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Yeast Today, Cancer Tomorrow

  • Title: Assistant Professor, University of Michigan
  • Education: PhD, Wright State University, 1997
  • Recommended by: Michael Snyder

Though he went for a year, Anuj Kumar didn’t really like medical school. And it’s a good thing, since now he’s devoting his attention full-time to using systems biology approaches to study the genetic changes associated with filamentous growth — threadlike growth that is also pathogenic — in the budding yeast, S. cerevisiae. Using large-scale phenotypic screens, Kumar looks at what kinds of effects gene disruption and overexpression can have on this type of growth in different knockout strains of the yeasts.

Kumar creates mutant alleles that he then introduces into a particular strain of yeast, following up with testing on DNA microarrays to see what gene expression changes occurred. “In some cases you’re interested in studying the effect of deletion, but also in a different [genetic background] — in a yeast strain where other mutations are also present that can help you understand the function of the gene you’re studying,” he says.

Kumar first became interested in studying yeast genomics as a postdoc in Mike Snyder’s lab at Yale. During his PhD work at Wright State University, Kumar was studying a pathway involved in sulfur regulation in Neurospora crassa, a type of non-pathogenic filamentous fungus. He was interested in doing more large-scale studies, and found that the budding yeast was better suited to that. “With the availability of whole genome sequence data and some other techniques that were being used,” Kumar says, “it seemed like we would be actually doing a disservice if we didn’t consider some of the information you can get using those techniques and that data.”

Snyder is also a leader in creating and using protein microarrays, and Kumar’s interest in using these as well as different visualization techniques for large-scale protein localization studies has allowed him to study eukaryotic protein localization and function. If technology advances according to Kumar’s wishes, he’d like to see “better techniques for large-scale visualization of cells, in a systematic, 96-well type format.”

Most of the challenges he sees the field facing are due to the still relatively rudimentary toolsets available. “Despite the fact that we’re making advances, we have fairly blunt tools to study some very fine processes,” he says. “We get incomplete and partial data sets and we try to make the best out of it.”  He sees advances coming in the fields of microfluidics and mass spectrometry, and predicts that chemical biology — using compound libraries to screen for protein interactions — will also make some waves.

Looking ahead

Kumar sees future implications for his work adding to the understanding of what actually goes wrong in cancer in terms of cell growth. “[My work] is applicable to our understanding of processes of fungal pathogenesis, and also basic gene signaling, cell cycle progression, cell growth, all processes that are compromised in cancer,” he says.  “Even when we assess all the genes in a genome, we’re not understanding any full process individually with that data set — so we still have a cumulative effect from numbers of studies, and I just contribute to that process. Hopefully I generate some datasets that are useful.”

Publications of note

In a paper published in the September 2007 issue of Genetics, Kumar and colleagues found a connection between the processes of filamentous growth and autophagy, a stress response in eukaryotic cells, both of which result from nitrogen stress. Their findings suggest that in an environment of nutrient stress, autophagy can delay the start of filamentous growth, and when autophagy is inhibited, it will overactivate and increase this growth.

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