Liquid Biopsies

Liquid biopsies and AI give insight into eye health and aging

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At a Glance

  • Researchers used a liquid biopsy technique to assess thousands of proteins in eye fluids and identify cellular drivers for disease and aging.
  • The approach could also be applied to other organs that have associated fluids.

Open eye in space.

Scientists developed a technique to gain insight into age- and disease-related changes within cells throughout the eye. adimas

Many diseases are diagnosed via biopsy, in which a physician removes a small sample of cells or tissues from an organ to look for evidence of disease. But biopsies can cause irreversible harm to organs that don’t regenerate, like the eyes or brain. This has made it hard for researchers to study cell-level activities and gene functions of these organs in living people.

A research team led by Dr. Vinit Mahajan of Stanford Medicine hit on the idea of analyzing fluids within the eye that are often accessible and removed during eye surgery. The scientists suspected that these eye fluids might be enriched with a variety of cell-specific proteins that could serve as biomarkers to indicate health or disease.

The researchers obtained liquid biopsies from 120 people undergoing eye surgery. Some had conditions that can lead to vision loss. These included diabetic retinopathy, which damages blood vessels in the retina, and uveitis, which is inflammation inside the eye. Other liquid biopsies were from healthy people, including some who had cataracts but otherwise healthy eyes. Results were reported in Cell on October 26, 2023.

The researchers used an analytic technique called proteomic profiling to identify all the proteins present in the liquid samples. They detected nearly 6,000 unique proteins, a significant improvement over previous techniques. Using available mRNA sequencing data from different eye cells, the team then created algorithms that could trace the proteins back to the types of cells that made them. The eye contains 57 known types of cells, including nerve cells, blood cells, immune cells, and blood vessel cells. Each type can release proteins into the eye’s fluid-filled regions. The team also included data on 15 cell types from outside the eye, including spleen and liver cells.

The researchers found that liquid biopsies from patients with diabetic retinopathy had distinctive protein patterns that shifted as the disease progressed. The markers of disease included proteins that affect blood vessel growth and immune cells. The findings could point to new strategies for treating the condition.

The team also found evidence that liquid biopsies from the eye might provide early clues to Parkinson’s disease. The scientists identified nine proteins, mostly from retina nerve cells, that were significantly elevated among participants with Parkinson’s disease. Further study would be needed to confirm this link.

Using machine learning and artificial intelligence, the researchers created “molecular clocks” that can predict the actual age of the eye and detect signs of accelerated aging. The eyes of people with early-stage diabetic retinopathy appeared to be about 12 years older than the eyes of healthy people. The eyes of those with the late-stage condition seemed to be about 30 years older than healthy eyes. And the eyes of patients with uveitis seemed an extra 29 years old.

With further study, the researchers say, the liquid biopsy technique might be applied to other organs that have associated fluids. These include the brain via spinal fluid, kidney via urine, lungs via lung fluids, and joints via synovial fluid.

“What’s amazing about the eye is we can look inside and see diseases happening in real time,” Mahajan says. “Our primary focus was to connect those anatomical changes to what’s happening at the molecular level inside the eyes of our patients.”

CHOP Researchers Show Liquid Biopsies Can Catch Disease Progression Early in High-Risk Neuroblastoma

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Neuroblastoma is an aggressive pediatric cancer that develops from early nerve cells and accounts for up to 10% of childhood cancer deaths. Survival rates are low – less than 50% of patients with the disease survive, and less than 5% with relapsed disease overcome it.

One challenge researchers face is monitoring how the cancer mutates in response to treatment, shapeshifting as it resists conventional treatments like chemotherapy, as well as newer targeted treatments. The tumors are often in difficult locations – around the spine, within the bone, or in the brain – so performing a tumor biopsy can be risky and may not capture mutations in tumors located elsewhere in the body. Yet identifying tumor changes early is key to successful treatment.

To circumvent this challenge, researchers at Children’s Hospital of Philadelphia (CHOP) investigated whether a series of “liquid biopsies” performed in partnership with Foundation Medicine could less invasively and more accurately identify tumor changes in patients with high-risk neuroblastoma. Patients with solid tumors like neuroblastoma often have tumor cells and tumor DNA circulating in their blood, and recent technological advances have allowed scientists to characterize this circulating tumor DNA (ctDNA). Serial ctDNA profiling is already used in many adult cancers and is even FDA approved for certain indications, so the CHOP researchers explored whether ctDNA profiling could be clinically useful in neuroblastoma.

Examining the blood from 48 patients with high-risk neuroblastoma, the researchers found 73% of patients had at least one ctDNA sample over the course of their treatment where a mutation was detected. The series of liquid biopsies revealed that some patients’ tumors mutated under the pressure of treatment, which not only correlated with disease progression, but also made them potentially eligible for other targeted therapies. For example, several of the mutations included clinically actionable variants, such as those related to ALK and RAS-MAPK pathways, for which targeted treatments exist.

