Researchers discover new fluorescent DNA label, likely to help detect cancer risk

Scientists develop a new fluorescent label that provides a sharper image of how DNA architecture is disturbed in cancer cells. Individuals’ cancer diagnosis and cancer risk categorization could be improved as a result of the research.

Yang Liu, PhD., associate professor of medicine and bioengineering at the University of Pittsburgh and member of the UPMC Hillman Cancer Center. Image Credit: University of Pittsburgh Medical Center.

The research discovered that the DNA-binding dye functioned well in processed clinical tissue samples and produced high-quality images through superresolution fluorescence microscopy. The study was published recently in the journal Science Advances.

My lab is focused on developing microscopy techniques to visualize the invisible. 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.”

Yang Liu PhD., Study Senior Author and Associate Professor, Medicine and Bioengineering, University of Pittsburgh

DNA strands are coiled around proteins like beads on a string inside the nucleus of the cell. Destruction of this DNA-protein complex, or chromatin, is commonly seen as a sign of cancer or precancerous lesions by pathologists using typical light microscopes.

Liu, who is also a member of the UPMC Hillman Cancer Center states, “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. This has bothered me for more than 10 years. To improve cancer diagnosis, we need tools to visualize nuclear structure at much greater resolution.”

In 2014, Liu’s vision became a reality—thanks to the Nobel Prize-winning discovery of superresolution fluorescence microscopy. A fluorescent dye, which blinks on and off like a flashing star, is used to mark a molecule of interest.

Unlike typical fluorescence microscopy, which utilizes labels that glow all the time, this method only switches on a subset of the labels at a time. When many photos are layered, the entire picture may be rebuilt—at a far better resolution than before.

Until now, the concern was that the fluorescent dyes did not function well on DNA or in cancer samples that had been processed. As a result, Liu and her colleagues developed Hoechst-Cy5, a novel label that combines the DNA-binding molecule Cy5 with a fluorescent dye called Hoechst that has optimal blinking qualities for superresolution imaging.

The scientists compared colorectal tissue from normal, precancerous, and cancerous tumors after demonstrating that the novel label yielded higher quality images than conventional dyes. In normal cells, chromatin is tightly packed, particularly at the nucleus’s borders. Since a larger density of labels generates a stronger signal, condensed DNA glows strongly; on the other hand, loosely packed chromatin produces a weaker signal.

The photos demonstrate that chromatin gets less tightly packed as cancer advances, and the compact structure at the nuclear boundary becomes badly disturbed.

While these results indicate that the new label can differentiate between normal tissue and precancerous and cancerous tumors, Liu believes that superresolution microscopy will not be able to substitute traditional microscopes for regular clinical diagnostics. Instead, risk categorization could benefit from this technology.

Early-stage lesions can have very different clinical outcomes. 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.”

Yang Liu PhD., Study Senior Author and Associate Professor, Medicine and Bioengineering, University of Pittsburgh

Liu and her colleagues studied Lynch syndrome patients to determine if chromatin structure could reveal information about future cancer risk. Lynch syndrome is a hereditary disorder that raises the chances of various cancer types, notably colon cancer. They studied non-cancerous colon tissue from Lynch syndrome patients with or without a family history of cancer, as well as individuals without Lynch syndrome.

The distinctions were remarkable. Chromatin was substantially less condensed in Lynch patients who previously had colon cancer than in healthy samples, indicating that chromatin instability could be an early indicator of cancer formation—even in tissue that pathologists thought was perfectly normal.

Some Lynch patients who do not have a family history of cancer may develop cancer, while others will not.

We see a much larger spread in this group, which is very interesting. Some patients resemble healthy controls, and some are closer to Lynch patients who previously had cancer. We think that patients with more open chromatin are those who are more likely to develop cancer. We need to follow these patients over time to measure outcomes, but we’re pretty excited that chromatin disruption in normal cells could potentially predict cancer risk.”

Yang Liu PhD., Study Senior Author and Associate Professor, Medicine and Bioengineering, University of Pittsburgh

Liu and her colleagues want to look at chromatin structure in endometrial tissue from Lynch patients, who have an increased risk of endometrial cancer. The scientists have also just acquired funding to examine sputum samples from smokers in the hopes of detecting lung cancer at an early stage.