Advanced Technology Cores: Genomic and RNA Profiling
Gene sequencing has the potential to paint a molecular picture of an individual cancer and help researchers identify its origin, its potential for metastasis, its responsiveness to specific drugs, and the likelihood of its recurrence. VIICTR.org spoke with Core Director Lisa D.White, Ph.D., about how Baylor's Genomic and RNA Profiling Core is providing next-generation sequencing services that help researchers analyze and alter genomic changes that occur in the most prevalent human diseases.
What is the purpose of the Genomic and RNA Profiling Core, and how has it expanded since its inception?
When I started as core director in 2001, our purpose was to provide microarray technology to Baylor researchers. We spotted our own homemade microarrays then using robots. However, we struggled with data capacity because we could only handle files in the megabyte range. Since then, technology has evolved to the extent that we offer massively parallel sequencing technologies such as those in Baylor’s Human Genome Sequencing Center. Today, we are using microarrays and sequencing to perform genomic profiling of DNA/RNA, protein interactions, and genetic modifications across the genome.
When we purchased our first sequencer in 2009, it cost $1 million. Only 4 years later, we upgraded our sequencing equipment to the Illumina® platform, which allows us to handle more than 15 times the data for the same cost. The new platform generates about 1 terabase of sequencing information, so we can now produce the same data in one week that formerly took 13 days.
We also have a NanoString® nCounter instrument - see above example of data from this instrument - that can screen large numbers of samples for up to 800 different genes (or assays) simultaneously. If a researcher sequences a entire transcriptomes (RNA) and identifies common gene list that links to pathways etc. involved in the disease being studied, he or she can test for those genes across all the samples in a tumor bank or another sample cohort to validate their gene list. Researchers can then use this information to develop biomarkers, diagnostic tests, or to identify certain types of cancer. As technology advances, some researchers are pushing the limits and trying to conduct single-cell genomic and transcriptomic profiling. So, it is very important that we are able to handle small samples sizes as well as very large ones.
Who uses this Core, and how do they benefit from it?
The best part of my job is that I get to interact with different researchers who are conducting very important research for Baylor. We work with several departments and groups to sequence the genes in cancer samples, stem cells, regeneration research samples, and samples of many different human diseases. We also work with researchers involved in the microbiome project to sequence different bacterial RNA transcriptomes.
In terms of benefits, we provide access to different types of high-throughput technologies that a typical researcher cannot afford to purchase and maintain alone. We also provide expertise in these types of technologies, so that researchers who are not involved in genomic science can use them. Our Core is often cheaper to use because we are subsidized by Baylor and by certain centers within Baylor. For example, researchers who are members of Baylor’s Dan L. Duncan Cancer Center pay 10% less (the researcher actually pays 90% of the cost and DLDCC pays the remaining 10%). Another benefit is the support and advantages that the Core offers to researchers during funding competitions. When they apply for grants, it is helpful to show that they already have access to the newest and most cutting-edge technologies.
How distinct is this Core when compared with similar cores at other institutions?
Through my involvement with the Association of Biomolecular Resource Facilities, I know that our Core is on par with other facilities across the country because we all acquire new technologies at the same time. Nevertheless, we have sequencing capabilities that are lacking at many other universities, which gives us an opportunity to assist researchers outside Baylor. Researchers at Texas A&M University have used our Core for sequencing and microarrays, and researchers at Rice University, especially the nanotechnology and bio/tissue engineering groups, have used our services. Researchers also come from the University of Houston and Tulane University to use our services, so we are a resource for the region.
Do researchers have a clear understanding of what they need, or do they often rely on your expertise?
I would say most rely on our expertise. Researchers usually want to sequence some samples, so we talk about their needs and the research questions they want to answer. Sometimes cost is a factor, so we work together to determine the best experiment that is both affordable and gets them the results they need.
What are some of the typical projects that the Core supports?
In the past 2 years, about 80% of the researchers who sought our services have wanted their samples sequenced for gene expression profiling. They typically are studying tumors versus normal tissue or primary tumors versus metastases and trying to determine what mutations have occurred that have then triggered tumor growth or metastases. We have also been studying cartilage as a candidate for tissue engineering and have worked with NASA to study the effects of gravity and microgravity on changes in gene expression in cartilage cells. So, we support many different experiments, all of which are very exciting.
Is there any project that stands out as being particularly innovative or that resulted in a major breakthrough?
Although some researchers are interested only in basic research, most of the researchers who use our services are aware that translation to the bedside is the goal. For example, we helped Larry Chan, M.B.B.S., D.Sc., a professor of endocrinology and molecular and human genetics at Baylor, with gene expression profiling, a technique that allows us to measure the activity of thousands of genes at once. Based on the results, he and his team were able to transform liver cells, induce them to produce insulin and “cure” diabetes in a mouse model. This work resulted in several published papers. Currently, Dr. Chan and his team are trying to translate their success into a human model.
Are there areas in which the Core could be used more fully?
We are interested in expanding some of our services to researchers who are not as familiar with molecular bench work and helping them to prepare samples before we get involved. For example, some researchers are having problems getting the right-sized gene fragments to undertake DNA sequencing, so that is an area in which we could serve more people. Also, we have more outside researchers using our NanoString technology than Baylor researchers. Baylor has many tumor banks and sample cohorts that could benefit from this technology, so often it is simply a matter of getting the word out to Baylor researchers.
Can you give us some examples of how the Core has helped to promote scientific knowledge that would not have been possible without these resources?
There are about 160 principal investigators who use our Core, so there are many examples of what can be achieved with our resources. We worked with one team who was investigating treatment response and breast cancer metastases. They used our Core to profile animal models that can serve as a renewable tissue resource for preclinical studies. Another team used high-throughput transcriptome sequencing to identify a cancer-specific interchromosomal fusion gene that is found in a significant portion of ovarian cancer samples. Ultimately, this breakthrough will increase our understanding of ovarian cancer and improve the classification of its subtypes
Are there any new Core services that are in the pipeline?
Last year, I started a program to provide sequencing at a significantly reduced rate for pilot projects. For the first grant we offered, we received 42 applications for 7 spots. I partnered with a vendor that supplied all of the sequencing reagents, and we charged a fraction of the usual cost for samples. Applicants submitted a two-page description of their research that included an experimental design and explained how this first step would help them get additional funding. The novelty of this program is that it allows Core grant recipients to use real sequencing data in their subsequent grant applications to federal agencies and foundations. The opportunity clearly increased awareness of our Core. About 70% of the applicants who did not receive a pilot project grant still used our sequencing services.
Investigators interested in using the Genomic and RNA Profiling (GARP) Core can learn more on the Baylor College of Medicine GARP Web site at https://www.bcm.edu/garp.