The researchers also found that most patients who received a variety of ALK inhibitors, which are targeted treatments, experienced genomic evolution of their tumors, as the tumors were put under the weight of therapy. The evolution of these tumors happens just before or at the same time as disease progression, showing that ctDNA profiling can identify clinically relevant genomic evolution perhaps even earlier than current standard disease surveillance methods.

“Based on our observations, we suggest that serial ctDNA profiling should be integrated into clinical practice for children with high-risk neuroblastoma to provide real-time data on genomic evolution and insights into mechanisms of therapy resistance, in addition to potentially identifying clinically targetable mutations,” said Kristopher Bosse, MD, an Assistant Professor of Pediatrics in the Cancer Center at Children’s Hospital of Philadelphia and first and corresponding author of the study describing the research. “Our goal is to implement less invasive and more sensitive tumor surveillance and detection of tumor heterogeneity.”

“In time, ctDNA profiling could allow for decreased use of standard radiographic methods used for disease surveillance, many of which require analgesia along with continued exposure to radiation for children who are already at high risk for development of secondary malignancies,” said senior study author Yael P. Mossé, MD, Professor of Pediatrics in CHOP’s Cancer Center. “We have developed our own pediatric-specific liquid biopsy assay that is now being commercialized such that it can be available for all children with high-risk solid tumors and eventually become part of the standard of care.”

New blood test may expand scope of liquid biopsies

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New blood test may expand scope of liquid biopsies
Along its length DNA loops around structures called nucleosomes (in gray) and is bound by proteins. When cells die, enzymes (represented by scissors) chop up the DNA by targeting the easily accessible areas between nucleosomes and proteins. The resulting DNA segments reveal where the nucleosomes and proteins were located. 

When cells die, they don’t vanish without a trace. Instead, they leave behind their fingerprints in the form of cell-free DNA. In people, these tiny fragments of DNA can be found in the bloodstream.

In recent years, research into cell-free DNA has led to a type of test, dubbed the “liquid biopsy,” that can diagnose and monitor some cancers, identify fetal abnormalities, and assess the health of transplanted organs, all with a simple blood draw. Despite the promise of these tests, at present the range of conditions they can detect is limited.

In a new study, UW Medicine researchers in Seattle show that it might be possible to overcome these limitations with a method for identifying what types of cells gave rise to the cell-free DNA.

This method could potentially expand the scope of the liquid biopsy. The new approach relies on analyzing the fragmentation patterns seen in the cell-free DNA in one individual, and comparing that pattern to what might be expected for cell death associated with various medical or physiological conditions.

The research was led by Matthew W. Snyder, a graduate student, and Dr. Martin Kircher, a postdoctoral fellow, in the laboratory of Dr. Jay Shendure, University of Washington professor of genome sciences and a Howard Hughes Medical Institute investigator.

Their results are reported this week in the scientific journal Cell. Their paper is titled, “Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin.”

“Our findings suggest it is possible to identify tissues contributing to cell-free DNA by looking at these fragmentation patterns, instead of looking for specific mutations in the DNA,” Shendure said. The test examines the ends of each fragment of DNA, and tries to identify hotspots, or parts of the DNA that get cut more frequently than others.

To fit into a cell’s nucleus, DNA has to be coiled, wound and folded into an incredibly compact package. Key to this process are structures called nucleosomes, which are composed of a protein core around which the DNA is wrapped like thread around a spool. Nucleosomes are strung out along the entire length of the genome, like beads on a string, with the DNA looping around one nucleosome after the next. Each cell type in the body packages DNA slightly differently. These differences leave their tell-tale mark in the resulting cell-free DNA.

The UW researchers hypothesized that they could use these fingerprints to work backwards to try to figure out where the cell-free DNA originated. To do this, they first needed to know which parts of the DNA were wrapped around the nucleosomes.

During , the DNA gets chopped into small pieces by enzymes that like to cut in the easily accessible, unprotected sections of DNA in between the nucleosomes. Research has pointed to 13 million positions in the human genome where nucleosomes are most likely to be located.

Using blood samples from cancer patients, the researchers showed that different types of cancer left different nucleosome fingerprints in the cell-free DNA. For some of the cancers, the researchers could identify the anatomical source of the tumor.

“This could be particularly relevant in the 5 percent of metastatic cancers whose original source is unknown,” Shendure said, adding that the test “could aid in diagnosing what kind of cancer it is and to help guide treatment.”

Most liquid biopsy approaches look for specific DNA mismatches between different cells in the body, such as the mutations found in tumor cells but not healthy cells. The researchers think that the advantage of the new test is that it may work even when the cells are genetically identical to one another.

The approach potentially could be used to diagnose a wide variety of conditions that kill off , but that as yet cannot be diagnosed with liquid biopsies. Examples of such serious, cell-destroying medical problems are heart attacks, strokes and autoimmune diseases.

‘Liquid Biopsies’ Could Be The First Noninvasive Way To Sample Cancer Tumors

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A new type of blood test is starting to transform cancer treatment, sparing some patients the surgical and needle biopsies long needed to guide their care.

The tests, called liquid biopsies, capture cancer cells or DNA that tumors shed into the blood, instead of taking tissue from the tumor itself. A lot is still unknown about the value of these tests, but many doctors think they are a big advance that could make personalized medicine possible for far more people.

