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Engelberg JA, Retallack H, Balassanian R, Dowsett M, Zabaglo L, Ram AA, Apple SK, Bishop JW, Borowsky AD, Carpenter PM, Chen YY, Datnow B, Elson S, Hasteh F, Lin F, Moatamed NA, Zhang Y, Cardiff RD. "Score the Core" Web-based pathologist training tool improves the accuracy of breast cancer IHC4 scoring. Hum Pathol 2015; 46:1694-704. [PMID: 26410019 DOI: 10.1016/j.humpath.2015.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 07/07/2015] [Accepted: 07/15/2015] [Indexed: 01/27/2023]
Abstract
Hormone receptor status is an integral component of decision-making in breast cancer management. IHC4 score is an algorithm that combines hormone receptor, HER2, and Ki-67 status to provide a semiquantitative prognostic score for breast cancer. High accuracy and low interobserver variance are important to ensure the score is accurately calculated; however, few previous efforts have been made to measure or decrease interobserver variance. We developed a Web-based training tool, called "Score the Core" (STC) using tissue microarrays to train pathologists to visually score estrogen receptor (using the 300-point H score), progesterone receptor (percent positive), and Ki-67 (percent positive). STC used a reference score calculated from a reproducible manual counting method. Pathologists in the Athena Breast Health Network and pathology residents at associated institutions completed the exercise. By using STC, pathologists improved their estrogen receptor H score and progesterone receptor and Ki-67 proportion assessment and demonstrated a good correlation between pathologist and reference scores. In addition, we collected information about pathologist performance that allowed us to compare individual pathologists and measures of agreement. Pathologists' assessment of the proportion of positive cells was closer to the reference than their assessment of the relative intensity of positive cells. Careful training and assessment should be used to ensure the accuracy of breast biomarkers. This is particularly important as breast cancer diagnostics become increasingly quantitative and reproducible. Our training tool is a novel approach for pathologist training that can serve as an important component of ongoing quality assessment and can improve the accuracy of breast cancer prognostic biomarkers.
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Affiliation(s)
- Jesse A Engelberg
- Center for Comparative Medicine, University of California Davis, Davis, CA 95616.
| | - Hanna Retallack
- School of Medicine, University of California San Francisco, San Francisco, CA 94143
| | - Ronald Balassanian
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143
| | - Mitchell Dowsett
- Centre for Molecular Pathology, Royal Marsden Hospital, London, SW3 6JJ United Kingdom
| | - Lila Zabaglo
- Institute of Cancer Research, London, SM2 5NG United Kingdom
| | - Arishneel A Ram
- Center for Comparative Medicine, University of California Davis, Davis, CA 95616
| | - Sophia K Apple
- Department of Pathology, University of California Los Angeles, Los Angeles, CA 90404
| | - John W Bishop
- Department of Pathology, University of California Davis, Davis, CA 95616
| | | | - Philip M Carpenter
- Department of Pathology, University of California Irvine, Orange, CA 92697
| | - Yunn-Yi Chen
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143
| | - Brian Datnow
- Department of Pathology, University of California San Diego, San Diego, CA 92093
| | - Sarah Elson
- Center for Comparative Medicine, University of California Davis, Davis, CA 95616
| | - Farnaz Hasteh
- Department of Pathology, University of California San Diego, San Diego, CA 92093
| | - Fritz Lin
- Department of Pathology, University of California Irvine, Orange, CA 92697
| | - Neda A Moatamed
- Department of Pathology, University of California Los Angeles, Los Angeles, CA 90404
| | - Yanhong Zhang
- Department of Pathology, University of California Davis, Davis, CA 95616
| | - Robert D Cardiff
- Department of Pathology, University of California Davis, Davis, CA 95616
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Chen JQ, Mori H, Cardiff RD, Trott JF, Hovey RC, Hubbard NE, Engelberg JA, Tepper CG, Willis BJ, Khan IH, Ravindran RK, Chan SR, Schreiber RD, Borowsky AD. Abnormal Mammary Development in 129:STAT1-Null Mice is Stroma-Dependent. PLoS One 2015; 10:e0129895. [PMID: 26075897 PMCID: PMC4468083 DOI: 10.1371/journal.pone.0129895] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 05/14/2015] [Indexed: 11/18/2022] Open
Abstract
