VTechWorks Repository :: Browsing by Author "Rajagopalan, Padmavathy"

Browsing by Author "Rajagopalan, Padmavathy"

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3D Hepatic Cultures Simultaneously Maintain Primary Hepatocyte and Liver Sinusoidal Endothelial Cell Phenotypes
Kim, Yeonhee; Rajagopalan, Padmavathy (PLOS, 2010-11-12)
Developing in vitro engineered hepatic tissues that exhibit stable phenotype is a major challenge in the field of hepatic tissue engineering. However, the rapid dedifferentiation of hepatic parenchymal (hepatocytes) and non-parenchymal (liver sinusoidal endothelial, LSEC) cell types when removed from their natural environment in vivo remains a major obstacle. The primary goal of this study was to demonstrate that hepatic cells cultured in layered architectures could preserve or potentially enhance liver-specific behavior of both cell types. Primary rat hepatocytes and rat LSECs (rLSECs) were cultured in a layered three-dimensional (3D) configuration. The cell layers were separated by a chitosan-hyaluronic acid polyelectrolyte multilayer (PEM), which served to mimic the Space of Disse. Hepatocytes and rLSECs exhibited several key phenotypic characteristics over a twelve day culture period. Immunostaining for the sinusoidal endothelial 1 antibody (SE-1) demonstrated that rLSECs cultured in the 3D hepatic model maintained this unique feature over twelve days. In contrast, rLSECs cultured in monolayers lost their phenotype within three days. The unique stratified structure of the 3D culture resulted in enhanced heterotypic cell-cell interactions, which led to improvements in hepatocyte functions. Albumin production increased three to six fold in the rLSEC-PEM-Hepatocyte cultures. Only rLSEC-PEM-Hepatocyte cultures exhibited increasing CYP1A1/2 and CYP3A activity. Well-defined bile canaliculi were observed only in the rLSEC-PEM-Hepatocyte cultures. Together, these data suggest that rLSEC-PEM-Hepatocyte cultures are highly suitable models to monitor the transformation of toxins in the liver and their transport out of this organ. In summary, these results indicate that the layered rLSEC-PEM-hepatocyte model, which recapitulates key features of hepatic sinusoids, is a potentially powerful medium for obtaining comprehensive knowledge on liver metabolism, detoxification and signaling pathways in vitro.
The assembly of integrated rat intestinal-hepatocyte cultures
Kothari, Anjaney; Rajagopalan, Padmavathy (2019-11)
The jejunum is the segment of the small intestine responsible for several metabolism and biotransformation functions. In this report, we have cultured rat jejunum explants in vitro and integrated them with hepatocyte cultures. We have also investigated the changes in jejunum function at different locations since spatial variations in intestinal functions have been reported previously. We divided the length of the rat jejunum into three distinct regions of approximately 9 cm each. We defined the regions as proximal (adjacent to the duodenum), medial, and distal (adjacent to the ileum). Spatiotemporal variations in functions were observed between these regions within the jejunum. Alkaline phosphatase activity (a marker of enterocyte function), decreased twofold between the proximal and distal regions at 4 hr. Lysozyme activity (a marker of Paneth cell function) increased from the proximal to the distal jejunum by 40% at 24 hr. Mucin-covered areas, a marker of goblet cell function, increased by twofold between the proximal and distal segments of the jejunum at 24 hr. When hepatocytes were integrated with proximal jejunum explants, statistically higher urea (similar to 2.4-fold) and mucin (57%) production were observed in the jejunum explants. The integrated intestine-liver cultures can be used as a platform for future investigations.