They give the first noninvasive way to repeatedly sample a cancer so doctors can profile its genes, target drugs to mutations, tell quickly whether treatment is working, and adjust it as the cancer evolves.

Two years ago, these tests were rarely used except in research. Now, several are sold, more than a dozen are in development, and some doctors are using them in routine care.

Gurpaul Bedi had one for colon cancer that spread to his lungs. About 10 percent of patients with metastatic colon cancer at the University of Texas MD Anderson Cancer Center now get liquid biopsies.

“I think it’s wonderful,” said Bedi, who lives in Atlanta and goes to Houston for his care. “A lung biopsy, many doctors told me, is not easy.”

In Philadelphia, a liquid biopsy detected Carole Linderman’s breast cancer recurrence months before it normally would have been found.

“Had this test not been available, we may not have known I had cancer on my spine until symptoms showed up,” which may have been too late for good treatment, she said.

The huge potential for these tests is clear. The problem: There are no big, definitive studies to show they help patients, how accurate they are, which type is best or who should get them and when.

Still, patients do better when drugs are matched to their tumors, and liquid biopsies may give a practical way to do that more often.

“I’m really excited about all of this,” said Dr. Razelle Kurzrock, a University of California, San Diego cancer specialist. “I spent most of my life giving drugs that were useless to people” because there was no good way to tell who would benefit or quickly tell when one wasn’t working, she said. “This is so much better.”

WHO GETS TESTED NOW

The tests are mostly used when a tissue biopsy can’t easily be done, when the cancer’s original site isn’t known, or when drugs have stopped working and doctors are unsure what to try next, said Dr. Scott Kopetz, a colon cancer specialist at MD Anderson. The tests are catching on “faster than I anticipated,” he said.

At Philadelphia’s Thomas Jefferson University, Dr. Massimo Cristofanilli has used them on about 120 breast cancer patients, including two dozen like Linderman with a high risk of recurrence.

A tissue biopsy typically samples one section of a tumor, and tumors can vary widely, with different genes and hormones active in different parts, he said. Also, cancer that has spread often differs from the original site, and tumors change rapidly in response to treatment.

With a tissue biopsy, “our treatments lag behind and they’re still based on limited information,” Cristofanilli said. With a liquid biopsy, “the power of this test has been to really find out how the disease changes, even in a short period of time.”

HOW THEY WORK

Early versions looked for whole tumor cells in blood. Newer ones look for free-floating cancer DNA, enabling gene profiling to see what mutations drive the cancer. Kopetz and Cristofanilli use one from Guardant Health Inc. of Redwood City, California, that has been sold in the U.S. since June 2014 and in parts of Europe and Asia.

Many companies are working on similar tests including Sequenom, a San Diego biotech that already sells one for prenatal screening, using fetal DNA in maternal blood. Many companies tried prenatal screening with fetal cells but it didn’t work, said chief science officer Dirk van den Boom. “Cell-free DNA really was the breakthrough” that enabled wide use, and the same could happen with these cancer tests, he said.

THE COST

Whether liquid biopsies will be cost-effective is unknown. Guardant’s test costs $5,400; some insurers cover it for certain types of patients. Gene profiling from a tissue biopsy costs about the same. The promise of liquid biopsies is that they can be done periodically to monitor care, but more tests means more cost.

They may save other costs, though. A traditional lung biopsy is thousands of dollars. Money could be saved by skipping cancer drugs that ultimately don’t work; many cost $10,000 to $15,000 a month.

With cell-free DNA tests, even doctors in rural areas can offer precision medicine because they can ship a blood sample to a lab. “We think that’s the future,” said Dr. Charles Baum, a former Pfizer cancer drug chief who now heads Mirati Therapeutics, a San Diego biotech company developing gene-targeting drugs

DO THEY WORK?

Many studies suggest that liquid biopsy results largely mirror those from tissue ones, and sometimes find more mutations. A study Kopetz presented in April at an American Association for Cancer Research meeting found the blood tests detected cancer mutations in the vast majority of 105 colorectal cancer patients. For 37 percent of them, doctors thought a drug could target a mutation that was found.

Still, no big studies show that liquid biopsies give better care or extend lives. Without that proof, how much they will be used by doctors and covered by insurers remains to be seen.

THE FUTURE

A San Diego company, Trovagene, is working on an even faster, easier liquid biopsy — a test to detect tumor DNA in urine. One scenario: a patient collects a urine sample every day for a week after starting a new drug and ships them to a lab.

“In as little as three to five days, you can observe dramatic changes” that suggest a response to treatment, said Trovagene’s chief executive, Antonius Schuh.

Work on this test is still very early.

Ultimately, liquid biopsies might offer a way to screen for cancer besides the mammograms, colonoscopies and other methods used now. That raises even more questions, including when to call something “cancer” and whether it needs treatment if there are only abnormal cells in the blood.

“Why does there have to be a tumor? The tumor is the symptom. The disease is the DNA,” Schuh said.