Female 129:Stat1-null mice (129S6/SvEvTac-Stat1tm1Rds homozygous) uniquely develop estrogen-receptor (ER)-positive mammary tumors. Herein we report that the mammary glands (MG) of these mice have altered growth and development with abnormal terminal end buds alongside defective branching morphogenesis and ductal elongation. We also find that the 129:Stat1-null mammary fat pad (MFP) fails to sustain the growth of 129S6/SvEv wild-type and Stat1-null epithelium. These abnormalities are partially reversed by elevated serum progesterone and prolactin whereas transplantation of wild-type bone marrow into 129:Stat1-null mice does not reverse the MG developmental defects. Medium conditioned by 129:Stat1-null epithelium-cleared MFP does not stimulate epithelial proliferation, whereas it is stimulated by medium conditioned by epithelium-cleared MFP from either wild-type or 129:Stat1-null females having elevated progesterone and prolactin. Microarrays and multiplexed cytokine assays reveal that the MG of 129:Stat1-null mice has lower levels of growth factors that have been implicated in normal MG growth and development. Transplanted 129:Stat1-null tumors and their isolated cells also grow slower in 129:Stat1-null MG compared to wild-type recipient MG. These studies demonstrate that growth of normal and neoplastic 129:Stat1-null epithelium is dependent on the hormonal milieu and on factors from the mammary stroma such as cytokines. While the individual or combined effects of these factors remains to be resolved, our data supports the role of STAT1 in maintaining a tumor-suppressive MG microenvironment.
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Affiliation(s)
- Jane Q. Chen
- Center for Comparative Medicine, University of California, Davis, California, United States of America
| | - Hidetoshi Mori
- Center for Comparative Medicine, University of California, Davis, California, United States of America
| | - Robert D. Cardiff
- Center for Comparative Medicine, University of California, Davis, California, United States of America
| | - Josephine F. Trott
- Department of Animal Science, University of California, Davis, California, United States of America
| | - Russell C. Hovey
- Department of Animal Science, University of California, Davis, California, United States of America
| | - Neil E. Hubbard
- Center for Comparative Medicine, University of California, Davis, California, United States of America
| | - Jesse A. Engelberg
- Center for Comparative Medicine, University of California, Davis, California, United States of America
| | - Clifford G. Tepper
- Division of Basic Sciences, Cancer Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Sacramento, California, United States of America
| | - Brandon J. Willis
- Mouse Biology Program, University of California, Davis, California, United States of America
| | - Imran H. Khan
- Center for Comparative Medicine, University of California, Davis, California, United States of America
| | - Resmi K. Ravindran
- Center for Comparative Medicine, University of California, Davis, California, United States of America
| | - Szeman R. Chan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Robert D. Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Alexander D. Borowsky
- Center for Comparative Medicine, University of California, Davis, California, United States of America
- Department of Pathology and Laboratory Medicine, University of California, Davis, School of Medicine, Sacramento, California, United States of America
- * E-mail:
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Engelberg JA, Giberson RT, Young LJT, Hubbard NE, Cardiff RD. The use of mouse models of breast cancer and quantitative image analysis to evaluate hormone receptor antigenicity after microwave-assisted formalin fixation. J Histochem Cytochem 2014; 62:319-34. [PMID: 24682322 DOI: 10.1369/0022155414529250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Microwave methods of fixation can dramatically shorten fixation times while preserving tissue structure; however, it remains unclear if adequate tissue antigenicity is preserved. To assess and validate antigenicity, robust quantitative methods and animal disease models are needed. We used two mouse mammary models of human breast cancer to evaluate microwave-assisted and standard 24-hr formalin fixation. The mouse models expressed four antigens prognostic for breast cancer outcome: estrogen receptor, progesterone receptor, Ki67, and human epidermal growth factor receptor 2. Using pathologist evaluation and novel methods of quantitative image analysis, we measured and compared the quality of antigen preservation, percentage of positive cells, and line plots of cell intensity. Visual evaluations by pathologists established that the amounts and patterns of staining were similar in tissues fixed by the different methods. The results of the quantitative image analysis provided a fine-grained evaluation, demonstrating that tissue antigenicity is preserved in tissues fixed using microwave methods. Evaluation of the results demonstrated that a 1-hr, 150-W fixation is better than a 45-min, 150-W fixation followed by a 15-min, 650-W fixation. The results demonstrated that microwave-assisted formalin fixation can standardize fixation times to 1 hr and produce immunohistochemistry that is in every way commensurate with longer conventional fixation methods.
