Biology subjects

Nigam, V.

Publications and source records attributed to Nigam, V..

5 recordsLinked to original sources

bioRxiv2026

Three-Dimensional Fluid-Structure Interaction Reveals Trade-offs Among Oxygen Delivery, Shear, and Washout in Pediatric Roller-Pump Cardiopulmonary Bypass

Objective: To determine how roller speed, tubing occlusion, and hematocrit jointly regulate oxygen delivery, shear, and washout in pediatric roller-pump cardiopulmonary bypass. Methods: A three-dimensional, closed-loop fluid-structure interaction model resolved roller-tube contact, tubing deformation, and blood flow. Forty simulations combined 4 roller speeds (38-95 revolutions per minute), 2 occlusion levels (77% and 83%), and 5 hematocrit levels (15%-50%). Cycle-averaged flow, oxygen delivery, peak shear stress, and viscosity-normalized relative residence time were quantified. Results: Roller compression produced retrograde leakage through the occluded gap, localized peak shear stress exceeding 100 pascals, and adjacent stagnation and recirculation. Flow increased nearly linearly with roller speed and was higher at greater occlusion, with little hematocrit dependence. Higher speed and occlusion increased peak shear stress while reducing relative residence time; higher hematocrit further increased peak shear stress. Similar oxygen delivery could arise from substantially different flow environments: among 10 conditions providing oxygen delivery of approximately 9-12 milliliters per minute, peak shear stress ranged from approximately 25 to 70 pascals. Within conditions satisfying an illustrative minimum oxygen-delivery threshold, lower hematocrit permitted speed and occlusion settings yielding lower peak shear stress and relative residence time. Conclusions: Pediatric roller-pump settings that provide similar oxygen delivery can expose blood to markedly different shear and washout environments. Joint evaluation of these metrics may guide selection of speed, occlusion, and hematocrit to meet a target oxygen delivery while reducing shear and improving washout. Keywords: Cardiopulmonary bypass; roller pump; pediatric cardiac surgery; fluid-structure interaction; shear stress; relative residence time

bioengineering↗

bioRxiv2026

Lineage-specific chromatin poising enforced by ETS-IRF composite elements determines the divergent interferon responses of plasmacytoid dendritic cells and epithelial cells

Plasmacytoid dendritic cells (pDCs) produce robust type I interferons (IFN-I) within hours of viral sensing, while epithelial cells at mucosal surfaces mount a delayed response dominated by type III interferons (IFN-III). Both cell types express pattern recognition receptors that activate similar downstream transcription factors, yet they produce distinct subsets of IFNs. The mechanisms underlying these differences have remained unclear. Here, using Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) in primary human pDCs and intestinal epithelial cells, we show that IFN-I and IFN-III gene loci carry opposing, constitutively established chromatin accessibility landscapes that determine cell-type-specific interferon induction. The IFN-I locus is broadly open in pDCs and constitutively closed in epithelial cells, while the IFN-III locus displays the reciprocal pattern. Motif enrichment analysis of accessible regions at the IFN-I locus in pDCs revealed unexpected and significant enrichment of ETS family binding motifs alongside IRF motifs, which determines the cell-type-specific locus accessibility. The ETS factor PU.1 and IRF8 bind IFN-I promoters, at composite ETS-IRF elements positioned at the Positive Regulatory Domain IV (PRDIV) site of IFNB1 promoter and adjacent to the TATA-proximal IRF motif of IFNA promoters. IFNL gene promoters lack ETS recognition sequences. PU.1-IRF8 composite factor binding extends across intergenic regions of the IFN-I locus, where candidate enhancer elements marked by H3K4me1, H3K27ac, and RNA Pol II occupancy were identified. We propose that this network of ETS-IRF composite-element-anchored enhancers maintains the IFN-I locus in a constitutively poised state in pDCs, licensing the rapid and robust IFN-I response that defines pDCs. In epithelial cells, the absence of PU.1 and IRF8 renders the IFN-I locus epigenetically silent, while the IFN-III locus is constitutively open. Despite this, the delayed IFN-III gene expression in epithelial cells is due to intrinsically weaker promoter activity relative to IFN-I. These findings reveal that the divergent IFN induction of pDCs and epithelial cells is determined by the chromatin architecture prior to infection. Overall, these observations show that lineage-specific ETS-IRF regulatory factors and promoter strength determine the cell-type-specific IFN activation.

immunology↗

bioRxiv2023

Monocyte Adhesion and Transmigration Through Endothelium Following Cardiopulmonary Bypass Shearing is Mediated by IL-8 Signaling

