Multimodal Learning for Mapping the Genotype-Phenotype Dynamics.

How complex phenotypes emerge from intricate gene expression patterns is a fundamental question in biology. Quantitative characterization of this relationship, however, is challenging due to the vast combinatorial possibilities and dynamic interplay between genotype and phenotype landscapes. Integrating high-content genotyping approaches such as single-cell RNA sequencing and advanced learning methods such as language models offers an opportunity for dissecting this complex relationship. Here, we present a computational integrated genetics framework designed to analyze and interpret the high-dimensional landscape of genotypes and their associated phenotypes simultaneously. We applied this approach to develop a multimodal foundation model to explore the genotype-phenotype relationship manifold for human transcriptomics at the cellular level. Analyzing this joint manifold showed a refined resolution of cellular heterogeneity, enhanced precision in phenotype annotating, and uncovered potential cross-tissue biomarkers that are undetectable through conventional gene expression analysis alone. Moreover, our results revealed that the gene networks are characterized by scale-free patterns and show context-dependent gene-gene interactions, both of which result in significant variations in the topology of the gene network, particularly evident during aging. Finally, utilizing contextualized embeddings, we investigated gene polyfunctionality which illustrates the multifaceted roles that genes play in different biological processes, and demonstrated that for VWF gene in endothelial cells. Overall, this study advances our understanding of the dynamic interplay between gene expression and phenotypic manifestation and demonstrates the potential of integrated genetics in uncovering new dimensions of cellular function and complexity.

Effect of anatomical variation on extracorporeal membrane oxygenation circulatory support: A computational study.

BACKGROUND: Extracorporeal membrane oxygenation (ECMO) via femoral cannulation is a vital intervention capable of rapidly restoring perfusion for patients in shock. Despite increasing use to provide circulatory support, its hemodynamic effects are poorly understood and the impact of patient-specific anatomical variation on perfusion is unknown. This study investigates the complex failing heart-mechanical circulatory support circulation and analyzes the effect of patient-specific vascular anatomical variations on hemodynamics and end-organ perfusion. METHODS: Patient-specific vascular geometries were constructed from segmenting clinical computerized tomography angiography images and quantitatively compared using tortuosity, curvature, torsion, and lumen diameter. Computational fluid dynamic simulations were performed on a subset of geometries selected to represent a range of anatomical variation. Heart failure severity was modeled by varying the relative fraction of total flow provided by the heart and the extracorporeal circuit. A 3-element lumped parameter model was applied to accurately and dynamically model distal perfusion boundary conditions. Hemodynamic parameters and end-organ perfusion were analyzed and compared to assess the effect of anatomical variation. RESULTS: Pulsatile antegrade cardiac perfusion and ECMO retrograde perfusion collide in the aorta to form a dynamic watershed region. The size, position, and variation of this region over the cardiac cycle is substantially altered by patient anatomical region. Increased vascular tortuosity reduces the proximal extent of flow from circulatory support and decreases the size of the watershed region. CONCLUSIONS: Patient vascular anatomy is a key determinant of the ECMO-failing heart circulation that alters the location and extent of the watershed region and affects the tissues at risk for differential hypoxia and circuit-derived thromboemboli for a given level of support.

Simulation of Fluid-Structure Interaction in Extracorporeal Membrane Oxygenation Circulatory Support Systems.

Extracorporeal membrane oxygenation (ECMO) is a vital mechanical circulatory support modality capable of restoring perfusion for the patient in circulatory failure. Despite increasing adoption of ECMO, there is incomplete understanding of its effects on systemic hemodynamics and how the vasculature responds to varying levels of continuous retrograde perfusion. To gain further insight into the complex ECMO:failing heart circulation, computational fluid dynamics simulations focused on perfusion distribution and hemodynamic flow patterns were conducted using a patient-derived aorta geometry. Three case scenarios were simulated: (1) healthy control; (2) 90% ECMO-derived perfusion to model profound heart failure; and, (3) 50% ECMO-derived perfusion to model the recovering heart. Fluid-structure interface simulations were performed to quantify systemic pressure and vascular deformation throughout the aorta over the cardiac cycle. ECMO support alters pressure distribution while decreasing shear stress. Insights derived from computational modeling may lead to better understanding of ECMO support and improved patient outcomes.

Understanding TAVR device expansion as it relates to morphology of the bicuspid aortic valve: A simulation study.