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Affiliation(s)
- Jesse A Engelberg
- Center for Comparative Medicine, University of California, Davis, California (JAE,LJTY,NEH,RDC)
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Hubbard NE, Chen QJ, Sickafoose LK, Wood MB, Gregg JP, Abrahamsson NM, Engelberg JA, Walls JE, Borowsky AD. Transgenic mammary epithelial osteopontin (spp1) expression induces proliferation and alveologenesis. Genes Cancer 2013; 4:201-12. [PMID: 24069507 DOI: 10.1177/1947601913496813] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 06/14/2013] [Indexed: 01/12/2023] Open
Abstract
Osteopontin (OPN) Spp1 is involved in differentiation of the mammary gland. We engineered mice to overexpress OPN in mammary epithelium and describe an altered mammary phenotype. Three transgenic (Tg) founder lines FVB/N Tg(MMTV-Opn)((1-3BOR)) were propagated after FVB/NJ pronuclear injections. Mammary glands from Tg-OPN mice compared to littermate controls showed, at 4 weeks of age, exaggerated terminal end buds; at 8 and 12 weeks, more numerous and complex ducts with increased luminal protein; and at 16 weeks, increased lobulogenesis. Lactational Tg-OPN mammary glands showed more rapid lobulogenesis and lactational changes with slower gland involution and regression following weaning. Ex vivo lobulogenesis was noticeably increased from organoids of Tg-OPN mice. Immunohistochemistry revealed cytoplasmic OPN accumulation and increased Ki-67 positive mammary epithelial cells in Tg-OPN mammary glands. OPN appears to convey a proliferative stimulus for mammary epithelial cells and alters development and differentiation. These OPN mammary overexpressing mice provide a means to study the role of OPN in cancer progression.
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Affiliation(s)
- Neil E Hubbard
- Center for Comparative Medicine, University of California at Davis, Davis, CA, USA
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Cardiff RD, Hubbard NE, Engelberg JA, Munn RJ, Miller CH, Walls JE, Chen JQ, Velásquez-García HA, Galvez JJ, Bell KJ, Beckett LA, Li YJ, Borowsky AD. Quantitation of fixative-induced morphologic and antigenic variation in mouse and human breast cancers. J Transl Med 2013; 93:480-97. [PMID: 23399853 PMCID: PMC3843496 DOI: 10.1038/labinvest.2013.10] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Quantitative Image Analysis (QIA) of digitized whole slide images for morphometric parameters and immunohistochemistry of breast cancer antigens was used to evaluate the technical reproducibility, biological variability, and intratumoral heterogeneity in three transplantable mouse mammary tumor models of human breast cancer. The relative preservation of structure and immunogenicity of the three mouse models and three human breast cancers was also compared when fixed with representatives of four distinct classes of fixatives. The three mouse mammary tumor cell models were an ER+/PR+ model (SSM2), a Her2+ model (NDL), and a triple negative model (MET1). The four breast cancer antigens were ER, PR, Her2, and Ki67. The fixatives included examples of (1) strong cross-linkers, (2) weak cross-linkers, (3) coagulants, and (4) combination fixatives. Each parameter was quantitatively analyzed using modified Aperio Technologies ImageScope algorithms. Careful pre-analytical adjustments to the algorithms were required to provide accurate results. The QIA permitted rigorous statistical analysis of results and grading by rank order. The analyses suggested excellent technical reproducibility and confirmed biological heterogeneity within each tumor. The strong cross-linker fixatives, such as formalin, consistently ranked higher than weak cross-linker, coagulant and combination fixatives in both the morphometric and immunohistochemical parameters.