Cell Migration on Opposing Rigidity Protein Gradients: Single Cell and Co-culture Studies
Jain, Gaurav (Virginia Tech, 2014-10-31)
Cell migration is a complex physiological process that is important from embryogenesis to senescence. In vivo, the migration of cells is guided by a complex combination of signals and cues. Directed migration is typically observed when one of these cues is presented to cells as a gradient. Several studies have been conducted into directed migration on gradients that are purely mechanical or chemical. Our goal was to investigate cellular migratory behavior when cells are presented with a choice and have to choose between increasing substrate rigidity or higher protein concentration. We chose to focus on this unique environment since it recapitulates several interfacial regions in vivo. We have designed novel hydrogels that exhibit dual and opposing chemical and mechanical profiles using photo-polymerization. Our studies demonstrate that durotaxis, a well-known phenomenon, can be reversed when cells sense a steep protein profile in the opposite direction. Fibroblasts were co-cultured with macrophages to obtain an understanding on how migration occurs when two different cell types are present in the same microenvironment. First, we investigated the migratory behavior of macrophages. These cell types exhibited a statistically significant preference to move towards the rigid/low collagen region of the interface. Interestingly, fibroblasts when co-cultured with macrophages, exhibited a preference for the low modulus-high collagen region of the interface. However, with the current sample size, these trends are statistically insignificant. On the contrary, the presence of fibroblasts in the cellular microenvironment did not result in the reversal of durotaxis exhibited by macrophages. Macrophages secreted significantly higher levels of secreted tumor necrosis factor (TNF-alpha) in mono-cultures in contrast to fibroblast-macrophage co-cultures. This trend could be an indication of macrophage plasticity between mono- and co-cultures. In summary, we have designed dual and opposing rigidity-protein gradients on a hydrogel substrate that can provide new insights into cellular locomotion. These results can be used to design biomimetic interfaces, biomaterial implants and for tissue engineering applications.
The Design and Assembly of 3D Liver Mimetic Cellular Architectures
Kim, Yeonhee (Virginia Tech, 2010-09-07)
We report the assembly of three-dimensional (3D) liver sinusoidal mimics comprised of primary rat hepatocytes, human or rat liver sinusoidal endothelial cells denoted as hLSECs and rLSECs respectively, and an intermediate chitosan-hyaluronic acid (HA) polyelectrolyte multilayer (PEM). The height of the PEMs ranged from 30-55nm and exhibited a shear modulus of ~ 100kPa. Primary rat hepatocytes coated with 5 and 15 PE layers exhibited stable urea and albumin production over a seven day period and these values were either comparable or superior to that in a collagen sandwich (CS). Hepatocyte-PEM-hLSEC liver mimics exhibited stable urea production and increasing albumin secretion over the culture period in comparison to hepatocyte-LSEC samples. In the 3D liver mimics, hLSEC phenotype was maintained and verified by the uptake of acetylated low-density lipoprotein (AcLDL). A sixteen-fold increase in CYP1A1/2 activity was observed for hepatocyte-PEM-10,000 hLSEC samples, thereby, suggesting that interactions between hepatocytes and hLSECs play a key role in enhancing hepatic phenotypes in in vitro cultures. As the first step towards elucidating key signaling pathways involved in cell-cell communications, global genome-wide transcriptional profiles of primary hepatocytes cultured in CS and hepatocyte monolayers (HMs) were performed over an eight-day period using DNA microarray measurements and Gene Set Enrichment Analysis (GSEA) in order to derive biologically meaningful information at the level of gene sets. The gene expression in CS cultures steadily diverged from that in HMs. Gene sets up-regulated in CS are those linked to liver metabolic and synthetic functions, such as lipid, fatty acid, alcohol and carbohydrate metabolism, urea production, and synthesis of bile acids. Monooxygenases such as CYP enzymes were significantly up-regulated starting on day 3 in CS cultures. These results serve as a baseline for further investigation into the systems biology of engineered liver tissues. 3D hepatic constructs were also assembled with primary rat hepatocytes and rLSECs, and a chitosan-HA PEM. In these hepatic models, the phenotype of hepatocytes and rLSECs were maintained. rLSEC phenotype was verified over a twelve-day period through immunostaining with the sinusoidal endothelial-1 (SE-1) antibody. In contrast, rLSECs cultured as monolayers lost their phenotype within 3 days. A two-fold increase in albumin production was observed only in the 3D liver models. rLSEC-PEM-hepatocyte cultures exhibited three- to six-fold increased CYP1A1/2 and CYP3A enzymatic activity. Well-defined bile canaliculi were observed in only 3D hepatic constructs. In summary, these results indicate that the layered rLSEC-PEM-hepatocyte constructs can be used as liver models for future studies.
