Close up of human biotechnologist testing testing blood for cancer in a laboratory
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A new fluorescent label helps better determine how DNA architecture is disrupted in cancer cells. These findings could improve cancer diagnoses for patients and classification of future cancer risk.

“We have been looking at chromatin compaction,” senior author Yang Liu, associate professor of medicine and bioengineering at the University of Pittsburgh, told Inside Precision Oncology.

Current tools for superresolution microscopy, such as stochastic optical reconstruction microscopy (STORM), can achieve a spatial resolution of 20–30 nm.  But a challenge has been single molecule localization.

Liu and her team have formulated a new label called Hoechst-Cy5 by combining the DNA-binding molecule Cy5 and a fluorescent dye called Hoechst with ideal blinking properties for superresolution microscopy.

Published this week in Science Advances, their study found that this new DNA-binding dye performed well in processed clinical tissue samples and generated high-quality images.

“We are one of the first groups to explore the capabilities of superresolution microscopy in the clinical realm. Previously, we improved its throughput and robustness for analysis of clinical cancer samples. Now, we have a DNA dye that is easy to use, which solves another big problem in bringing this technology to patient care,” said Liu.

“Although we know that chromatin is changed at the molecular scale during cancer development, we haven’t been able to clearly see what those changes are,” said Liu. “To improve cancer diagnosis, we need tools to visualize nuclear structure at much greater resolution.”

In superresolution fluorescence microscopy, a molecule is labelled with a special fluorescent dye that flashes on and off like a blinking star. Unlike traditional fluorescence microscopy, which uses labels that glow constantly, this approach involves switching on only a subset of the labels at each moment. When several images are overlayed, the complete picture can be reconstructed—at a much higher resolution than previously possible.

The images in this study show that as cancer progresses, chromatin becomes less densely packed, and the compact structure at the nuclear border is severely disrupted. While the new label can distinguish normal tissue from precancerous and cancerous lesions, Liu said that superresolution microscopy is unlikely to replace traditional microscopes for routine clinical diagnoses. Instead, this technology could shine in risk stratification.

Pathologists use traditional light microscopes to visualize disruption to the DNA-protein complex, or chromatin, as a marker of cancer or precancerous lesions.

“Early-stage lesions can have very different clinical outcomes,” said Liu. “Some people develop cancer very quickly, and others stay at the precursor stage for a long time. Stratifying cancer risk is a major challenge in cancer prevention.”

To see if chromatin structure could hold clues about future cancer risk, Liu and her team evaluated patients with Lynch syndrome, a heritable condition that increases the risk of several cancer types, including colon cancer. They looked at non-cancerous colorectal tissue from healthy people without the syndrome and Lynch patients with or without a personal history of cancer.

After showing that their new label produced higher resolution images than other dyes, Liu’s group compared colorectal tissue from normal, precancerous, and cancerous lesions.

The differences were striking. In Lynch patients who previously had colon cancer, chromatin was much less condensed than in healthy samples, suggesting that chromatin disruption could be an early sign of cancer development — even in tissue that looks completely normal to pathologists.

To further this research, they are working with Robert Schoen, Professor of Medicine and Epidemiology at the University Pittsburgh, who has helped develop a database of over 154,000 individuals that has been used to evaluate Prostate, Lung, Colorectal, and Ovarian (PLOC) cancer.

“We are now expanding our studies to other organs,” Liu told Inside Precision Oncology.



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