My postdoc research proposal

November 21, 2013

I was recently asked by an applicant to Princeton’s Lewis-Sigler Institute Fellows program for a copy of my successful research proposal. For those who don’t know, I was a LSI Fellow from 2007 to 2012. In the spirit of paying it forward, I’ve reproduced the document in its entirety below. (Keep in mind that I wrote this in late 2006/early 2007). I realize that independent postdocs are bougie, but I suspect grad students applying for a regular postdoc – or perhaps second or third postdoc — may find this material useful, too. In today’s Malthusian academic hiring environment, which is also notoriously opaque to the uninitiated, God knows any bit of transparency will be useful to someone, somewhere.


Research Interests and Goals


My research interests are focused at the intersection of evolutionary, molecular and chemical biology. Specifically, I am interested in examining the effects of natural genetic variation on the complex response of simple model organisms to small-molecule drugs. This cross-disciplinary approach will not only yield a deeper basic understanding of complex evolutionary processes, but may also illuminate the evolutionarily conserved bases of complex human diseases.


Previous Doctoral Research



My doctoral work centered on developing and applying an evolutionary perspective on the interdisciplinary context of chemical biology, and gave promise, inter alia, of improvement of the traditional drug-development process, and of the deepening of our understanding of the root evolutionary causes of complex human disease.


Compound responses as complex traits

In work published earlier this year in Chemistry & Biology, I and others showed that the cellular response of naturally recombinant yeast strains to small molecules can constitute a model system for the study of complex traits. This initial study was followed by an extensive genetic linkage study, now under revision at Nature Genetics, which identified numerous naturally-occurring polymorphisms that affect resistance/sensitivity of 104 meiotic segregants to small-molecule drugs. I and others also identified quantitative-trait loci (QTL) “hot spots” that affected the response to multiple compounds, and then successfully verified that a single-nucleotide polymorphism (SNP) in an inorganic phosphate transporter protein confers resistance to two small-molecule uncouplers of oxidative phosphorylation.


Small-molecule screening

In another project involving yeast and small molecules, which is in preparation for submission, I and others demonstrated that small-molecule enhancers of the cytostatic effects of rapamycin in yeast induce autophagy (a protein- and organelle-degradation process) in mammalian cells, and ameliorate the toxicity associated with human disease models of neurodegeneration.


Therapeutic relevance

In ongoing unpublished work, I’ve explored the mechanism of action of the unexpected growth-inhibiting effects on yeast of select psychiatric-disease therapeutic drugs, including sertraline (Zoloft). These preliminary studies indicate that the growth-inhibiting effects of sertraline and several other psychiatric-disease drugs on yeast may be therapeutically relevant to mental illness, rather than a pharmacological curiosity or coincidence.


Proposed Research



The use of model organisms in the study of, and development of pharmaceutical treatments for, complex human diseases is a commonly used approach that seeks to balance the limitations of reductionism with the demands of systems-level reality. Typically, a deliberately simplified disease model is hypothesized upfront, reducing the causation of a complex human illness to a few crucial components (usually mutations in one or more human genes); then the ancestral analogs of those human genes are each identified and individually studied in surrogates. However, this process is expensive, slow and inefficient, and many resulting drugs have harmful side effects. Even armed with new insights gained from knowledge of the human genome sequence, coupled with the catalogue of all DNA differences in humans, it is nonetheless inherently limited by its incomplete theoretical perspective.



In contrast, I propose a non-reductionist, two-stage approach to the study of complex evolutionary processes and their links to human diseases. My approach examines the whole-organism effects of therapeutic drugs, whether known or experimental, on the budding yeast Saccharomyces cerevisiae and comparable unicellular eukaryotes. Stage One is an “evolutionarily-informed clinical trial,” which objectively identifies, without a priori theorizing, the naturally-occurring genetic mutations that predispose yeast, and eventually other unicellular eukaryotes, to sensitivity to a specific therapeutic drug. Stage Two is an “evolutionarily-informed drug-discovery search engine,” which, similarly, identifies other compounds that either synergize with, or antagonize, the effects of that specific therapeutic drug on yeast, and eventually other unicellular eukaryotes.