The Design of Antimicrobial Detachable Thin Films for the Study of Hepatic Infections
Cassin, Margaret Emily (Virginia Tech, 2015-10-27)
Microbial infections are a global problem. Due to the over and misuse of antibiotics, drug-resistant pathogens are becoming more common. It is imperative to explore broad spectrum antimicrobial approaches. In this work, we modified collagen/hyaluronic acid polyelectrolyte multilayers (PEMs) with the natural antimicrobial peptide, LL-37 to study hepatic infections. LL-37 was physisorbed and covalently linked to the surface of the PEMs. Escherichia coli DH10B were cultured in the presence of LL-37modified PEMs in bacterial adhesion and contact killing models. Physisorbed LL-37 PEMs prevented bacterial adhesion and could also kill pathogens in the surrounding environment due to the release of LL-37 from the film. Immobilized LL-37 PEMs resulted in less bacterial adhesion on the surface due to the presence of the peptide. Films were then placed in contact with primary rat hepatocytes as well as in hepatocyte/bacteria co-cultures. LL-37 input concentrations up to of 16μM did not exhibit cytotoxic effects on hepatocytes. The LL-37 modified PEMs exhibited a hepatoprotective effect on albumin and urea secretion functions in co-cultures. The hepatoprotective effects were dependent on the ratio of hepatocytes and bacteria as well as the concentration of LL-37. These findings are encouraging and demonstrate that LL-37 modified PEMs can be used to investigate hepatic infections caused by bacteria.
The Design of Polyelectrolyte Multilayers Using Galactosylated Chitosan
Arca, Hale Cigdem (Virginia Tech, 2012-04-26)
A major challenge in hepatic tissue engineering is that liver cells rapidly lose their phenotype in in vitro cell culture systems. For this reason, it is necessary to design biomaterials that can support and enhance hepatic functions. Hepatocytes have a surface protein, called the asialoglycoprotein receptor (ASGP-R), which interacts with galactose via a specific receptor-ligand interaction. Polyelectrolyte multilayers (PEMs) were prepared by the layer by layer method, which is based on electrostatic attractions between oppositely charged polyelectrolytes (PEs). Anionic (hyaluronic acid) and cationic (chitosan and galactosylated chitosan) PEs were used in the fabrication of detachable, free-standing PEMs. The main focus of this study is the design of PEMs comprised of 50 bilayers of PEs. PEMs that contained galactose functional groups were assembled with either 5 or 10 bilayers of galactosylated chitosan (5 - 10 % of galactosylation). Optical properties, solvent stability and surface topography of the PEMs were measured.
The Design of Three-Dimensional Multicellular Liver Models Using Detachable, Nanoscale Polyelectrolyte Multilayers
Larkin, Adam Lyston (Virginia Tech, 2012-08-29)
We report the design and assembly of three-dimensional (3D) multi-cellular liver models comprised of primary rat hepatocytes, liver sinusoidal endothelial cells (LSECs), and Kupffer cells (KCs). LSECs and KCs in the liver model were separated from hepatocytes by a nanoscale, detachable, optically transparent chitosan and hyaluronic acid (HA) polyelectrolyte multilayer (PEM) film. The properties of the PEM were tuned to mimic the Space of Disse found in liver. The thickness of the detachable PEM was 650 to 1000 nm under hydrated conditions. The Young's modulus of the PEM was approximately 42 kPa, well within the range of modulus values reported for bulk liver. The 3D liver models comprised of all three cell types and a detachable PEM exhibited stable urea production and increased albumin secretion over a 12 day culture period. Additionally, the 3D liver model maintained the phenotype of both LSECs and KCs over the 12 day culture period, verified by CD32b and CD163 staining, respectively. Additionally, CYP1A1 enzyme activity increased significantly in the 3D liver models. The number of hepatocytes in the 3D liver model increased by approximately 60% on day 16 of culture compared to day 4 indicating. Furthermore, only the 3D hepatic model maintained cellular compositions virtually identical to those found in vivo. DNA microarray measurements were conducted on the hepatocyte fractions of the 3D liver mimic to obtain insights into hepatic processes. Gene sets up-regulated in the 3D liver model were related to proliferation, migration, and deposition of extracellular matrix, all functions observed in regenerating hepatocytes. Taken together, these results suggest that inter-cellular signaling between the different cell types in the 3D liver model led to increased hepatic functions. To the best of our knowledge, this is the first study where three of the major hepatic cell types have been incorporated into a model that closely mimics the structure of the sinusoid. These studies demonstrate that the multi-cellular liver models are physiologically relevant. Such models are very promising to conduct detailed investigations into hepatic inter-cellular signaling.
