Trudy Mackay and Robert Anholt work with tiny fruit flies to make big discoveries.

Trudy Mackay (right) and Robert Anholt work with tiny fruit flies to make big discoveries.
Image Credit: College of Science

GREENWOOD, South Carolina – Trudy Mackay and Robert Anholt of Clemson University’s Center for Human Genetics in Greenwood have received $1.87 million from the National Institutes of Health to advance research aimed at significantly increasing our fundamental understanding of the complex roles molecular variations play in human disease.

Human beings share 99.9 percent of all DNA (the carrier of genetic information), but the 0.1 percent that isn’t shared is what makes each person unique. Everyone’s genome (an organism’s complete set of DNA) contains millions of genetic variants that affect everything from lifespan to eye color.

In an irony of sorts, the invisible inner workings of Drosophila melanogaster, a fruit fly smaller than a grain of rice, appears to hold the key to unlocking huge mysteries that have puzzled geneticists for decades. About 70 percent of fly genes have human counterparts, enabling the construction of genetic networks that are comparable in makeup and scope. Mackay and Anholt use the flies to perform genome-wide association analysis, which studies genetic variants in large numbers of different individuals to see if any variant is associated with a distinguishing quality or characteristic.

Mackay is director of the Center for Human Genetics, which is part of the College of Science. She is also the Self Family Endowed Chair in Human Genetics. Anholt is Provost’s Distinguished Professor of Genetics and Biochemistry and is also director of faculty excellence initiatives in the College of Science. Both are co-principal Investigators of the four-year NIH project titled “Reverse Engineering Quantitative Genetic Variation.” Their work will focus on quantitative (or complex) traits that depend on the cumulative actions of many interacting genes.

“My lab and Robert’s lab have developed the Drosophila melanogaster Genetic Reference Panel (DGRP), which was derived from an outcrossed population of wild fruit flies collected from the Raleigh (N.C.) State Farmer’s Market,” Mackay said. “The DGRP is a sequenced suite of 200 fruit-fly lines that has been inbred over multiple generations so that each member of any one genotype (an organism’s complete heritable genetic identity) has minimal genetic variation. We developed these lines so that we can statistically analyze a variety of quantitative traits. In doing so, we are identifying candidate genes and candidate variants – and are also beginning to learn how variants can create a rippling effect throughout an entire complex of genes.”

Mackay and Anholt are using a gene-editing technique called CRISPR/Cas9, which controls gene insertion, deletion or mutations in the genome. They use a NovaSeq 6000 DNA sequencer and advanced computational and bioinformatics analyses to extract information from the large data sets that are generated by this powerful high-throughput instrument.

“Using novel gene-editing techniques, we are able to reverse-engineer complex traits in living flies so that we can identify the variants in the genome that can be added together to determine risk for alterations in traits,” Anholt said. “We have essentially clones of individuals of each line which enable us to measure the same individual, more or less, over and over again. And we are comparing lines in which the genetic background is identical. In this way, we can achieve the type of statistical power of analyses that cannot be accomplished in other systems. The type of work that we describe can only be done in the Drosophila melanogaster Genetic Reference Panel.”

The NIH project has three aims: 1) validate the findings of Mackay’s and Anholt’s previous research; 2) validate the effects of rare variants using CRISPR/Cas9 variant replacement; 3) validate novel transcribed regions and transcriptional networks and evaluate their effects on genome-wide expression and quantitative traits.

“In our 200 different genotypes, we have already profiled a lot of different quantitative traits. So our first aim will be to validate these profiles,” Mackay said. “Our second aim involves validating our findings regarding rare diseases, which individually don’t affect many people but which in combination affect a large number of children who are born with them.”

The third aim in many ways is the most interesting one. Mackay and Anholt have sequenced complete transcriptomes (the sum total of all the messenger RNA molecules expressed from the genes of an organism) in the 200 different lines and have discovered a whole slew of what they call “novel transcribed regions (NTRs).”

“We have increased the number of previously known non-coding RNAs by eight-fold, and what we’ve learned thus far is that the transcriptomes form an amazing interaction network that is in part sex-specific and in part shared between males and females,” Mackay said. “We want to figure out what these networks do. And the approach a geneticist takes is to break it. By using the gene-editing technique, we’re going to break them systematically and discover what their effects are on the regulatory networks and what their effects are on fly phenotypes.”

The Center for Human Genetics is based in Greenwood and is part of Clemson University's College of Science.

The Center for Human Genetics is based in Greenwood and is part of Clemson University’s College of Science.
Image Credit: University Relations

The Center for Human Genetics works in partnership with the Greenwood Genetic Center, a nonprofit institute that focuses on clinical genetic services, diagnostic laboratory testing, educational programs and research. Mackay and her team interact regularly with Greenwood Genetic Center personnel.

Mackay is a renowned geneticist and a fellow of the National Academy of Sciences, the American Association for the Advancement of Science, the American Academy of Arts and Sciences and the Royal Society of London. Anholt is also a fellow of the American Association for the Advancement of Science.

Others involved in the project include Miyoung Shin, a molecular geneticist who came to Clemson from the University of Miami; Rebecca Jones, a Clemson graduate student; and Wen Huang, a faculty-member collaborator from Michigan State. Recruitment of postdoctoral fellows to participate in this project is under way.

END

Clemson University College of Science
The College of Science transcends boundaries and bridges connections across life, physical, and mathematical sciences. Its mission is to pursue excellence in scientific discovery, learning and engagement that is both locally relevant and globally impactful. For more information, visit https://cualumni.clemson.edu/give/science.

Clemson Center for Human Genetics
The mission of the Clemson Center for Human Genetics is to advance and disseminate knowledge of the principles and mechanisms by which genetic and environmental factors affect human health and disease through discovery, education and engagement to benefit the health and well-being of the people of South Carolina, the nation and the world. For more information, visit https://www.clemson.edu/science/research/chg.html.

National Institutes of Health Grants and Funding
This research is supported by the National Institutes of Health’s department of health and human services under award number 1 R01 GM1128974. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.