BackgroundThe use of cardiopulmonary bypass (CPB) can induce sterile systemic inflammation that contributes to morbidity and mortality, especially in children. Patients have been found to have increased expression of cytokines and transmigration of leukocytes during and after CPB. Previous work has demonstrated that the supraphysiologic shear stresses present during CPB are sufficient to induce proinflammatory behavior in non-adherent monocytes. The interactions between shear stimulated monocytes and vascular endothelial cells have not been well studied and have important translational implications. MethodsTo test the hypothesis that non-physiological shear stress experienced by monocytes during CPB affects the integrity and function of the endothelial monolayer via IL-8 signaling pathway, we have used an in vitro CPB model to study the interaction between THP-1 monocyte-like cells and human neonatal dermal microvascular endothelial cells (HNDMVECs). THP-1 cells were sheared in polyvinyl chloride (PVC) tubing at 2.1 Pa, twice of physiological shear stress, for 2 hours. Interactions between THP-1 cells and HNDMVECs were characterized after coculture. ResultsWe found that sheared THP-1 cells adhered to and transmigrated through the HNDMVEC monolayer more readily than static controls. When co-culturing, sheared THP-1 cells also disrupted in the VE-cadherin and led to reorganization of cytoskeletal F-actin of HNDMVECs. Treating HNDMVECs with IL-8 resulted in upregulation of vascular cell adhesion molecule 1 (VCAM-1) and intercellular adhesion molecule 1 (ICAM-1) while also increasing the adherence of non-sheared THP-1 cells. Preincubating HNDMVECs with Reparixin, an inhibitor of CXCR2/IL-8 receptor inhibited sheared THP-1 cell adhesion to the HNDMVECs. ConclusionsThese results suggested that IL-8 not only increases the endothelium permeability during monocyte migration, but also affects the initial adhesion of monocytes in a CPB setup. This study revealed a novel mechanism of post-CPB inflammation and will contribute to the development of targeted therapeutics to prevent and repair the damage to neonatal patients. HighlightsO_LIShear stress in a CPB-like environment promoted the adhesion and transmigration of monocytes to and through endothelial monolayer. C_LIO_LITreating endothelial monolayer with sheared monocytes led to disruption of VE-cadherin and reorganization of F-actin. C_LIO_LIInteraction between sheared monocytes resulted in a significant increase of IL-8 release. C_LIO_LIInhibiting IL-8 receptor prevented sheared monocyte adhesion, while IL-8 promoted naive monocyte adhesion. C_LI

cell biology↗

bioRxiv2022

Hemodynamic stress activates inflammatory responses and cell death through spectrin-dependent modulation of Store Operated Calcium Entry

Patients undergoing cardiac surgery face significant inflammatory induced by exposure to cardiopulmonary bypass (CPB), contributing to heightened morbidity and mortality. The molecular and cellular mechanisms that underpin this inflammatory process remain unknown. To address this knowledge gap, we performed snRNA/ATAC-Sequencing on leukocytes from neonatal CPB patients. Classical monocytes become more prevalent and have dysregulation of inflammatory genes after CPB, indicating their role in CPB-associated inflammation. A genome-wide CRISPR screen and in vitro experiments in non-adherent monocytic cells identified two novel genes, SPTAN1 and RAF1, as effectors of hemodynamic stress. SPTAN1 and RAF1 activate store-operated calcium entry that results inflammation and cell death. snATAC-Seq revealed dynamically changing patterns of chromatin accessibility and AP-1 transcription factor binding after CPB exposure. These findings provide novel insights into the pathogenesis of CPB-associated inflammation, with broad implications for understanding the early stages of sterile inflammation and how non-adherent cells sense shear stress.

cell biology↗

bioRxiv2021

microRNA Expression Levels Change in Neonatal Patients During and After Exposure to Cardiopulmonary Bypass

ObjectivesThe systemic inflammation that occurs after exposure to cardiopulmonary bypass (CPB), which is especially severe in neonatal patients, is associated with poorer outcomes and is not well understood. In order to gain deeper insight into how exposure to bypass activates inflammatory responses in circulating leukocytes, we studied changes in microRNA (miRNA) expression during and after exposure to bypass. miRNAs are small non-coding RNAs that have important roles in modulating protein levels and function of cells. MethodsWe performed miRNA-Sequencing on leukocytes isolated from neonatal cardiopulmonary bypass patients (N=5) at 7 timepoints during the process of CPB, including prior to the initiation of bypass, during bypass, and at three time points during the first 24 hours after weaning from bypass. We identified significant differentially expressed miRNAs using generalized linear regression models, and miRNAs were defined as statistically significant using an FDR adjusted p <0.05. We identified gene targets of these miRNAs using the Targetscan database, and identified significantly enriched biological pathways for these gene targets. ResultsWe identified 54 miRNAs with differential expression during and after CPB. These miRNAs clustered into 3 groups, including miRNAs that were increased during and after CPB (3 miRNAs), miRNAs that decreased during and after CPB (10 miRNAs), and miRNAs that decreased during CPB but then increased 8-24 hours after CPB. 38.9% of the target genes of these miRNAs were significantly differentially expressed in our previous study. miRNAs with altered expression levels are predicted to significantly modulate pathways related to inflammation and signal transduction. ConclusionsThe unbiased profiling of the miRNA changes that occur in the circulating leukocytes of bypass patients provides deeper insight into the mechanisms that underpin the systemic inflammatory response that occurs in patients after exposure to cardiopulmonary bypass. These data will help the development of novel treatments and biomarkers for bypass associated inflammation.

developmental biology↗