Development and Application of Network Algorithms for Prediction of Gene Function and Response to Viral Infection and Chemicals
Law, Jeffrey Norman (Virginia Tech, 2020-12-09)
The complex molecular machinery of the cell controls its response to various signals and environmental conditions. A natural approach to study these molecular mechanisms and cellular processes is with protein interaction networks. Due to the complexity of these networks, sophisticated computational techniques are required to extract biological insights from them. In this thesis, I develop and apply network-based algorithms for three different challenges. 1. I develop a novel, highly-scalable algorithm for network-based label prediction methods that enables the integration of functional annotations and interaction networks across many species in order to predict the functions of genes in newly-sequenced bacteria. 2. To overcome the limitations of experimental approaches to find human proteins and processes that are hijacked by SARS-CoV-2, I adapt network propagation approaches for predicting human interactors of the virus. 3. Large-scale experimental techniques to screen chemicals for toxicity have tested their effects on many individual proteins. I integrate human protein-protein interactions with this data to gain insights into the molecular networks those chemicals affect. For each of these research problems, I perform comprehensive evaluations and downstream analyses to demonstrate both the accuracy of our approaches and their utility in obtaining a broader understanding of the molecular systems in question.
Discovering contextual connections between biological processes using high-throughput data
Lasher, Christopher Donald (Virginia Tech, 2011-09-12)
Hearkening to calls from life scientists for aid in interpreting rapidly-growing repositories of data, the fields of bioinformatics and computational systems biology continue to bear increasingly sophisticated methods capable of summarizing and distilling pertinent phenomena captured by high-throughput experiments. Techniques in analysis of genome-wide gene expression (e.g., microarray) data, for example, have moved beyond simply detecting individual genes perturbed in treatment-control experiments to reporting the collective perturbation of biologically-related collections of genes, or "processes". Recent expression analysis methods have focused on improving comprehensibility of results by reporting concise, non-redundant sets of processes by leveraging statistical modeling techniques such as Bayesian networks. Simultaneously, integrating gene expression measurements with gene interaction networks has led to computation of response networks--subgraphs of interaction networks in which genes exhibit strong collective perturbation or co-expression. Methods that integrate process annotations of genes with interaction networks identify high-level connections between biological processes, themselves. To identify context-specific changes in these inter-process connections, however, techniques beyond process-based expression analysis, which reports only perturbed processes and not their relationships, response networks, composed of interactions between genes rather than processes, and existing techniques in process connection detection, which do not incorporate specific biological context, proved necessary. We present two novel methods which take inspiration from the latest techniques in process-based gene expression analysis, computation of response networks, and computation of inter-process connections. We motivate the need for detecting inter-process connections by identifying a collection of processes exhibiting significant differences in collective expression in two liver tissue culture systems widely used in toxicological and pharmaceutical assays. Next, we identify perturbed connections between these processes via a novel method that integrates gene expression, interaction, and annotation data. Finally, we present another novel method that computes non-redundant sets of perturbed inter-process connections, and apply it to several additional liver-related data sets. These applications demonstrate the ability of our methods to capture and report biologically relevant high-level trends.
Discovering Networks of Perturbed Biological Processes in Hepatocyte Cultures
Lasher, Christopher D.; Rajagopalan, Padmavathy; Murali, T. M. (PLOS, 2011-01-05)
The liver plays a vital role in glucose homeostasis, the synthesis of bile acids and the detoxification of foreign substances. Liver culture systems are widely used to test adverse effects of drugs and environmental toxicants. The two most prevalent liver culture systems are hepatocyte monolayers (HMs) and collagen sandwiches (CS). Despite their wide use, comprehensive transcriptional programs and interaction networks in these culture systems have not been systematically investigated. We integrated an existing temporal transcriptional dataset for HM and CS cultures of rat hepatocytes with a functional interaction network of rat genes. We aimed to exploit the functional interactions to identify statistically significant linkages between perturbed biological processes. To this end, we developed a novel approach to compute Contextual Biological Process Linkage Networks (CBPLNs). CBPLNs revealed numerous meaningful connections between different biological processes and gene sets, which we were successful in interpreting within the context of liver metabolism. Multiple phenomena captured by CBPLNs at the process level such as regulation, downstream effects, and feedback loops have well described counterparts at the gene and protein level. CBPLNs reveal high-level linkages between pathways and processes, making the identification of important biological trends more tractable than through interactions between individual genes and molecules alone. Our approach may provide a new route to explore, analyze, and understand cellular responses to internal and external cues within the context of the intricate networks of molecular interactions that control cellular behavior.