This approach leverages many millions of years of  wisdom embodied in evolutionarily-conserved cell processes, and could greatly expedite the process not only of developing ”cocktails” or refined version of drugs with better therapeutic effects, and/or diminished side effects, but also of refining and/or testing models of complex disease causation. Among others, I will apply this two-stage approach to the study of the mechanism of action of growth inhibition in yeast by small-molecule drugs, including psychiatric-disease therapeutic drugs. However, this approach, if successful, could be generalized for application to many complex human diseases and drugs, and using other genetically-tractable unicellular eukaryotes in addition to yeast.


Expansion of genetic linkage studies in S. cerevisiae

My doctoral work demonstrated that treating segregating populations of S. cerevisiae with small-molecule drugs is a suitable experimental model for the general study of complex traits. However, these early studies constitute only a portion of possible explorations of natural variation in S. cerevisiae. As a Lewis-Sigler Fellow, I would continue to map and verify the SNPs that underlie the cellular response to small-molecule drugs using published strains. Also, the genomes of three S. cerevisiae strains have been sequenced to date: a laboratory strain (S288c), a vineyard isolate (RM11) and a clinical isolate (YJM). This collection of sequenced strains presents a unique opportunity for comparative functional genomics. Using existing genotyping technologies (e.g., yeast SNP array), I would genotype meiotic segregants (at least 100, possibly several hundred) from a cross between the wildtype vineyard and wildtype clinical isolates, and between the wildtype laboratory strain and the clinical isolate. Then I would examine compound response of select small-molecule drugs in these new segregating populations of S. cerevisiae strains.


Expansion into comparative chemical genomics

In addition to the above studies of S. cerevisiae, I would take the next logical step and explore creating a genotyping platform for segregating populations derived from a different unicellular eukaryote. The fission yeast Schizosaccharomyces pombe, whose genome has already been sequenced, and whose genetic homology to more complex multicellular organisms is already well established, is an attractive first candidate for expansion of my approach. In addition to their value for understanding the evolutionarily conserved basis of drug action, and for providing additional perspective when compared to results with S. cerevisiae, these genotyped segregating populations would also be valuable reagents for the greater community of researchers with an interest in the burgeoning field of comparative functional genomics.


Small-molecule modifier screening with therapeutically relevant drugs

I will conduct drug-discovery screens for small molecules that either antagonize or enhance the cellular effects of small-molecule drugs in S. cerevisiae, and the other unicellular eukaryotes. For example, we have already shown that treating yeast with rapamycin places cells in a physiological state that may be the evolutionarily-simplified equivalent of diseased tissues in humans. Therefore small molecules that either suppress or enhance the cellular effects of rapamycin on yeast may be readily identified as effective therapeutic agents in diseases as diverse as neurodegeneration and cancer.


Elucidation of the mechanism of action of human therapeutic small-molecule drugs

I will also use classical genetic approaches, coupled with enabling technologies, to identify spontaneous mutations that alter sensitivity of yeast cells to select small-molecule drugs, including psychiatric-disease therapeutic drugs. I will also take advantage of the phenomenon called haploinsufficiency as a method to identify the targets of small-molecule drugs. These approaches will shed light on the precise molecular function of those drugs in unicellular eukaryotes, and spur concrete hypotheses about their function in multicellular organisms. For example, currently there are few known molecular phenotypes associated with most psychiatric-disease therapeutic drugs. Therefore, I will test, in collaboration with the appropriate experts, whether molecular phenotypes induced by psychiatric-disease drugs in yeast are germane to human cells.



In summary, my approach to understanding complex evolutionary processes and their links to human diseases differs from previous approaches, in that it begins from the assumption, which my work to date has shown to be promising, that the biological processes of our ancestors, the ancient unicellular eukaryotes, are still preserved in humans, although masked by eons of evolutionary overlay, and await discovery.

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  • هيثم الشيشاني

    Thank you.