Department of Biomedical Sciences faculty publish book on cancer epigenetics protocols

“As human beings, we share 99.9% of 3.3 billion base-pairs of DNA,” said Archana Dhasarathy, Ph.D., from her office at the UND School of Medicine & Health Sciences (SMHS). “This means that what makes us unique as individuals is only 0.1% of our genome.”

The number, which still represents hundreds of millions of base pairs, still astounds the associate professor of biomedical sciences.

“How is it that each cell in our body has the same genome, but we have different cell types that look different and perform a myriad of functions,” Dhasarathy asked rhetorically. “If DNA is the ‘blueprint of life’ that helps make all the proteins in our cells, why don’t all our cells look alike?”

Dhasarathy knows the answers to such questions, of course: The turning on or off of each gene within a cell’s nucleus determines each cell’s shape, size, and function within the organism.

And it was the prospect of learning more about how the overwhelming genetic similarity between humans nonetheless results in the diversity of the population today – particularly in health outcomes – that drew Dhasarathy to her field of study years ago.

Methods and Protocols

The study of this genetic on-off switching – “think of genes within a cell’s nucleus as a set of about 23,000 switches,” Dhasarathy said – is known as epigenetics. Meaning “above the gene,” this expression of genes over a lifetime has profound consequences for human health, including an individual’s likelihood of developing cancer.

All of this is why Dhasarathy and her colleague, Motoki Takaku, Ph.D., also an associate professor of biomedical sciences at SMHS, set about developing a textbook dedicated to cancer epigenetics.

Released last month by academic publisher Springer Nature, the pair’s book, Cancer Epigenetics: Methods and Protocols, features 19 chapters by an international collection of epigenetic researchers studying cancer.

“Epigenetics is well recognized as playing an important role in cancer, Alzheimer’s disease, Parkinson’s, as well as several infectious diseases,” Dhasarathy continued. “But we need the proper tools and techniques to understand what the changes are, how they influence cell behaviors, and, importantly, to determine how to best treat disease.”

This need prompted her and Takaku’s book project, which features several faculty and graduate students from UND, including Associate Professor Sergei Nechaev, Ph.D., biomedical sciences graduate student Brooke Froelich, Professor Manu, Ph.D., from UND’s Department of Biology, graduate student Trevor Long, former UND graduate student and current medical student Kaitlyn Gura, Ph.D., and UND medical student Srikrishna Kandooru. Damien Parrello, Ph.D., and Mike Hill, from the UND Genomics Core, also contributed.

The speed of science

Established over a decade ago, UND’s Epigenetics Working Group has grown steadily over the years, thanks largely to repeat financial support from the National Institutes of Health. Faculty, postdocs, and students connected to the group have produced multiple studies on how genes impact not only cancer but aging, infection, and behavioral health.

Expressing gratitude to their colleagues across the U.S. and the world who contributed their expertise to the book, both Takaku and Dhasarathy reflected on the speed of change in the sciences – hoping that their book won’t be obsolete too quickly.

“Technologies in the field of epigenetics evolve at a rapid pace – it seems like there is a new technique published every other week,” said Takaku, adding that the book’s assembly and editing took over two years from start to finish. “We felt that this collection would provide researchers in the field, and especially those new to the field, with detailed protocols, including lists of materials and reagents and tips for troubleshooting epigenetic techniques.”

Such protocols include detecting epigenetic changes using DNA and RNA, the use of single-cell multiomics data, and advanced microscopy methods for visualizing cells. Many of these protocols include ways to collect these materials from challenging clinical samples.

“We were approached by Springer to help curate and edit a collection of methods and protocols for detection of epigenetic changes in cancer,” concluded Takaku. “To the beginner, some of these protocols can seem daunting, as they are usually multi-step. We just wanted to help new researchers orient themselves.”

Cancer Epigenetics: Methods and Protocols is available via Springer or wherever academic books are sold online.