Engineering Organoids for Stem Cell Maturation
Gandhi, Neeti Nimish (Virginia Tech, 2024-12-06)
Examining Cellular Interactions and Response to Chemotherapy in The Glioblastoma Perivascular Niche
Hatlen, Rosalyn Rae (Virginia Tech, 2023-01-17)
Glioblastoma multiforme (GBM) is the most deadly and common form of brain cancer and is responsible for over 50% of adult brain tumors. A specific region within the GBM environment is known as the perivascular niche (PVN). We have designed a 3D in vitro model of the PVN comprised of either collagen Type 1 or HyStem-C®, human umbilical vein endothelial cells (HUVECs) or human brain microvascular endothelial cells (HBMECs), and LN229 (GBM) cells. A synergistic response between HUVECs and LN229 cells was observed in co-culture, including 10 – 16-fold increased cell proliferation, a decrease in the height of hydrogels of up to 68%, as well as elevated secretion of TGF-β and CXCL12 up to 2.6-fold from Day 8 to 14. These trends correlated with cell colocalization, indicating a chemotactic role for CXCL12 in enabling the migration of LN229 cells towards HUVECs in co-cultures. Von Willebrand factor (vWF) was co-expressed with glial fibrillary acidic protein (GFAP) in up to 40% of LN229 cells after 14 days in co-culture in collagen (2.2 mg/mL) and HyStem-C® gels. The expression of vWF indicates the early stages of trans-differentiation of LN229 cells to an endothelial cell phenotype. We then investigated the effect of chemotherapeutic drugs temozolomide (TMZ) and Avastin® on EC networks, LN229 cell morphology and alignment, cytotoxicity, colocalization, and trans-differentiation. TMZ was observed to primarily affect LN229 cells, with treatment at high concentrations resulting in up to 2.3-fold reduced alignment as well as an increase in cell circularity. Cytotoxicity of up to 94% was also observed up to in LN229 monocultures, and was significantly higher in collagen (1.1 mg/mL) gels. Avastin® treatment resulted in changes to ECs. Network features were significantly reduced and EC cellular proliferation decreased up to 69% with Avastin® treatment. Significant increases in percentages of colocalized and GFAP+/vWF+ cells were also observed when treated with 8 µg/mL Avastin®. This suggests that chemotactic signaling may have been altered. TGF-β secretion was reduced in co-cultures when 150 µM TMZ or 8 µg/mL Avastin® were administered.
The hepatocyte proteome in organotypic rat liver models and the influence of the local microenvironment
Vu, Lucas T.; Orbach, Sophia M.; Ray, W. Keith; Cassin, Margaret E.; Rajagopalan, Padmavathy; Helm, Richard F. (Biomed Central, 2017-06-20)
Background: Liver models that closely mimic the in vivo microenvironment are useful for understanding liver functions, capabilities, and intercellular communication processes. Three-dimensional (3D) liver models assembled using hepatocytes and liver sinusoidal endothelial cells (LSECs) separated by a polyelectrolyte multilayer (PEM) provide a functional system while also permitting isolation of individual cell types for proteomic analyses. Methods: To better understand the mechanisms and processes that underlie liver model function, hepatocytes were maintained as monolayers and 3D PEM-based formats in the presence or absence of primary LSECs. The resulting hepatocyte proteomes, the proteins in the PEM, and extracellular levels of urea, albumin and glucose after three days of culture were compared. Results: All systems were ketogenic and found to release glucose. The presence of the PEM led to increases in proteins associated with both mitochondrial and peroxisomal-based β-oxidation. The PEMs also limited production of structural and migratory proteins associated with dedifferentiation. The presence of LSECs increased levels of Phase I and Phase II biotransformation enzymes as well as several proteins associated with the endoplasmic reticulum and extracellular matrix remodeling. The proteomic analysis of the PEMs indicated that there was no significant change after three days of culture. These results are discussed in relation to liver model function. Conclusions: Heterotypic cell-cell and cell-ECM interactions exert different effects on hepatocyte functions and phenotypes.
