pancreatic cancer
New Approach to ‘Liquid Biopsy’ Relies on Repetitive RNA in the Bloodstream
Posted on by Lawrence Tabak, D.D.S., Ph.D.
It’s always best to diagnose cancer at an early stage when treatment is most likely to succeed. Unfortunately, far too many cancers are still detected only after cancer cells have escaped from a primary tumor and spread to distant parts of the body. This explains why there’s been so much effort in recent years to develop liquid biopsies, which are tests that can pick up on circulating cancer cells or molecular signs of cancer in blood or other bodily fluids and reliably trace them back to the organ in which a potentially life-threatening tumor is growing.
Earlier methods to develop liquid biopsies for detecting cancers often have relied on the presence of cancer-related proteins and/or DNA in the bloodstream. Now, an NIH-supported research team has encouraging evidence to suggest that this general approach to detecting cancers—including aggressive pancreatic cancers—may work even better by taking advantage of signals from a lesser-known form of genetic material called noncoding RNA.
The findings reported in Nature Biomedical Engineering suggest that the new liquid biopsy approach may aid in the diagnosis of many forms of cancer [1]. The studies show that the sensitivity of the tests varies—a highly sensitive test is one that rarely misses cases of disease. However, they already have evidence that millions of circulating RNA molecules may hold promise for detecting cancers of the liver, esophagus, colon, stomach, and lung.
How does it work? The human genome contains about 3 billion paired DNA letters. Most of those letters are transcribed, or copied, into single-stranded RNA molecules. While RNA is best known for encoding proteins that do the work of the cell, most RNA never gets translated into proteins at all. This noncoding RNA includes repetitive RNA that can be transcribed from millions of repeat elements—patterns of the same few DNA letters occurring multiple times in the genome.
Common approaches to studying RNA don’t analyze repetitive RNA, so its usefulness as a diagnostic tool has been unclear—until recently. Last year, the lab of Daniel Kim at the University of California, Santa Cruz reported [2] that a key genetic mutation that occurs early on in some cancers causes repetitive RNA molecules to be secreted in large quantities from cancer cells, even at the earliest stages of cancer. Non-cancerous cells, by comparison, release much less repetitive RNA.
The findings suggested that liquid biopsy tests that look for this repetitive, noncoding RNA might offer a powerful new way to detect cancers sooner, according to the authors. But first they needed a method capable of measuring it. Due to its oftentimes uncertain functions, the researchers have referred to repetitive, noncoding RNA as “dark matter.”
Using a liquid biopsy platform they developed called COMPLETE-seq, Kim’s team trained computers to detect cancers by looking for patterns in RNA data. The platform enables sequencing and analysis of all protein coding and noncoding RNAs—including any RNA from more than 5 million repeat elements—present in a blood sample. They found that their classifiers worked better when repetitive RNAs were included. The findings lend support to the idea that repetitive, noncoding RNA in the bloodstream is a rich source of information for detecting cancers, which has previously been overlooked.
In a study comparing blood samples from healthy people to those with pancreatic cancer, the COMPLETE-seq technology showed that nearly all people in the study with pancreatic cancer had more repetitive, noncoding RNA in their blood samples compared to healthy people, according to the researchers. They used the COMPLETE-seq test on blood samples from people with other types of cancer as well. For example, their test accurately detected 91% of colorectal cancer samples and 93% of lung cancer samples.
They now plan to look at many more cancer types with samples from additional patients representing a broad range of cancer stages. The goal is to develop a single RNA liquid biopsy test that could detect multiple forms of cancer with a high degree of accuracy and specificity. They note that such a test might also be used to guide treatment decisions and more readily detect a cancer’s recurrence. The hope is that one day a comprehensive liquid biopsy test including coding and noncoding RNA will catch many more cancers sooner, when treatment can be most successful.
References:
[1] RE Reggiardo et al. Profiling of repetitive RNA sequences in the blood plasma of patients with cancer. Nature Biomedical Engineering DOI: 10.1038/s41551-023-01081-7 (2023).
