Albert Gough - Academia.edu (original) (raw)

Papers by Albert Gough

The automated interactive microscope (AIM) for investigating the functional dynamics of living cells: Status and vision

Proceedings, annual meeting, Electron Microscopy Society of America, 1994

The current status and future development plans for the Automated Interactive Microscope (AIM), t... more The current status and future development plans for the Automated Interactive Microscope (AIM), to better define the mechanisms of the function of living cells, is described. The development of AIM is fueled by biologists need to spatially and temporally correlate biochemical, molecular and genetic patterns to study cell functions such as division, locomotion and endocytosis. AIM will allow the investigator to use the cell as a “living microcuvette”.AIM redefines the meaning of the term “microscope” to include the functional capability of the microscope system provided by computerization, in addition to the more classical definition which emphasizes the opto-mechanical hardware. AIM is an next generation electronic light microscope imaging system which has grown out of our work in the development of the multimode light microscope. New functionality includes new experiment control facilities as well as related multidimensional image processing, image analysis and interactive data vis...

Experimental Biology and Medicine, 2021

Metabolic syndrome is a complex disease that involves multiple organ systems including a critical... more Metabolic syndrome is a complex disease that involves multiple organ systems including a critical role for the liver. Non-alcoholic fatty liver disease (NAFLD) is a key component of the metabolic syndrome and fatty liver is linked to a range of metabolic dysfunctions that occur in approximately 25% of the population. A panel of experts recently agreed that the acronym, NAFLD, did not properly characterize this heterogeneous disease given the associated metabolic abnormalities such as type 2 diabetes mellitus (T2D), obesity, and hypertension. Therefore, metabolic dysfunction-associated fatty liver disease (MAFLD) has been proposed as the new term to cover the heterogeneity identified in the NAFLD patient population. Although many rodent models of NAFLD/NASH have been developed, they do not recapitulate the full disease spectrum in patients. Therefore, a platform has evolved initially focused on human biomimetic liver microphysiology systems that integrates fluorescent protein biosens...

Metabolites

Non-alcoholic fatty liver disease (NAFLD) has a high global prevalence with a heterogeneous and c... more Non-alcoholic fatty liver disease (NAFLD) has a high global prevalence with a heterogeneous and complex pathophysiology that presents barriers to traditional targeted therapeutic approaches. We describe an integrated quantitative systems pharmacology (QSP) platform that comprehensively and unbiasedly defines disease states, in contrast to just individual genes or pathways, that promote NAFLD progression. The QSP platform can be used to predict drugs that normalize these disease states and experimentally test predictions in a human liver acinus microphysiology system (LAMPS) that recapitulates key aspects of NAFLD. Analysis of a 182 patient-derived hepatic RNA-sequencing dataset generated 12 gene signatures mirroring these states. Screening against the LINCS L1000 database led to the identification of drugs predicted to revert these signatures and corresponding disease states. A proof-of-concept study in LAMPS demonstrated mitigation of steatosis, inflammation, and fibrosis, especial...

831-P: Tocilizumab Is Effective in Reducing Inflammation in T2D–COVID-Organ-on-a-Chip Model

Diabetes

The COVID-pandemic has contributed to more than 5 million deaths worldwide in the last two years.... more The COVID-pandemic has contributed to more than 5 million deaths worldwide in the last two years. Co-morbid conditions such as Type 2 Diabetes (T2D) , HTN, obesity, and CKD have been associated with increased mortality with COVID-19. In a large meta-analysis, the relative risk of mortality was 1.54 for patients with T2D and COVID-19. Thus, there is an imperative need to develop a platform for rapid and reliable drug screening/selection against COVID-related morbidity/mortality in T2D patients. With limited translatability of in vitro and small animal models to humans, human organ-on-a-chip models are an attractive platform to model in vivo disease conditions and test potential therapeutics. We seeded T2D or nondiabetes patient-derived macrophage and human liver sinusoidal endothelial cells along with normal hepatocytes and kupffer cells in the liver-on-a-chip (LAMPS - Liver Acinus MicroPhysiological System) developed by our group, perfused with media mimicking normal fasting or late...