Identification of Cell Biomechanical Signatures Using Three Dimensional Isotropic Microstructures
Nikkhah, Mehdi (Virginia Tech, 2010-12-03)
Micro and nanofabrication technologies have been used extensively in many biomedical and biological applications. Integration of MEMS technology and biology (BioMEMS) enables precise control of the cellular microenvironments and offers high throughput systems. The focus of this research was to develop three dimensional (3-D) isotropic microstructures for comprehensive analysis on cell-substrate interactions. The aim was to investigate whether the normal and cancerous cells differentially respond to their underlying substrate and whether the differential response of the cells leads to a novel label-free technique to distinguish between normal and cancerous cells. Three different generations of 3-D isotropic microstructures comprised of curved surfaces were developed using a single-mask, single-etch step process. Our experimental model included HS68 normal human fibroblasts, MCF10A normal human breast epithelial cells and MDA-MB-231 metastatic human breast cancer cells. Primary findings on the first generation of silicon substrates demonstrated a distinct adhesion and growth behavior in HS68 and MDA-MB-231 cells. MDA-MB-231 cells deformed while the fibroblasts stretched and elongated their cytoskeleton on the curved surfaces. Unlike fibroblasts, MDA-MB-231 cells mainly trapped and localized inside the deep microchambers. Detailed investigations on cytoskeletal organization, adhesion pattern and morphology of the cells on the second generation of the silicon substrates demonstrated that cytoskeletal prestress and microtubules organization in HS68 cells, cell-cell junction and cell-substrate adhesion strength in MCF10A cells, and deformability of MDA-MB-231 cells (obtained by using AFM technique) affect their behavior inside the etched cavities. Treatment of MDA-MB-231 cells with experimental breast cancer drug, SAHA, on the second generation of substrates, significantly altered the cells morphology, cytoarchitecture and adhesion pattern inside the 3-D microstructures. Third generation of silicon substrates was developed for comprehensive analysis on behavior of MDA-MB-231 and MCF10A cells in a co-culture system in response to SAHA drug. Formation of colonies of both cell types was evident inside the cavities within a few hours after seeding the cells on the chips. SAHA selectively altered the morphology and cytoarchitecture in MDA-MB-231 cells. Most importantly, the majority of MDA-MB-231 cells stretched inside the etched cavities, while the adhesion pattern of MCF10A cells remained unaltered. In the last part of this dissertation, using AFM analysis, we showed that the growth medium composition has a pronounced effect on cell elasticity. Our findings demonstrated that the proposed isotropic silicon microstructures have potential applications in development of biosensor platforms for cell segregation as well as conducting fundamental biological studies.
Identifying Human Interactors of SARS-CoV-2 Proteins and Drug Targets for COVID-19 using Network-Based Label Propagation
Law, Jeffrey N.; Akers, Kyle; Tasnina, Nure; Della Santina, Catherine M.; Kshirsagar, Meghana; Klein-Seetharaman, Judith; Crovella, Mark; Rajagopalan, Padmavathy; Kasif, Simon; Murali, T. M. (Virginia Tech, 2020-06-22)
Motivated by the critical need to identify new treatments for COVID- 19, we present a genome-scale, systems-level computational approach to prioritize drug targets based on their potential to regulate host- virus interactions or their downstream signaling targets. We adapt and specialize network label propagation methods to this end. We demonstrate that these techniques can predict human-SARS-CoV- 2 protein interactors with high accuracy. The top-ranked proteins that we identify are enriched in host biological processes that are potentially coopted by the virus. We present cases where our methodology generates promising insights such as the potential role of HSPA5 in viral entry. We highlight the connection between endoplasmic reticulum stress, HSPA5, and anti-clotting agents. We identify tubulin proteins involved in ciliary assembly that are targeted by anti-mitotic drugs. Drugs that we discuss are already undergoing clinical trials to test their efficacy against COVID-19. Our prioritized list of human proteins and drug targets is available as a general resource for biological and clinical researchers who are repositioning existing and approved drugs or developing novel therapeutics as anti-COVID-19 agents.
Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2
Law, Jeffrey N.; Akers, Kyle; Tasnina, Nure; Della Santina, Catherine M.; Deutsch, Shay; Kshirsagar, Meghana; Klein-Seetharaman, Judith; Crovella, Mark; Rajagopalan, Padmavathy; Kasif, Simon; Murali, T. M. (Oxford University Press, 2021-12-01)
BACKGROUND: Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance tracing in this context, e.g., determining how much any experimental observation in the input contributes to the score of every prediction. RESULTS: We design a network propagation framework with 2 novel components and apply it to predict human proteins that directly or indirectly interact with SARS-CoV-2 proteins. First, we trace the provenance of each prediction to its experimentally validated sources, which in our case are human proteins experimentally determined to interact with viral proteins. Second, we design a technique that helps to reduce the manual adjustment of parameters by users. We find that for every top-ranking prediction, the highest contribution to its score arises from a direct neighbor in a human protein-protein interaction network. We further analyze these results to develop functional insights on SARS-CoV-2 that expand on known biology such as the connection between endoplasmic reticulum stress, HSPA5, and anti-clotting agents. CONCLUSIONS: We examine how our provenance-tracing method can be generalized to a broad class of network-based algorithms. We provide a useful resource for the SARS-CoV-2 community that implicates many previously undocumented proteins with putative functional relationships to viral infection. This resource includes potential drugs that can be opportunistically repositioned to target these proteins. We also discuss how our overall framework can be extended to other, newly emerging viruses.
Investigating Induced Pluripotent Stem Cells for Tissue Engineering and Hepatotoxicity Applications
Wills, Lauren Raquel (Virginia Tech, 2019-06-12)
Induced pluripotent stem cells (iPSCs) can be differentiated into multiple cell types in the body while maintaining proliferative capabilities. The generation of human iPSC-derived hepatocytes (iPSC-Heps) has resulted in a new source for hepatic cells. The current available options for human hepatocytes are primary human hepatocytes (PHHs) and cell lines. PHHs isolated from healthy human donors are difficult to obtain, while cell lines exhibit reduced hepatotoxic sensitivity. iPSC-Heps are being investigated as an alternative option as they are derived from a continuous, stable source and are able to maintain their original donor genotype, which opens the door for patient-specific studies. iPSC-Heps show promise for utilization in tissue engineering, hepatotoxicity studies as well as screening for patient-specific therapeutics. Various reports have concluded that iPSC-Heps exhibit reduced hepatocyte function in comparison to PHHs. Prior reports on iPSC-Heps have focused on improving their adult phenotype functions through variations in differentiation protocols or by altering their in vitro culturing environment. This thesis focuses on incorporating hepatic non-parenchymal cells to more closely mimic the tissue and cell architecture found in the liver tissue. We designed and assembled a 3D iPSC-Hep model that integrates liver sinusoidal endothelial cells, with the goal of achieving functional maturity. Hepatotoxicants were administered to our models and various hepatic markers were measured to analyze the toxic response. This work demonstrates the need for the inclusion of hepatic non-parenchymal cells in iPSC-derived liver tissues, specifically for hepatotoxicity applications.
Investigating the Interplay between Inflammation and Matrix Stiffness: Evaluation of Cell Phenotype and Cytoplasmic Stiffness In Vitro
Ford, Andrew Joseph (Virginia Tech, 2018-08-13)
The cellular microenvironment in vivo consists of both mechanical and chemical signals, which drive cell function and fate. These signals include the composition, architecture, and mechanical properties of the extracellular matrix (ECM), signaling molecules secreted by cells into their surroundings, as well as physical interactions between neighboring cells. Cells are able to interact with their surroundings through a number of different mechanisms such as remodeling of the ECM through adhesion, contraction, degradation, and deposition of proteins, as well as the secretion of pro- or anti-inflammatory molecules. In diseased states, where homeostasis has been perturbed, inflammatory signals are secreted which can modify the cellular microenvironment. Diseased states such as cancer and fibrosis are often associated with the excessive production of ECM proteins that subsequently lead to an increase in tissue stiffness and changes to ECM architecture. Such changes to the mechanical properties of the cellular microenvironment affect the cytoskeletal arrangement, migration and adhesion of both the parenchymal cells, as well as immune response cells, which migrate to the sites of injury. Further understanding of the inflammatory responses and their relationships to tissue stiffness and ECM architecture could aid in the development of novel strategies to predict diseases as well as to target and monitor therapies. Since inflammation and mechanical properties of the affected tissue are closely interlinked, obtaining a detailed understanding of the interplay between the properties of the microenvironment and the cells that reside within it will be very beneficial to obtain physiologically relevant information. We have investigated the combinatorial effects of matrix stiffness, and architecture in the presence of co-cultures of cells to determine the overall effect on cellular responses and phenotypes. We have conducted studies on co-cultures of cells in 2D and 3D environments to identify how cellular behavior is affected by dimensionality.