[2] RE Reggiardo et al. Mutant KRAS regulates transposable element RNA and innate immunity via KRAB zinc-finger genes. Cell Reports DOI: 10.1016/j.celrep.2022.111104 (2022).
Links:
Daniel Kim Lab (UC Santa Cruz)
Cancer Screening Overview (National Cancer Institute/NIH)
Early Detection (National Cancer Institute/NIH)
NIH Support: National Cancer Institute, National Heart, Lung, and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases
Fighting Cancer with Next-Gen Cell Engineering
Posted on by Dr. Francis Collins
Researchers continue to make progress with cancer immunotherapy, a type of treatment that harnesses the body’s own immune cells to attack cancer. But Kole Roybal wants to help move the field further ahead by engineering patients’ immune cells to detect an even broader range of cancers and then launch customized attacks against them.
With an eye toward developing the next generation of cell-based immunotherapies, this synthetic biologist at University of California, San Francisco, has already innovatively hacked into how certain cells communicate with each other. Now, he and his research team are using a 2018 NIH Director’s New Innovator Award to build upon that progress.
Roybal’s initial inspiration is CAR-T therapy, one of the most advanced immunotherapies to date. In CAR-T therapy, some of a cancer patient’s key immune cells, called T cells, are removed and engineered in a way that they begin to produce new surface proteins called chimeric antigen receptors (CARs). Those receptors allow the cells to recognize and attack cancer cells more effectively. After expanding the number of these engineered T cells in the lab, doctors infuse them back into patients to enhance their immune systems’s ability to seek-and-destroy their cancer.
As helpful as this approach has been for some people with leukemia, lymphoma, and certain other cancers, it has its limitations. For one, CAR-T therapy relies solely on a T cell’s natural activation program, which can be toxic to patients if the immune cells damage healthy tissues. In other patients, the response simply isn’t strong enough to eradicate a cancer.
Roybal realized that redirecting T cells to attack a broader range of cancers would take more than simply engineering the receptors to bind to cancer cells. It also would require sculpting novel immune cell responses once those receptors were triggered.
Roybal found a solution in a new class of lab-made receptors known as Synthetic Notch, or SynNotch, that he and his colleagues have been developing over the last several years [1, 2]. Notch protein receptors play an essential role in developmental pathways and cell-to-cell communication across a wide range of animal species. What Roybal and his colleagues found especially intriguing is the protein receptors’ mode of action is remarkably direct.
When a protein binds the Notch receptor, a portion of the receptor breaks off and heads for the cell nucleus, where it acts as a switch to turn on other genes. They realized that engineering a cancer patient’s immune cells with synthetic SynNotch receptors could offer extraordinary flexibility in customized sensing and response behaviors. What’s more, the receptors could be tailored to respond to a number of user-specified cues outside of a cell.
In his NIH-supported work, Roybal will devise various versions of SynNotch-engineered cells targeting solid tumors that have proven difficult to treat with current cell therapies. He reports that they are currently developing the tools to engineer cells to sense a broad spectrum of cancers, including melanoma, glioblastoma, and pancreatic cancer.
They’re also engineering cells equipped to respond to a tumor by producing a range of immune factors, including antibodies known to unleash the immune system against cancer. He says he’ll also work on adding engineered SynNotch molecules to other immune cell types, not just T cells.
Given the versatility of the approach, Roybal doesn’t plan to stop there. He’s also interested in regenerative medicine and in engineering therapeutic cells to treat autoimmune conditions. I’m looking forward to see just how far these and other next-gen cell therapies will take us.
References:
[1] Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors. Morsut L, Roybal KT, Xiong X, Gordley RM, Coyle SM, Thomson M, Lim WA. Cell. 2016 Feb 11;164(4):780-91.
[2] Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors. Roybal KT, Williams JZ, Morsut L, Rupp LJ, Kolinko I, Choe JH, Walker WJ, McNally KA, Lim WA. Cell. 2016 Oct 6;167(2):419-432.e16.
