Analysis of Drug Pharmacology towards Predicting Drug Behavior by Expression Profiling Using High‐Density Oligonucleotide Arrays

Hu, Jing-Shan; Durst, Mark; Kerb, Reinhold; Truong, Vivi; Ma, Jing-Tyan; Khurgin, Elina; Balaban, David; Gingeras, T; Hoffman, Brian B.

doi:10.1111/j.1749-6632.2000.tb06862.x

Cited by 18 publications

(6 citation statements)

References 3 publications

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“…Genomic approaches are widely accepted in the context of biomarker generation (reviewed in Hook ), however, these transcriptional approaches need to be validated with a phenotypic anchor, i.e., clearly defined and measurable effects at organ, tissue, or physiological levels. For example, whole tissue transcriptome profiling has been effectively used for screening adverse outcomes associated with drug and chemical toxicity in mammalian studies (Hu et al ; Martin et al ). Microarray approaches may be particularly useful in determining the contributions of various classes of environmental contaminants toward sublethal toxicity in mixture scenarios (Tilton et al ; Osborn and Hook ; Hook et al ).…”

Section: Classes Of Biomarkers and Their Application To Aquatic Ecosymentioning

confidence: 99%

The role of biomarkers in the assessment of aquatic ecosystem health

Hook

Gallagher

Batley

2014

Integr Envir Assess & Manag

278

135

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Ensuring the health of aquatic ecosystems and identifying species at risk from the detrimental effects of environmental contaminants can be facilitated by integrating analytical chemical analysis with carefully selected biological endpoints measured in tissues of species of concern. These biological endpoints include molecular, biochemical and physiological markers (i.e. biomarkers) that when integrated, can clarify issues of contaminant bioavailability, bioaccumulation and ecological effects while enabling a better understanding of the effects of non-chemical stressors. In the case of contaminant stressors, an understanding of chemical modes of toxicity can be incorporated with diagnostic markers of aquatic animal physiology to help understand the health status of aquatic organisms in the field. Furthermore, new approaches in functional genomics and bioinformatics can help discriminate individual chemicals, or groups of chemicals among complex mixtures that may contribute to adverse biological effects. While the use of biomarkers is not a new paradigm, such approaches have been underutilized in the context of ecological risk assessment and natural resource damage assessment. From a regulatory standpoint, these approaches can help better assess the complex effects from coastal development activities to assessing ecosystem integrity pre- and post-development or site remediation.

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Section: Classes Of Biomarkers and Their Application To Aquatic Ecosymentioning

confidence: 99%

The role of biomarkers in the assessment of aquatic ecosystem health

Hook

Gallagher

Batley

2014

Integr Envir Assess & Manag

278

135

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“…44 A second use for the oligonucleotide microarray is that of biopharmacology, where anticancer agent efficacy can be correlated to gene expression in tissue. 45,46 Complimentary to these novel genomic initiatives is proteomics, the study of expressed proteins in tissue and cell types. 47 Both proteomic and other tissue microarray studies are enhanced by the use of laser capture microdissection which enables isolation of critical neoplastic cells.…”