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Affiliation(s)
- Robert D Cardiff
- Center for Comparative Medicine, University of California, Davis, CA, USA,Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Neil E Hubbard
- Center for Comparative Medicine, University of California, Davis, CA, USA
| | - Jesse A Engelberg
- Center for Comparative Medicine, University of California, Davis, CA, USA
| | - Robert J Munn
- Center for Comparative Medicine, University of California, Davis, CA, USA,Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Claramae H Miller
- Center for Comparative Medicine, University of California, Davis, CA, USA,Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Judith E Walls
- Center for Comparative Medicine, University of California, Davis, CA, USA
| | - Jane Q Chen
- Center for Comparative Medicine, University of California, Davis, CA, USA
| | | | - Jose J Galvez
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institute of Health, Washington, DC, USA
| | - Katie J Bell
- Center for Comparative Medicine, University of California, Davis, CA, USA
| | - Laurel A Beckett
- Division of Biostatistics, Department of Public Health Sciences, School of Medicine, University of California, Davis, CA, USA
| | - Yue-Ju Li
- Division of Biostatistics, Department of Public Health Sciences, School of Medicine, University of California, Davis, CA, USA
| | - Alexander D Borowsky
- Center for Comparative Medicine, University of California, Davis, CA, USA,Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, CA, USA
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Medici V, Shibata NM, Kharbanda KK, LaSalle JM, Woods R, Liu S, Engelberg JA, Devaraj S, Török NJ, Jiang JX, Havel PJ, Lönnerdal B, Kim K, Halsted CH. Wilson's disease: changes in methionine metabolism and inflammation affect global DNA methylation in early liver disease. Hepatology 2013; 57:555-65. [PMID: 22945834 PMCID: PMC3566330 DOI: 10.1002/hep.26047] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 08/14/2012] [Indexed: 12/18/2022]
Abstract
UNLABELLED Hepatic methionine metabolism may play an essential role in regulating methylation status and liver injury in Wilson's disease (WD) through the inhibition of S-adenosylhomocysteine hydrolase (SAHH) by copper (Cu) and the consequent accumulation of S-adenosylhomocysteine (SAH). We studied the transcript levels of selected genes related to liver injury, levels of SAHH, SAH, DNA methyltransferases genes (Dnmt1, Dnmt3a, Dnmt3b), and global DNA methylation in the tx-j mouse (tx-j), an animal model of WD. Findings were compared to those in control C3H mice, and in response to Cu chelation by penicillamine (PCA) and dietary supplementation of the methyl donor betaine to modulate inflammatory and methylation status. Transcript levels of selected genes related to endoplasmic reticulum stress, lipid synthesis, and fatty acid oxidation were down-regulated at baseline in tx-j mice, further down-regulated in response to PCA, and showed little to no response to betaine. Hepatic Sahh transcript and protein levels were reduced in tx-j mice with consequent increase of SAH levels. Hepatic Cu accumulation was associated with inflammation, as indicated by histopathology and elevated serum alanine aminotransferase (ALT) and liver tumor necrosis factor alpha (Tnf-α) levels. Dnmt3b was down-regulated in tx-j mice together with global DNA hypomethylation. PCA treatment of tx-j mice reduced Tnf-α and ALT levels, betaine treatment increased S-adenosylmethionine and up-regulated Dnmt3b levels, and both treatments restored global DNA methylation levels. CONCLUSION Reduced hepatic Sahh expression was associated with increased liver SAH levels in the tx-j model of WD, with consequent global DNA hypomethylation. Increased global DNA methylation was achieved by reducing inflammation by Cu chelation or by providing methyl groups. We propose that increased SAH levels and inflammation affect widespread epigenetic regulation of gene expression in WD.