The bicuspid aortic valve (BAV) is a common and heterogeneous congenital heart abnormality that is often complicated by aortic stenosis. Although initially developed for tricuspid aortic valves (TAV), transcatheter aortic valve replacement (TAVR) devices are increasingly applied to the treatment of BAV stenosis. It is known that patient-device relationship between TAVR and BAV are not equivalent to those observed in TAV but the nature of these differences are not well understood. We sought to better understand the patient-device relationships between TAVR devices and the two most common morphologies of BAV. We performed finite element simulation of TAVR deployment into three cases of idealized aortic anatomies (TAV, Sievers 0 BAV, Sievers 1 BAV), derived from patient-specific measurements. Valve leaflet von Mises stress at the aortic commissures differed by valve configuration over a ten-fold range (TAV: 0.55 MPa, Sievers 0: 6.64 MPa, and Sievers 1: 4.19 MPa). First principle stress on the aortic wall was greater in Sievers 1 (0.316 MPa) and Sievers 0 BAV (0.137 MPa) compared to TAV (0.056 MPa). TAVR placement in Sievers 1 BAV demonstrated significant device asymmetric alignment, with 1.09 mm of displacement between the center of the device measured at the annulus and at the leaflet free edge. This orifice displacement was marginal in TAV (0.33 mm) and even lower in Sievers 0 BAV (0.23 mm). BAV TAVR, depending on the subtype involved, may encounter disparate combinations of device under expansion and asymmetry compared to TAV deployment. Understanding the impacts of BAV morphology on patient-device relationships can help improve device selection, patient eligibility, and the overall safety of TAVR in BAV.

A Computational Fluid Dynamics Study of the Extracorporeal Membrane Oxygenation-Failing Heart Circulation.

Extracorporeal membrane oxygenation (ECMO) is increasingly deployed to provide percutaneous mechanical circulatory support despite incomplete understanding of its complex interactions with the failing heart and its effects on hemodynamics and perfusion. Using an idealized geometry of the aorta and its major branches and a peripherally inserted return cannula terminating in the iliac artery, computational fluid dynamic simulations were performed to (1) quantify perfusion as function of relative ECMO flow and (2) describe the watershed region produced by the collision of antegrade flow from the heart and retrograde ECMO flow. To simulate varying degrees of cardiac failure, ECMO flow as a fraction of systemic perfusion was evaluated at 100%, 90%, 75%, and 50% of total flow with the remainder supplied by the heart calculated from a patient-derived flow waveform. Dynamic boundary conditions were generated with a three-element lumped parameter model to accurately simulate distal perfusion. In profound failure (ECMO providing 90% or more of flow), the watershed region was positioned in the aortic arch with minimal pulsatility observed in the flow to the visceral organs. Modest increases in cardiac flow advanced the watershed region into the thoracic aorta with arch perfusion entirely supplied by the heart.

Incomplete expansion of transcatheter aortic valves is associated with propensity for valve thrombosis.

OBJECTIVES: Clinical and subclinical leaflet thromboses are increasingly recognized complications following transcatheter aortic valve replacement. Identification of the risk factors is important to mitigate the occurrence of leaflet thrombosis in transcatheter aortic valves (TAVs) and ensure their long-term function. The goal of this study was to determine the effect of incomplete expansion of TAVs on the likelihood of leaflet thrombosis following transcatheter aortic valve replacement. METHODS: Using experimental and computational methods, 3-dimensional unsteady flow fields of 26-mm SAPIEN 3 valves expanded to 3 different diameters (i.e. 26.0 mm, 23.4 mm and 20.8 mm) were determined in patient-specific geometries. The diameters corresponded to 100%, 90% and 80% stent expansion, respectively. To address the potential difference in the likelihood of leaflet thrombosis, blood residence time (i.e. stasis) and viscous shear stress on the surface of TAV leaflets were quantified and compared. RESULTS: The results indicated that TAV underexpansion increased blood stasis on the TAV leaflets. Blood residence time on the surface of the leaflets after 80% and 90% TAV expansion on average was 9.4% and 4.1% more than that of the fully expanded TAV, respectively. In addition, areas of blood stasis time of more than 0.5 s, which are highly prone to platelet activation, increased linearly as the degree of TAV underexpansion increased. CONCLUSIONS: Incomplete expansion of TAVs increases blood stasis on the surface of TAV leaflets. Regions of blood stasis promote platelet activation and thrombotic events. TAV underexpansion can therefore increase the risk of leaflet thrombosis in patients with transcatheter aortic valve replacement.

Analysis of mechanical parameters on the thromboembolism using a patient-specific computational model.

Ischemic stroke is a major cause of death and long-term disabilities worldwide. In this paper, we aim to represent a comprehensive simulation of the motion of emboli through cerebrovascular network within patient-specific computational model. The model consists of major arteries of the circle of Willis reconstructed from magnetic resonance angiography images, pulsatile flow and emboli with different sizes and material properties. Here, the fluid-structure interactions method was used to simulate the motion of deformable and rigid emboli through cerebral arteries. Hemodynamic changes in the circle of Willis due to the entrance of embolus are observed. The effect of material properties on the distribution ratio and dynamics of motion of the emboli in the cerebral arterial network is also analyzed. Our results reveal that as the rigidity of emboli increases, higher proportion of them tend to enter to the larger arteries (e.g., middle cerebral artery). Scrutinizing the amount of stress acting on the emboli represented in this paper can broaden our understanding of the rheological phenomenon (e.g., lysis or growth of emboli during embolism). The approach of considering different material properties of the thrombus in a patient-specific computational model not only enable us to better understand the roll of biomechanical parameters causing the embolism, but also lead to a better clinical decision making to manage patients with stroke.