Whole-Organism Cellular Pathology: A Systems Approach to Phenomics

Keith Cheng, S. R. Katz, A. Y. Lin, X. Xin, Y. Ding

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Citations (Scopus)

Abstract

Phenotype is defined as the state of an organism resulting from interactions between genes, environment, disease, molecular mechanisms, and chance. The purpose of the emerging field of phenomics is to systematically determine and measure phenotypes across biology for the sake of understanding. Phenotypes can affect more than one cell type and life stage, so ideal phenotyping would include the state of every cell type within the context of both tissue architecture and the whole organism at each life stage. In medicine, high-resolution anatomic assessment of phenotype is obtained from histology. Histology's interpretative power, codified by Virchow as cellular pathology, is derived from its ability to discern diagnostic and characteristic cellular changes in diseased tissues. Cellular pathology is observed in every major human disease and relies on the ability of histology to detect cellular change in any cell type due to unbiased pan-cellular staining, even in optically opaque tissues. Our laboratory has shown that histology is far more sensitive than stereomicroscopy for detecting phenotypes in zebrafish mutants. Those studies have also shown that more complete sampling, greater consistency in sample orientation, and the inclusion of phenotypes extending over longer length scales would provide greater coverage of common phenotypes. We are developing technical approaches to achieve an ideal detection of cellular pathology using an improved form of X-ray microtomography that retains the strengths and addresses the weaknesses of histology as a screening tool. We are using zebrafish as a vertebrate model based on the overlaps between zebrafish and mammalian tissue architecture, and a body size small enough to allow whole-organism, volumetric imaging at cellular resolution. Automation of whole-organism phenotyping would greatly increase the value of phenomics. Potential societal benefits would include reduction in the cost of drug development, a reduction in the incidence of unexpected severe drug and environmental toxicity, and more rapid elucidation of the contributions of genes and the environment to phenotypes, including the validation of candidate disease alleles identified in population and personal genetics.

Original languageEnglish (US)
Title of host publicationGenetics, Genomics and Fish Phenomics, 2016
EditorsNicholas S. Foulkes, Nicholas S. Foulkes
PublisherAcademic Press Inc.
Pages89-115
Number of pages27
ISBN (Print)9780128048009
DOIs
StatePublished - Jan 1 2016

Publication series

NameAdvances in Genetics
Volume95
ISSN (Print)0065-2660

Fingerprint

Systems Analysis
Pathology
Phenotype
Histology
Zebrafish
X-Ray Microtomography
Gene-Environment Interaction
Drug Costs
Automation
Population Genetics
Body Size
Drug-Related Side Effects and Adverse Reactions
Vertebrates
Alleles
Medicine
Staining and Labeling
Incidence
Genes

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Cheng, K., Katz, S. R., Lin, A. Y., Xin, X., & Ding, Y. (2016). Whole-Organism Cellular Pathology: A Systems Approach to Phenomics. In N. S. Foulkes, & N. S. Foulkes (Eds.), Genetics, Genomics and Fish Phenomics, 2016 (pp. 89-115). (Advances in Genetics; Vol. 95). Academic Press Inc.. https://doi.org/10.1016/bs.adgen.2016.05.003
Cheng, Keith ; Katz, S. R. ; Lin, A. Y. ; Xin, X. ; Ding, Y. / Whole-Organism Cellular Pathology : A Systems Approach to Phenomics. Genetics, Genomics and Fish Phenomics, 2016. editor / Nicholas S. Foulkes ; Nicholas S. Foulkes. Academic Press Inc., 2016. pp. 89-115 (Advances in Genetics).
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Cheng, K, Katz, SR, Lin, AY, Xin, X & Ding, Y 2016, Whole-Organism Cellular Pathology: A Systems Approach to Phenomics. in NS Foulkes & NS Foulkes (eds), Genetics, Genomics and Fish Phenomics, 2016. Advances in Genetics, vol. 95, Academic Press Inc., pp. 89-115. https://doi.org/10.1016/bs.adgen.2016.05.003

Whole-Organism Cellular Pathology : A Systems Approach to Phenomics. / Cheng, Keith; Katz, S. R.; Lin, A. Y.; Xin, X.; Ding, Y.

Genetics, Genomics and Fish Phenomics, 2016. ed. / Nicholas S. Foulkes; Nicholas S. Foulkes. Academic Press Inc., 2016. p. 89-115 (Advances in Genetics; Vol. 95).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Cheng K, Katz SR, Lin AY, Xin X, Ding Y. Whole-Organism Cellular Pathology: A Systems Approach to Phenomics. In Foulkes NS, Foulkes NS, editors, Genetics, Genomics and Fish Phenomics, 2016. Academic Press Inc. 2016. p. 89-115. (Advances in Genetics). https://doi.org/10.1016/bs.adgen.2016.05.003