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Affiliation(s)
- Valentina Medici
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of California Davis
| | - Noreene M. Shibata
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of California Davis
| | - Kusum K. Kharbanda
- Research Service, Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, Nebraska
| | - Janine M. LaSalle
- Department of Medical Microbiology and Immunology, University of California Davis
| | - Rima Woods
- Department of Medical Microbiology and Immunology, University of California Davis
| | - Sarah Liu
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of California Davis
| | | | | | - Natalie J. Török
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of California Davis
| | - Joy X. Jiang
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of California Davis
| | - Peter J. Havel
- Department of Molecular Biosciences, University of California Davis
- Department of Nutrition, University of California Davis
| | - Bo Lönnerdal
- Department of Nutrition, University of California Davis
| | - Kyoungmi Kim
- Department of Public Health Sciences, Division of Biostatistics, University of California Davis
| | - Charles H. Halsted
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of California Davis
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Engelberg JA, Datta A, Mostov KE, Hunt CA. MDCK cystogenesis driven by cell stabilization within computational analogues. PLoS Comput Biol 2011; 7:e1002030. [PMID: 21490722 PMCID: PMC3072361 DOI: 10.1371/journal.pcbi.1002030] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 02/24/2011] [Indexed: 12/17/2022] Open
Abstract
The study of epithelial morphogenesis is fundamental to increasing our
understanding of organ function and disease. Great progress has been made
through study of culture systems such as Madin-Darby canine kidney (MDCK) cells,
but many aspects of even simple morphogenesis remain unclear. For example, are
specific cell actions tightly coupled to the characteristics of the cell's
environment or are they more often cell state dependent? How does the single
lumen, single cell layer cyst consistently emerge from a variety of cell
actions? To improve insight, we instantiated in silico analogues that used
hypothesized cell behavior mechanisms to mimic MDCK cystogenesis. We tested them
through in vitro experimentation and quantitative validation. We observed novel
growth patterns, including a cell behavior shift that began around day five of
growth. We created agent-oriented analogues that used the cellular Potts model
along with an Iterative Refinement protocol. Following several refinements, we
achieved a degree of validation for two separate mechanisms. Both survived
falsification and achieved prespecified measures of similarity to cell culture
properties. In silico components and mechanisms mapped to in vitro counterparts.
In silico, the axis of cell division significantly affects lumen number without
changing cell number or cyst size. Reducing the amount of in silico luminal cell
death had limited effect on cystogenesis. Simulations provide an observable
theory for cystogenesis based on hypothesized, cell-level operating
principles. Epithelial cells perform essential functions throughout the body, acting as both
barrier and transporter and allowing an organism to survive and thrive in varied
environments. Although the details of many processes that occur within
individual cells are well understood, we still lack a thorough understanding of
how cells coordinate their behaviors to create complex tissues. In order to
achieve deeper insight, we created a list of targeted attributes and plausible
rules for the growth of multicellular cysts formed by Madin-Darby canine kidney
(MDCK) cells grown in vitro. We then designed in silico analogues of MDCK
cystogenesis using object-oriented programming. In silico components (such as
the cells and lumens) and their behaviors directly mapped to in vitro components
and mechanisms. We conducted in vitro experiments to generate data that would
validate or falsify the in silico analogues and then iteratively refined the
analogues to mimic that data. Cells in vitro begin to stabilize at around the
fifth day even as cysts continue to expand. The in silico system mirrored that
behavior and others, achieving new insights. For example, luminal cell death is
not strictly required for cystogenesis, and cell division orientation is very
important for normal cyst growth.