Supplemental material, LMNB1_Assay_Development_paper_REV2_Supplemental for Development and Optimi... more Supplemental material, LMNB1_Assay_Development_paper_REV2_Supplemental for Development and Optimization of a High-Content Analysis Platform to Identify Suppressors of Lamin B1 Overexpression as a Therapeutic Strategy for Autosomal Dominant Leukodystrophy by Bruce Nmezi, Laura L. Vollmer, Tong Ying Shun, Albert Gough, Harshvardhan Rolyan, Fang Liu, Yumeng Jia, Quasar S. Padiath and Andreas Vogt in SLAS Discovery

Supplemental material, SUPPLEMENTAL_MATERIAL_final_R1 for A High-Throughput Assay for DNA Replica... more Supplemental material, SUPPLEMENTAL_MATERIAL_final_R1 for A High-Throughput Assay for DNA Replication Inhibitors Based upon Multivariate Analysis of Yeast Growth Kinetics by Marilyn Ngo, Nick Wechter, Emily Tsai, Tong Ying Shun, Albert Gough, Mark E. Schurdak, Anthony Schwacha and Andreas Vogt in SLAS Discovery

Integrating Analysis of Cellular Heterogeneity in High-Content Dose-Response Studies

Cellular Heterogeneity, 2018

Heterogeneity is a complex property of cellular systems and therefore presents challenges to the ... more Heterogeneity is a complex property of cellular systems and therefore presents challenges to the reliable identification and characterization. Large-scale biology projects may span many months, requiring a systematic approach to quality control to track reproducibility and correct for instrumental variation and assay drift that could mask biological heterogeneity and preclude comparisons of heterogeneity between runs or even between plates. However, presently there is no standard approach to the tracking and analysis of heterogeneity. Previously, we demonstrated the use of the Kolmogorov-Smirnov statistic as a metric for monitoring the reproducibility of heterogeneity in a screen and described the use of three heterogeneity indices as a means to characterize, filter, and browse cellular heterogeneity in big data sets (Gough et al., Methods 96:12-26, 2016). In this chapter, we present a detailed method for integrating the analysis of cellular heterogeneity in assay development, validation, screening, and post screen. Importantly, we provide a detailed method for quality control, to normalize cellular data, track heterogeneity over time, and analyze heterogeneity in big data sets, along with software tools to assist in that process. The example screen for this method is from an HCS project, but the approach applies equally to other experimental methods that measure populations of cells.

Method for modeling a disease

Cellular Systems Biology Applied to Preclinical Safety Testing: A Case Study of CellCiphrTM Profiling

Vernetti, L., Irwin, W., Giuliano, KA, Gough, A., Johnston, K. and Taylor, DL (2008) Cellular Sys... more Vernetti, L., Irwin, W., Giuliano, KA, Gough, A., Johnston, K. and Taylor, DL (2008) Cellular Systems Biology Applied to Preclinical Safety Testing: A Case Study of CellCiphr TM Profiling, in Drug Efficacy, Safety, and Biologics Discovery: Emerging Technologies and ...

One of the greatest challenges in biomedical research, drug discovery and diagnostics is understa... more One of the greatest challenges in biomedical research, drug discovery and diagnostics is understanding how seemingly identical cells can respond differently to perturbagens including drugs for disease treatment. Although heterogeneity has become an accepted characteristic of a population of cells, in drug discovery it is not routinely evaluated or reported. The standard practice for cell-based, high content assays has been to assume a normal distribution and to report a well-to-well average value with a standard deviation. To address this important issue we sought to define a method that could be readily implemented to identify, quantify and characterize heterogeneity in cellular and small organism assays to guide decisions during drug discovery and experimental cell/tissue profiling. Our study revealed that heterogeneity can be effectively identified and quantified with three indices that indicate diversity, non-normality and percent outliers. The indices were evaluated using the induction and inhibition of STAT3 activation in five cell lines where the systems response including sample preparation and instrument performance were well characterized and controlled. These heterogeneity indices provide a standardized method that can easily be integrated into small and large scale screening or profiling projects to guide interpretation of the biology, as well as the development of therapeutics and diagnostics. Understanding the heterogeneity in the response to perturbagens will become a critical factor in designing strategies for the development of therapeutics including targeted polypharmacology.

Systems cell biology based on high-content screening

Methods in enzymology, 2006

A new discipline of biology has emerged since 2004, which we call "systems cell biology&quot... more A new discipline of biology has emerged since 2004, which we call "systems cell biology" (SCB). Systems cell biology is the study of the living cell, the basic unit of life, an integrated and interacting network of genes, proteins, and myriad metabolic reactions that give rise to function. SCB takes advantage of high-content screening platforms, but delivers more detailed profiles of cellular systemic function, including the application of advanced reagents and informatics tools to sophisticated cellular models. Therefore, an SCB profile is a cellular systemic response as measured by a panel of reagents that quantify a specific set of biomarkers.

SLAS Discovery, 2010

The integration of high-content screening (HCS) readers with organ-specific cell models, panels o... more The integration of high-content screening (HCS) readers with organ-specific cell models, panels of functional biomarkers, and advanced informatics is a powerful approach to identifying the toxic liabilities of compounds early in the development process and forms the basis of “early safety assessment.” This cellular systems biology (CSB™) approach (CellCiphr® profile) has been used to integrate rodent and human cellular hepatic models with panels of functional biomarkers measured at multiple time points to profile both the potency and specificity of the cellular toxicological response. These profiles also provide initial insights on the mechanism of the toxic response. The authors describe here mechanistic assay profiles designed to further dissect the toxic mechanisms of action and elucidate subtle effects apparent in subpopulations of cells. They measured 8 key mechanisms of toxicity with multiple biomarker feature measurements made simultaneously in populations of living primary h...

