Grinstein, J. | Search bioRxiv

bioRxiv2022

Blood flow modeling under LVAD physiology. From global circulation to local hemodynamics

This document presents the modeling strategy to address the in-silico study of different LVAD patho-physiological scenarios. The proposed approach employs a closed-loop lumped-parameter compartmental representation of the global circulation in the cardiovascular system (CVS). The CVS is coupled to a HeartMate 3 LVAD, and different cardiovascular conditions are proposed by modification of model parameters. Once the simulation for these conditions are performed, the cardiac function is analyzed in detail, and the global circulation model delivers flow rate waveforms which are employed as boundary conditions in a 3D hemodynamic simulation. This local circulation model is built using a patient-specific geometry of the aortic arch, containing 7 inlet/outlet boundaries, namely: LVAD cannula, aortic root, left and right subclavian arteries, left and right common carotid arteries and thoracic aorta. This model is exploited to investigate the impact of global cardiovascular conditions in the local hemodynamic features, particularly the wall shear stress (WSS) in different spatial regions.

bioengineering↗

bioRxiv2018

3D Chromatin Architecture Remodeling during Human Cardiomyocyte Differentiation Reveals A Novel Role of HERV-H In Demarcating Chromatin Domains

Dynamic restructuring of chromatin architecture has been implicated in cell-type specific gene regulatory programs; yet, how chromatin remodels during lineage specification remains to be elucidated. Through interrogating chromatin reorganization during human cardiomyocyte differentiation, we uncover dynamic chromatin interactions between genes and distal regulatory elements harboring noncoding variants associated with adult and congenital heart diseases. Unexpectedly, we also discover a new class of human pluripotent stem cell (PSC)-specific topologically associating domains (TAD) that are created by the actively transcribed endogenous retrotransposon HERV-H. Deletion or silencing of specific HERV-H elements eliminates corresponding TAD boundaries, while de novo insertion of HERV-H can introduce new chromatin domain boundaries in human PSCs. Furthermore, comparative analysis of chromatin architecture in other species that lack HERV-H sequences supports a role for actively transcribed HERV-H in demarcating human PSC-specific TADs. The biological role of HERV-H is further underscored by the observation that deletion of a specific HERV-H reduces transcription of genes upstream and facilitates cell differentiation. Overall, our results highlight a previously unrecognized role for retrotransposons in restructuring genome architecture in the human genome and delineate dynamic gene regulatory networks during cardiomyocyte development that inform how non-coding genetic variants contribute to human heart diseases.

genomics↗