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Affiliation(s)
- Jesse A. Engelberg
- UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of
California, San Francisco, California, United States of America
| | - Anirban Datta
- Department of Anatomy, University of California, San Francisco,
California, United States of America
| | - Keith E. Mostov
- Department of Anatomy, University of California, San Francisco,
California, United States of America
| | - C. Anthony Hunt
- UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of
California, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of
California, San Francisco, California, United States of America
- * E-mail:
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Hunt CA, Ropella GEP, Lam TN, Tang J, Kim SHJ, Engelberg JA, Sheikh-Bahaei S. At the biological modeling and simulation frontier. Pharm Res 2009; 26:2369-400. [PMID: 19756975 PMCID: PMC2763179 DOI: 10.1007/s11095-009-9958-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 08/13/2009] [Indexed: 01/03/2023]
Abstract
We provide a rationale for and describe examples of synthetic modeling and simulation (M&S) of biological systems. We explain how synthetic methods are distinct from familiar inductive methods. Synthetic M&S is a means to better understand the mechanisms that generate normal and disease-related phenomena observed in research, and how compounds of interest interact with them to alter phenomena. An objective is to build better, working hypotheses of plausible mechanisms. A synthetic model is an extant hypothesis: execution produces an observable mechanism and phenomena. Mobile objects representing compounds carry information enabling components to distinguish between them and react accordingly when different compounds are studied simultaneously. We argue that the familiar inductive approaches contribute to the general inefficiencies being experienced by pharmaceutical R&D, and that use of synthetic approaches accelerates and improves R&D decision-making and thus the drug development process. A reason is that synthetic models encourage and facilitate abductive scientific reasoning, a primary means of knowledge creation and creative cognition. When synthetic models are executed, we observe different aspects of knowledge in action from different perspectives. These models can be tuned to reflect differences in experimental conditions and individuals, making translational research more concrete while moving us closer to personalized medicine.
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Affiliation(s)
- C Anthony Hunt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA.
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Engelberg JA, Kim M, Mostov KE, Hunt CA. An agent-based model of epithelial cell cystogenesis implemented with a cellular Potts model. J Crit Care 2009. [DOI: 10.1016/j.jcrc.2009.06.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
By improving our understanding of epithelial cell tubulogenesis in vitro we should improve our understanding of how these cells organize to form normal tissues such as the ducts and lobules that make up breast tissue. We do not fully understand how these ducts and lobules form. Because it is difficult to directly control and observe epithelial cell morphogenesis in vivo, we study it using in vitro culture systems. They are more easily controlled and observed. One of the most well studied models of tubulogenesis uses Madin-Darby canine kidney (MDCK) cells in culture systems: single cell layered cysts form tubules when exposed to hepatocyte growth factor (HGF). We have developed an in silico analogue that mimics the fundamental cell-level operating principles and system-level phenotypes of in vitro MDCK tubulogenesis. The creation and validation of the analogue required the specification and questioning of currently held assumptions. The analogue can be used to test hypotheses about mechanisms and in silico operating principles that may have in vitro counterparts. By increasing our understanding of the operating principles that govern in vitro epithelial cell growth and organization we are better positioned to understand how best to manipulate these operating principles to achieve specific tissue engineering objectives.
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Affiliation(s)
- Jesse A Engelberg
- UCSF / UC Berkeley Joint Graduate Group in Bioengineering, San Francisco, CA 94143, USA.
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Abstract
BACKGROUND Our objective was to discover in silico axioms that are plausible representations of the operating principles realized during characteristic growth of EMT6/Ro mouse mammary tumor spheroids in culture. To reach that objective we engineered and iteratively falsified an agent-based analogue of EMT6 spheroid growth. EMT6 spheroids display consistent and predictable growth characteristics, implying that individual cell behaviors are tightly controlled and regulated. An approach to understanding how individual cell behaviors contribute to system behaviors is to discover a set of principles that enable abstract agents to exhibit closely analogous behaviors using only information available in an agent's immediate environment. We listed key attributes of EMT6 spheroid growth, which became our behavioral targets. Included were the development of a necrotic core surrounded by quiescent and proliferating cells, and growth data at two distinct levels of nutrient. RESULTS We then created an analogue made up of quasi-autonomous software agents and an abstract environment in which they could operate. The system was designed so that upon execution it could mimic EMT6 cells forming spheroids in culture. Each agent used an identical set of axiomatic operating principles. In sequence, we used the list of targeted attributes to falsify and revise these axioms, until the analogue exhibited behaviors and attributes that were within prespecified ranges of those targeted, thereby achieving a level of validation. CONCLUSION The finalized analogue required nine axioms. We posit that the validated analogue's operating principles are reasonable representations of those utilized by EMT6/Ro cells during tumor spheroid development.
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Affiliation(s)
- Jesse A Engelberg
- UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, San Francisco, CA, USA
- The Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Glen EP Ropella
- The Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - C Anthony Hunt
- UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, San Francisco, CA, USA
- The Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
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