In this edition:
Research from the Raman Lab in the Department of Biochemistry paves the way for scientists to explore the mechanisms driving potentially dangerous mutations in cells — possibly hundreds of mutations — with a single experiment. Here’s the run down on their latest research, published recently in the journal Nature Biotechnology:
- Oncofusions, a type of genetic mutation known as a chromatin mutation, can result in childhood cancers. Though hundreds of oncofusions have been identified, little is known about the functional impact of each mutation.
- Research characterizing genetic mutations is time-consuming and expensive because mutations are sequenced individually.
- Using oncofusions, scientists in the Raman Lab have developed a method to sequence hundreds of chromatin-altering mutations at once, drastically cutting down on time and costs for identifying how individual mutations disrupt the ways cells function.
What background information do you need to know?
Oncofusions are mutations that can occur when pieces of chromosomes, which are packages of DNA within a cell, break off and reattach in the wrong place, leading to “Frankenstein genes” that are mashups of two different genes. Such mutations are naturally occurring and can often be benign. But, as the prefix “onco” implies, these mis-matched pieces of chromosome can also lead to cancers including aggressive pediatric cancers.
Disease-causing oncofusions can result in mutated proteins. Like other genetic mutations affecting chromatin, oncofusions affect the way DNA is folded and packaged. The result is a disruption of cellular pathways, turning on cellular functions that should be left off or failing to induce necessary functions.
However, how each oncofusion — or other types of chromatin mutations, for that matter — impairs cellular function remains unknown.
Why is it difficult to identify a mutation’s functional impacts?
Researchers can compile libraries of information about genetic mutations associated with human diseases. Knowing that a mutation is associated with a disease, however, does not tell us how the mutation results in disease — information that can be critical for developing effective drugs and other treatments.
Scientists hoping to explore whether and how mutations influence protein function have been limited by the tools available to study these mutations. The tools are expensive and require that every possible mutation in a protein be characterized individually, a process that can laborious and time-consuming.
How have scientists made progress?
Researchers in the Raman Lab have developed a method that allows them to study the effects of individual genetic mutations at a significantly larger scale. Using their high-throughput methodology, they were able to characterize the effects of more than 100 oncofusions at once for a fraction of what it would have cost to study such a large array of mutations using other methods.
Raman and his lab grew cells, each with its own oncofusion, and sequenced genomes from all of the cells at once to identify how the oncofusions changed chromatin state (the way DNA was packaged) in each cell. DNA barcodes inserted into each cell allowed them to identify which chromatin changes were associated with individual oncofusions.
Through this efficient process, dubbed PROD-ATAC, the researchers were able to identify how oncofusions impact cellular function. Common mechanisms included inducing cellular functions that would otherwise be silenced and pioneering new cellular activities. These convergent mechanisms by which oncofusions cause dysregulation may offer insights into targets for gene therapy and other treatments to attack aggressive pediatric cancers.
The researchers’ methods may also have applications beyond oncofusions, as human diseases such as diabetes, heart disease, and Alzheimer’s are also associated with chromatin mutations. Scientists may now be able to characterize mutations correlated with disease en masse in search of causes and treatments.
Written by Renata Solan.
In Research In Brief: The What, Why, and How, we explore new research from the UW–Madison Department of Biochemistry to learn more about the world around us — and inside us.
This edition of Research in Brief: The What, Why, and How is based on the following publication:
Frenkel, Hujoel, Morris, and Raman. Discovering chromatin dysregulation induced by protein-coding perturbations at scale. Nature Biotechnology, 2024 Jul 24.
This research was funded in party by grants from the National Institutes of Health (NIH) fellowship T32HG2760-17, NIH Director’s New Innovator Award DP2GM132682 and University of Wisconsin Carbone Cancer Center Core Grant P30CA104520).