SLAS Discovery, 1997

Recent improvements in target discovery and high throughput screening (HTS) have increased the pr... more Recent improvements in target discovery and high throughput screening (HTS) have increased the pressure at key points along the drug discovery pipeline. High-content screening (HCS) was developed to ease bottlenecks that have formed at target validation and lead optimization points in the pipeline. HCS defines the role of targets in cell functions by combining fluorescence-based reagents with the ArrayScan™ System to automatically extract temporal and spatial information about target activities within cells. The ArrayScan System is a tabletop instrument that includes optics for subcellular resolution of fluorescence signals from many cells in a field within a well of a microtiter plate. One demonstrated application is a high-content screen designed to measure the drug-induced transport of a green fluorescent protein-human glucocorticoid receptor chimeric protein from the cytoplasm to the nucleus of human tumor cells. A high-content screen is also described for the multiparametric me...

Experimental Biology and Medicine, 2014

The liver is a heterogeneous organ with many vital functions, including metabolism of pharmaceuti... more The liver is a heterogeneous organ with many vital functions, including metabolism of pharmaceutical drugs and is highly susceptible to injury from these substances. The etiology of drug-induced liver disease is still debated although generally regarded as a continuum between an activated immune response and hepatocyte metabolic dysfunction, most often resulting from an intermediate reactive metabolite. This debate stems from the fact that current animal and in vitro models provide limited physiologically relevant information, and their shortcomings have resulted in “silent” hepatotoxic drugs being introduced into clinical trials, garnering huge financial losses for drug companies through withdrawals and late stage clinical failures. As we advance our understanding into the molecular processes leading to liver injury, it is increasingly clear that (a) the pathologic lesion is not only due to liver parenchyma but is also due to the interactions between the hepatocytes and the residen...

Annals of the New York Academy of Sciences, 1997

Multimode Light Microscopy and the Dynamics of Molecules, Cells, and Tissues

Annual Review of Physiology, 1993

There is a renaissance and revolution in light microscopy and its use in biological research, bio... more There is a renaissance and revolution in light microscopy and its use in biological research, biotechnology, and clinical diagnostics (139, 163). This renaissance has been driven primarily by the need to define the interplay of ions, metabolites, and macromolecules in time and space in living cells and tissues. The goal is to understand fundamental biological functions by temporal-spatial mapping of chemical and molecular events in vivo. The revolution has been fueled by the integration of advances in the heretofore distinct fields of biology, chemistry, physical optics, robotics, and computer science. Powerful new reagents are being used in conjunction with automated light microscope imaging workstations to investigate the contents, activity, and dynamics of living cells and tissues. There are also great challenges. Some challenges involve instrumental

Automated interactive microscopy: measuring and manipulating the chemical and molecular dynamics of cells and tissues

Optical Diagnostics of Living Cells and Biofluids, 1996

Automated interactive microscopy: measuring and manipulating the chemical and molecular dynamics ... more Automated interactive microscopy: measuring and manipulating the chemical and molecular dynamics of cells and tissues. [Proceedings of SPIE 2678, 15 (1996)]. D. Lansing Taylor, Lowell D. Harris, R. DeBiasio, Scott E. Fahlman ...

Human biomimetic liver microphysiology systems in drug development and precision medicine

Nature Reviews Gastroenterology & Hepatology

A 3D microfluidic liver model for high throughput compound toxicity screening in the OrganoPlate®

Toxicology

Nature Communications

An unmet clinical need in solid tumor cancers is the ability to harness the intrinsic spatial inf... more An unmet clinical need in solid tumor cancers is the ability to harness the intrinsic spatial information in primary tumors that can be exploited to optimize prognostics, diagnostics and therapeutic strategies for precision medicine. Here, we develop a transformational spatial analytics computational and systems biology platform (SpAn) that predicts clinical outcomes and captures emergent spatial biology that can potentially inform therapeutic strategies. We apply SpAn to primary tumor tissue samples from a cohort of 432 chemo-naïve colorectal cancer (CRC) patients iteratively labeled with a highly multiplexed (hyperplexed) panel of 55 fluorescently tagged antibodies. We show that SpAn predicts the 5-year risk of CRC recurrence with a mean AUROC of 88.5% (SE of 0.1%), significantly better than current state-of-the-art methods. Additionally, SpAn infers the emergent network biology of tumor microenvironment spatial domains revealing a spatially-mediated role of CRC consensus molecula...