Shared Resources Spotlight: Cytogenetics

There is tremendous power in simply seeing. However, in biomedical research, where investigators need to understand the physical arrangement of components inside cells, seeing isn’t that simple. Showing where DNA, RNA and proteins exist relative to each other and following how these components interact is the expertise of the St. Jude Cytogenetics Shared Resource. This team uses cutting-edge technologies to visualize where tiny macromolecules reside and how they interact with their sub-cellular environments. 

Using cytogenetics approaches, genetic mutations that contribute to the biology of cancer can be directly visualized inside individual cells. Researchers can also begin to unravel their complex interactions. By directly visualizing the genome in its native cellular environment, investigators can gain insights that might be otherwise overlooked.

The Cytogenetics Shared Resource is essential for the clinical and research operations of St. Jude – understanding how chromosomes are broken and reassembled in patient genomes and advancing understanding of the dynamic interactions among sub-cellular components. 

“We are coming up on 50 years of cytogenetic assay combined experience for the members of our team,” says Steve Burden, PhD, Cytogenetics Shared Resource director. “It requires a lot of education and experience to accurately understand and interpret cytogenetic assays.”

Pioneering techniques

The Cytogenetics Shared Resource aims to empower St. Jude researchers in their quest to understand childhood diseases. “We’re taking images of cells, identifying normal or abnormal chromosome morphology, and delivering crucial data back to our collaborators,” Burden elaborates. This approach is critical to understanding the genetic landscape of many diseases. 

Fluorescent in situ hybridization (FISH) is a mainstay experiment for cytogenetics. This assay has several flavors, each targeting a different type of nucleic acid (DNA or RNA). The pioneering combination of RNA FISH, DNA FISH, and immunofluorescence called “sequential FISH” is a cytogenetics innovation. Research can combine information about nucleic acid locations to gain unparalleled insights into nuclear organization, cellular function and gene regulation.

Seq-FISH enables scientists to detect where specific RNA molecules are produced from their corresponding DNA sequences, providing a more comprehensive picture of gene expression patterns. It also helps identify how spatial arrangements of genes, transcripts and proteins within the nucleus influence their activity, shedding light on the mechanisms of gene regulation. This combined technique can reveal critical interactions and co-localizations that might not be apparent when examining DNA, RNA, or immunofluorescence alone or by taking averages across pools of cells. Ultimately, integrating RNA FISH, DNA FISH and immunofluorescence enriches the toolkit available to cytogeneticists, empowering them to make more informed discoveries and advancements in the fight against childhood diseases.

However, the Cytogenetics Shared Resource does more than run innovative, gold-standard analyses—their approach is one of collaboration. By working closely with researchers across various disciplines, they aim to help translate genetic insights into meaningful scientific advancements.

Collaborations and personalized support

The cytogenetics team works with researchers across 11 diverse departments with over 23 investigators at St. Jude, ensuring a tailored approach to each project. “We work very closely with our collaborators. It’s not just the send-out service. We understand the objectives, what their model systems look like normally, and the history behind the systems they’re using,” Burden explains. This personalized approach fosters deeper insights and accelerates scientific discovery.

For example, Brian Abraham, PhD, Department of Computational Biology, collaborates closely with the cytogenetics team. Abraham's research focuses on genome topology in mammalian cells. He emphasizes the importance of the Cytogenetics Shared Resource in providing essential tools and methodologies for his work. "Our lab is studying the coordinated localization of DNA, of RNAs produced from those DNAs, and of transcription-regulating proteins called co-factors," Abraham explains. By using fluorescent probes, the Cytogenetics Shared Resource helps pinpoint where these elements are within a cell's nucleus, making complex spatial analyses possible.

The Cytogenetics Shared Resource enables Abraham to explore intricate patterns and interactions within the genome. “We’re working with Dr. Burden’s team on a complex challenge in trying to determine the locations of five different types of macromolecules, such as nucleic acids and proteins, and to disentangle their patterns of interaction in individual cells instead of averaging millions of cells,” Abraham details. This project includes studying how distant parts of DNA can physically interact despite being separated by large genomic distances, a phenomenon crucial for understanding gene expression and regulation.

By working closely with the cytogenetics team, Abraham’s lab can faithfully incorporate genome topology data into their research, advancing the understanding of genetic regulation in cancer. This partnership exemplifies how the Cytogenetics Shared Resource leverages innovative tools and methodologies to combat childhood diseases. 

Personal perspective on mission-driven science

Burden’s journey to St. Jude reflects a commitment to mission-driven science. “The emphasis on curing catastrophic childhood diseases is what drives us every day,” Burden states. Before joining St. Jude, Burden owned and operated a biotech company for four years, bringing his PhD research to life. His background in biotechnology, particularly his work with fluorogenic aptamers, tiny DNA or RNA structures that bind non-fluorescent dyes, causing them to become fluorescent, showcases his knack for creating cutting-edge methodologies, which he uses in his work at St. Jude.

Burden resonates deeply with the collaborative environment and the mission-driven focus of St. Jude. “The nonprofit aspect of St. Jude, the mission, you can’t beat it,” he adds. The Cytogenetics Shared Resource embodies the spirit of innovation and collaboration essential for advancing science.

The future of cytogenetics promises even more significant advancements. The focus is on developing technologies that enable real-time tracking of RNA within live cells. This capability could revolutionize our understanding of dynamic cellular processes and inform novel therapeutic strategies. “Live cell nucleic acid imaging will become a focal point for us. It offers insights into cellular dynamics over time, which is crucial for understanding disease mechanisms," Burden states.