Whole-Organism Cellular Pathology

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.

Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

“…Histotomographic images provide a mechanism for quantitative histopathological analysis that facilitates the objective and reproducible study of volume, shape, and texture of cells across organisms and tissue types. Histotomography’s potential throughput and analytical power may be applied to computational histological phenotyping of whole organisms to probe the diversity of organismal tissue architecture and relationships between genotype, environment, and microanatomy (Austin et al, 2004; Cheng et al, 2016b; Varshney et al, 2013).…”

Rigid Embedding of Fixed and Stained, Whole, Millimeter-Scale Specimens for Section-free 3D Histology by Micro-Computed Tomography

“…Importantly, differences in traits between wild-type organisms and genetic mutants can provide key insight into the mechanisms and functions of affected genes. With respect to morphology, histopathology is the gold standard for assessing phenotypes at the cellular level but suffers from mechanical artifacts and does not allow accurate quantitative volumetric analysis 1 . Our laboratory is motivated to overcome the barriers to the application of the diagnostic power of histology to full tissue volumes at submicron resolution.…”

“…A survey of available technologies suggests that imaging by X-ray micro-computed tomography (micro-CT) may provide ideal capabilities needed for millimeter-scale whole-animal 3-dimensional (3D) histology. Micro-CT enables non-destructive, isotropic, 3D visualization and the ability to conduct quantitative analysis of tissue architecture 1 2 . In recent years, 3D imaging of unstained and metal-stained zebrafish by micro-CT has gained increasing traction and has been utilized for volumetric analysis of several tissues, including muscle, teeth, bone, and adipose tissues 3 4 5 6 7 8 9 10 .…”

OmicsOne: associate omics data with phenotypes in one-click

“…A phenotype can be defined as any observable characteristic or state of an organism resulting from interactions between genes, environment, disease, molecular mechanisms, and chance [1]. The purpose of phenotype association analysis in genomics and proteomics for disease studies is to illustrate the relationship between protein expression and clinical phenotypes.…”