Investigating the Spatiotemporal Variation in Functional Markers, Gut Metabolites and Ethanol Toxicity in In Vitro Cultures of the Rat Jejunum and Hepatocytes
Kothari, Anjaney (Virginia Tech, 2019-10-22)
The small intestine and the liver regulate several physiological functions together including the absorption and bioavailability of drugs and bile and nitrogen homeostasis. It is important to study these two organs together to gain a holistic understanding of their communication with each other. However, there is a lack of culture models that investigate the use of primary cells/tissues from the liver and the intestine to study their interaction and importance in manifestation of drug toxicity. The studies described in this dissertation were conducted using inverted rat intestinal explants obtained from three regions of the jejunum, named as the proximal, medial and distal jejunum. Markers of enterocyte, goblet cell and Paneth cell function in the jejunum followed in vivo – like spatial trends reported for the entire small intestine. Jejunum explants were integrated with hepatocytes to model the intestine-liver axis. Integration of jejunum explants from the proximal region with hepatocytes had a beneficial effect on both hepatocyte urea secretion and jejunum mucin secretion, hinting at communication between these organs in culture. Integrated cultures of the rat jejunum and hepatocytes were used to investigate ethanol toxicity in vitro. Trends in activities of enzymes involved in ethanol metabolism and mucus secretion in integrated cultures with proximal jejunum explants corroborated with in vivo reports on ethanol toxicity. Various metabolites secreted and metabolized in vitro were also identified using mass spectrometry. Spatial trends in concentrations of several lipids including bile acids, lysophosphatidylcholines and fatty acids corroborated with in vivo reports of lipid metabolism. The integrated intestine-liver cultures can be used as a platform for future investigations of drug toxicity, lipid metabolism and inter-organ communication.
Multi-Cellular Organotypic Liver Models for the Investigation of Chemical Toxicity and Liver Fibrosis
Orbach, Sophia Michelle (Virginia Tech, 2018-03-07)
The liver is responsible for lipid and glucose metabolism, protein and bile synthesis and the biotransformation of xenobiotics. These functions, performed by hepatocytes, are dependent on heterotypic interactions with other liver cell types and the stratified microarchitecture of the organ. In vitro liver models provide insights into the role of each cell type and perturbations upon external stimuli. Despite the dissimilarities to in vivo and rapid dedifferentiation, most liver studies utilize hepatocyte monocultures. These models lack heterotypic interactions causing inaccurate assessments of toxicity and disease. Only a limited number of 3D hepatic models incorporate the major liver cell types, and these cultures primarily focus on the hepatocyte response. We have developed 3D liver models that include all major hepatic cell types and recapitulate the layered architecture of the organ. These models maintain hepatic functions for up to four weeks and can be used to isolate the role and response of each cell type. We used these models to study two critical aspects of the organ -- acute hepatotoxicity and liver fibrosis. There are tens of thousands of chemicals with undetermined effects on the human body. High concentrations of xenobiotics can cause acute liver damage and failure. Liver impairment can result in multiple organ failure, hepatic encephalopathy and death. Therefore, it becomes critically important to investigate hepatotoxicity in a time, cost and resource effective manner. Our 3D liver models were validated for hepatotoxicity testing with acetaminophen, a prototypic drug. We then adapted and optimized the models for high-throughput hepatotoxicity testing with automated procedures and primary human hepatic cells. Liver fibrosis and cirrhosis are well-established consequences of chronic chemical exposure, infection and alcoholism. The initiating factors, end stages and resolution of fibrosis have been extensively studied. However, there is minimal information on the role of the local microenvironment in the progression of the disease from diseased to healthy tissue. We designed 3D liver cultures with a mechanical gradient to gradually model this transition through spatial and temporal perspectives. These findings demonstrate the versatility and accuracy of these 3D hepatic models in the investigation of liver toxicity and fibrosis.

Browsing by Author "Rajagopalan, Padmavathy"

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