Links:
Car-T Cells: Engineering Patients’ Immune Cells to Treat Cancers (National Cancer Institute/NIH)
Synthetic Biology for Technology Development (National Institute of Biomedical Imaging and Bioengineering/NIH)
Roybal Lab (University of California, San Francisco)
Roybal Project Information (NIH RePORTER)
NIH Support: Common Fund; National Cancer Institute
KRAS Targeted Cancer Strategy Shows Early Promise
Posted on by Dr. Francis Collins
Caption: Mutant KRAS protein (white) keeps switch (red/pink) open in active state for GTP (arrow). After treatment with ARS-1620 (blue), switch is trapped in inactive GDP-bound state.
Credit: Adapted from Cell. 2018 Jan 25;172(3):578-589.
Of the more than 1.7 million Americans expected to be diagnosed with cancer this year, nearly one-third will have tumors that contain at least one mutation in the RAS family of genes [1]. That includes 95 percent of pancreatic cancers and 45 percent of colon cancers. These mutations result in the production of defective proteins that can drive cancer’s uncontrolled growth, as well as make cancers resistant to therapies. As you might expect, RAS has emerged as a major potential target for fighting cancer. Unfortunately, it is a target that’s proven very difficult to “hit” despite nearly three decades of work by researchers in both the private and public sectors, leading NIH’s National Cancer Institute to begin The RAS Initiative in 2013. This important effort has made advances with RAS that have translational potential.
Recently, I was excited to hear of progress in targeting a specific mutant form of KRAS, which is a protein encoded by a RAS gene involved in many lung cancers and some pancreatic and colorectal cancers. The new study, carried out by a pharmaceutical research team in mouse models of human cancer, is the first to show that it is possible to shrink a tumor in a living creature by directly inhibiting mutant KRAS protein [2].
New ‘Liquid Biopsy’ Shows Early Promise in Detecting Cancer
Posted on by Dr. Francis Collins
Caption: Liquid biopsy. Tumor cells shed protein and DNA into bloodstream for laboratory analysis and early cancer detection.
Early detection usually offers the best chance to beat cancer. Unfortunately, many tumors aren’t caught until they’ve grown relatively large and spread to other parts of the body. That’s why researchers have worked so tirelessly to develop new and more effective ways of screening for cancer as early as possible. One innovative approach, called “liquid biopsy,” screens for specific molecules that tumors release into the bloodstream.
Recently, an NIH-funded research team reported some encouraging results using a “universal” liquid biopsy called CancerSEEK [1]. By analyzing samples of a person’s blood for eight proteins and segments of 16 genes, CancerSEEK was able to detect most cases of eight different kinds of cancer, including some highly lethal forms—such as pancreatic, ovarian, and liver—that currently lack screening tests.
In a study of 1,005 people known to have one of eight early-stage tumor types, CancerSEEK detected the cancer in blood about 70 percent of the time, which is among the best performances to date for a blood test. Importantly, when CancerSEEK was performed on 812 healthy people without cancer, the test rarely delivered a false-positive result. The test can also be run relatively cheaply, at an estimated cost of less than $500.
Snapshots of Life: A Van Gogh Moment for Pancreatic Cancer
Posted on by Dr. Francis Collins
Salt Lake City
Last year, Nathan Krah sat down at his microscope to view a thin section of pre-cancerous pancreatic tissue from mice. Krah, an MD/PhD student in the NIH-supported lab of Charles Murtaugh at the University of Utah, Salt Lake City, had stained the tissue with three dyes, each labelling a different target of interest. As Krah leaned forward to look through the viewfinder, he fully expected to see the usual scattershot of color. Instead, he saw enchanting swirls reminiscent of the famous van Gogh painting, The Starry Night.
In this eye-catching image featured in the University of Utah’s 2016 Research as Art exhibition, red indicates a keratin protein found in the cytoskeleton of precancerous cells; green, a cell adhesion protein called E-cadherin; and yellow, areas where both proteins are present. Finally, blue marks the cell nuclei of the abundant immune cells and fibroblasts that have expanded and infiltrated the organ as a tumor is forming. Together, they paint a fascinating new portrait of pancreatic ductal adenocarcinoma (PDAC), the most common form of pancreatic cancer.
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