Section: Molecular Adjuncts To Diagnosis: the Microarraymentioning

confidence: 99%

The future of dermatopathology

Crowson

2006

Modern Pathology

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Of the major issues that dermatopathology will face in the immediate future, two powerful challenges loom large. The first is the application of novel nondestructive imaging technologies to in vivo diagnosis in humans. The second is the application of molecular technologies to a diagnostic arena which formerly belonged exclusively to the light microscopist. The first to be considered in this context is the application of near infrared spectroscopy to the noninvasive in vivo diagnosis of neoplastic skin disease. The second will be a discussion of application, methodology and the current state of the art in microarray technologies as they apply to neoplastic dermatopathology and, in particular, the diagnosis and prognostication of melanoma. Modern Pathology (2006) 19, S155-S163. doi:10.1038/modpathol.3800513Keywords: in vivo microscope; tissue microarray; basal cell carcinoma; infrared spectroscopy Noninvasive assessment of skin lesions by near infrared (IR) spectroscopyIn the late 1990s, working with Dr Laura McIntosh and colleagues at the National Research Council of Canada, the University of Manitoba, Central Medical Laboratories and the Misericordia General Hospital in Winnipeg, Canada, we designed and patented a noninvasive tool for the diagnosis of skin tumors using visible and near IR spectroscopy in the 400-2500 nm size wavelength range. 1-5 Initially, we excised neoplasms, and processed them in the fresh state with sections for formaldehyde fixation and paraffin embedding matched to tissue elements snap frozen in liquid nitrogen and stored at À801F. Thick sections from the frozen tissue elements were interrogated by mid-IR wavelength light (Figure 1). The transmitted light generated significant spectral differences; water, hemoglobin, cytochromes, lipids and proteins all absorb light at specific frequencies ( Figure 2). In particular, the mid-IR range is rich with information about proteins including in the context of collagen and RNA. When analyzed by a sophisticated leave-one-out hierarchical classification algorithm, distinction between microanatomic compartments of the skin could be made (Figure 3). Using this methodology, we were able with an accuracy of 90-95% to distinguish basal cell carcinoma (BCC) from melanocytic nevi, seborrheic keratoses and squamous cell carcinomata in vitro. Melanocytic nevi could be subdivided into banal vs dysplastic nevi based upon their spectral differences and melanomas could be separately recognized as well. Furthermore, the different types of lesion were shown to have distinct mid-IR signatures when compared to adjacent normal epidermal and dermal compartments.Unfortunately, the diagnostic potential of mid-IR spectroscopy for in vivo applications is limited, as complete absorption of mid-IR light occurs with samples greater than 10-15 mm in thickness. In contrast, near-IR light scatters to a much greater extent than it absorbs and in consequence, tissues are relatively transparent in the near-IR region which permits the examination of larger tissue volumes and led to...

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“…Global gene expression, or transcriptional profiling, has been used to identify molecular markers for various pathological states, and can be used to generate novel hypotheses to characterize different disease states [19][20][21][22][23]. DNA microarrays have been used to identify candidate genes for disease diagnosis, and to characterize gene expression patterns associated with potential disease treatments including diabetes [24][25][26]. However, the genetic changes involved in the pathology of diabetes have not been fully identified so far [27].…”

Section: Introductionmentioning

confidence: 99%

Gene expression profiling in streptozotocin-induced diabetic rat liver in response to fungal polysaccharide treatment

Hwang

Kim

Baek

et al. 2009

Korean J. Chem. Eng.

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We established the gene expression profiling in streptozotocin (STZ)-induced diabetic rat liver in response to hypoglycemic fungal polysaccharides (EPS), using oligonucleotide microarray analysis. Differentially regulated genes showing higher fold change than 2 were identified and categorized through hierarchical clustering analysis. Among the 835 genes analyzed, 244 were up-regulated, while 321 were down-regulated after diabetes induction. Interestingly, many gene expressions altered after STZ-treatment mimicked a normal rat liver by EPS therapy. Most of these genes included genes involving cell structure and motility, immunity and defense, lipid, fatty acid and steroid metabolism, protein metabolism and modification, and signal transduction. More importantly, we found a total of 36 genes that showed significant fold changes in their expression that have not previously been examined in the context of diabetes. To validate the microarray results, we further confirmed the gene expression patterns by RT-PCR using four genes of interest (carboxylesterase 2, stearoyl-coenzyme A desaturase 1, insulin-like growth factor 1, and insulin-like growth factor binding protein 2). Taken together, EPS acted as a potent regulator of gene expression for a wide variety of genes in diabetic rat liver.

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Analysis of Drug Pharmacology towards Predicting Drug Behavior by Expression Profiling Using High‐Density Oligonucleotide Arrays

Cited by 18 publications

References 3 publications

The role of biomarkers in the assessment of aquatic ecosystem health

The role of biomarkers in the assessment of aquatic ecosystem health

The future of dermatopathology

Gene expression profiling in streptozotocin-induced diabetic rat liver in response to fungal polysaccharide treatment

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