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Examining molecular biology in humans
 
Alex Parker1, Ian McCaffery2, and Scott D. Patterson2
1Molecular Sciences, Amgen Inc., Cambridge, MA, USA
2Molecular Sciences, Amgen, Inc., Thousand Oaks, CA, USA
BioTechniques Special Issue, Vol. 46, No. 5, April 2009, pp. 358–360
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Abstract

Significant advances in biological knowledge have been made through the application of genomic, proteomic, and metabolomic technologies to the interrogation of static samples in model systems of human disease. The integration of the results of these technologies under the banner of systems biology holds much promise. In this forward-looking essay, we posit that to fully understand human biology, such measurements not only need to be integrated, but conducted in humans in real time through the merging of molecular biology and imaging technologies.

Introduction

The evolution of our understanding of cell biology has been driven by the steady advance of available technologies for analysis of nucleic acids, proteins, and metabolites, culminating in their more recent implementation as ‘omic (or massively parallel) applications. These approaches provide a static view of a biological sample obtained at a discrete point in time, with the temporal dimension being captured through multiple sampling over time. If the entity to be studied is an organism, this often requires removal of the particular tissue(s) under investigation. From such measurements of in vitro systems and in vivo model systems, reconstruction of organismal physiology (or pathophysiology) is attempted.

Here, we will consider how the landscape of biological understanding might change over the next 25 years and what technological advances such change would require. We will examine those technologies that hold the potential to enhance our understanding of human physiology, and therefore provide valuable information for the introduction of more efficacious therapeutics. It should also be noted that this essay is not intended to be an extensive review of the literature of any of the fields mentioned; only a few representative references have been included. We theorize that in coming decades, molecular biology will be interrogated directly in humans through a merging of the technologies of molecular biology and imaging, thereby enabling real-time experimental biology in the appropriate physiological setting using non-invasive and non-destructive techniques.

Approaches that permit continuous, real-time data collection through various tagging methodologies coupled with high-resolution imaging (1) remain at an early stage of development and some are only relevant to in vitro experimentation. Development of real-time imaging models for preclinical research is being realized through the use of engineered transgenic animals or xenograft cell lines that express reporter constructs (e.g., luciferase) under control of promoters that confer cell type–specific expression or responsiveness to specific physiological conditions. These approaches have extended as far as micro–positron emission tomography (PET) imaging of gene expression using the HSV thymidine kinase, which can be imaged through the use of [8-18F]-fluoroganciclovir (2), and more recently, the determination of phosphorylation through optical bioluminescence imaging of a genetically encoded complementation system (3). Although useful in preclinical context to monitor real-time changes, these approaches do not appear directly translatable to clinical development. However, given the pace of progress in the PET imaging probe field, it is not difficult to imagine that the ability to image activity of specific endogenous enzymes is not too far in the future. The biggest limitation to these approaches comes in the form of our limited understanding of the basic biology behind most underlying cellular processes in vivo: where they are coupled with the dynamic extracellular physiological environment.

A major goal of biological research is to provide a greater understanding of human physiology as it relates to pathological processes involved in disease. Much of our knowledge of pathogenesis and disease progression originates from studies using animal models of disease, which are often poor reflections of the human counterpart (4). Furthermore, many animal model systems involve the use of inbred animals and thus fail to represent the true heterogeneity of human disease that arises from polymorphisms and mutations.

A more complete understanding of the dynamic processes that underlie human physiology at the level of cellular regulatory processes would ultimately inform targeted and precise pharmacological intervention with the aim of modifying the course or symptoms of disease. Although achievements have been made in the rational design of drugs, these efforts are limited by our lack of understanding of the molecular basis of many diseases and the adaptive nature of human physiology; the result is efficacy that is limited to patient subsets and idiosyncratic toxicology (5). As such, our ability to accurately determine the best targets for therapeutic pharmacologic intervention, as well as which patients will benefit from a particular intervention, is restricted. When insights are gained into these questions, it is often only during later stages of the drug development process.

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