigations. We propose that the technique represents a significant step in virtual autopsy methods for studying structural heart disease, facilitating research into abnormalities across scales and age-groups. It opens up possibilities for understanding and treating disease; and provides a cardiac blueprint with potential for in-silico simulation, device design, virtual surgical training, and bioengineered heart in the future.

pathology↗

bioRxiv2022

PKN2 deficiency leads both to prenatal congenital cardiomyopathy and defective angiotensin II stress responses.

BackgroundThe protein kinase PKN2 is required for embryonic development, and PKN2 knockout mice die as a result of failure in expansion of mesoderm tissues, cardiac development and neural tube closure. In the adult, cardiomyocyte PKN2 and PKN1 (in combination) are required for cardiac adaptation to pressure-overload. The role of PKN2 in contractile cardiomyocytes during development and its role in the adult heart remain to be fully established. MethodsWe used mice with cardiomyocyte-directed knockout of PKN2 or global PKN2 haploinsufficiency. Cardiac function and dimensions were assessed with high resolution episcopic microscopy, MRI, micro-CT and echocardiography. Biochemical and histological changes were assessed. ResultsCardiomyocyte-directed PKN2 knockout embryos displayed striking abnormalities in the compact myocardium, with frequent myocardial clefts and diverticula, ventricular septal defects and abnormal heart shape. The sub-Mendelian homozygous knockout survivors developed cardiac failure. RNASeq data showed upregulation of PKN2 in patients with dilated cardiomyopathy, suggesting an involvement in adult heart disease. Given the rarity of homozygous survivors with cardiomyocyte-specific deletion of PKN2, this was explored using mice with constitutive heterozygous PKN2 knockout. Cardiac hypertrophy resulting from hypertension induced by angiotensin II was reduced in haploinsufficient PKN2 mice relative to wild-type littermates, with suppression of cardiomyocyte hypertrophy and cardiac fibrosis. ConclusionsCardiomyocyte PKN2 is essential for heart development and formation of compact myocardium, and is also required for cardiac hypertrophy in hypertension. Thus, PKN signalling may offer therapeutic options for managing congenital and adult heart diseases.

developmental biology↗