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colorectal cancer

New Approach to ‘Liquid Biopsy’ Relies on Repetitive RNA in the Bloodstream

Posted on by Lawrence Tabak, D.D.S., Ph.D.

A nurse draws blood from the arm of a patient. To the side, RNA floats inside a vial of blood. The vial is labeled RNA from cancer cells.
Researchers have identified segments of noncoding RNA circulating in the blood that are early signs of cancer. Credit: Modified from Adobe Stock/ Andrey Popov; Donny Bliss, NIH

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.


[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).


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

New 3D Atlas of Colorectal Cancer Promises Improved Diagnosis, Treatment

Posted on by Lawrence Tabak, D.D.S., Ph.D.

Brightly colored light microscopy showing locations for DNA, Pan-cytokeratin, alpha-SMA, CD4, CD20, CD31, Glandular, Solid, Mucinous
Caption: Tissue from a colorectal cancer. The multi-colored scale (top right) reveals layers of hidden information, including types of tissue and protein. Credit: Sorger Lab, Harvard Medical School, Cambridge, MA

This year, too many Americans will go to the doctor for tissue biopsies to find out if they have cancer. Highly trained pathologists will examine the biopsies under a microscope for unusual cells that show the telltale physical features of a suspected cancer. As informative as the pathology will be for considering the road ahead, it would be even more helpful if pathologists had the tools to look widely inside cells for the actual molecules giving rise to the tumor.

Working this “molecular information” into the pathology report would bring greater diagnostic precision, drilling down to the actual biology driving the growth of the tumor. It also would help doctors to match the right treatments to a patient’s tumor and not waste time on drugs that will be ineffective.

That’s why researchers have been busy building the needed tools and also mapping out molecular atlases of common cancers. These atlases, really a series of 3D spatial maps detailing various biological features within the tumor, keep getting better all the time. That includes the comprehensive atlas of colorectal cancer just published in the journal Cell [1].

This colorectal atlas comes from an NIH-supported team led by Sandro Santagata, Brigham and Women’s Hospital, Boston, and Peter Sorger, Harvard Medical School, Cambridge, MA, in collaboration with investigators at Vanderbilt University, Nashville, TN. The colorectal atlas joins their previously published high-definition map of melanoma [2], and both are part of the Human Tumor Atlas Network that’s supported by NIH’s National Cancer Institute.

What’s so interesting with the colorectal atlas is the team combined traditional pathology with a sophisticated technique for imaging single cells, enabling them to capture their fine molecular details in an unprecedented way.

They did it using a cutting-edge technique known as cyclic immunofluorescence, or CyCIF. In CyCIF, researchers use many rounds of highly detailed molecular imaging on each tissue sample to generate a rich collection of molecular-level data, cell by cell. Altogether, the researchers captured this fine-scale visual information for nearly 100 million cancer cells isolated from tumor samples representing 93 individuals diagnosed with colorectal cancer.

With this single-cell information in hand, they next created detailed 2D maps covering the length and breadth of large portions of the colorectal cancers under study. Finally, with the aid of first author Jia-Ren Lin, also at Harvard Medical School, and colleagues they stitched together their 2D maps to produce detailed 3D reconstructions showing the length, breadth, and height of the tumors.

This more detailed view of colorectal cancer has allowed the team to explore differences between normal and tumor tissues, as well as variations within an individual tumor. In fact, they’ve uncovered physical features that had never been discovered.

For instance, an individual tumor has regions populated with malignant cells, while other areas look less affected by the cancer. In between are transitional areas that correspond to molecular gradients of information. With this high-resolution map as their guide, researchers can now study what this all might mean for the diagnosis, treatment, and prognosis of colorectal cancer.

The atlas also shows that the presence of immune cells varies dramatically within a single tumor. That’s an important discovery because of its potential implications for immunotherapies, in which treatments aim to unleash the immune system in the fight against cancer.

The maps also provide new insights into tumor structure. For example, scientists had previously identified what they thought were 2D pools of a mucus-like substance called mucin with clusters of cancer cells suspended inside. However, the new 3D reconstruction make clear that these aren’t simple mucin pools. Rather, they are cross sections of larger intricate caverns of mucin interconnected by channels, into which cancer cells make finger-like projections.

The good news is the researchers already are helping to bring these methods into the cancer clinic. They also hope to train other scientists to build their own cancer atlases and grow the collection even more.

In the meantime, the team will refine its 3D tumor reconstructions by integrating new imaging technologies and even more data into their maps. It also will map many more colorectal cancer samples to capture the diversity of their basic biology. Also of note, having created atlases for melanoma and colorectal cancer, the team has plans to tackle breast and brain cancers next.

Let me close by saying, if you’re between the ages of 45 and 75, don’t forget to stay up to date on your colorectal cancer screenings. These tests are very good, and they could save your life.


[1] Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Lin JR, Wang S, Coy S, Chen YA, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S, Sorger PK. Cell. 2023 Jan 19;186(2):363-381.e19.

[2] The spatial landscape of progression and immunoediting in primary melanoma at single-cell resolution. Nirmal AJ, Maliga Z, Vallius T, Quattrochi B, Chen AA, Jacobson CA, Pelletier RJ, Yapp C, Arias-Camison R, Chen YA, Lian CG, Murphy GF, Santagata S, Sorger PK. Cancer Discov. 2022 Jun 2;12(6):1518-1541.


Colorectal Cancer (National Cancer Institute/NIH)

Human Tumor Atlas Network (NCI)

CyCIF-Cyclic Immunofluorescence (Harvard Medical School, Cambridge, MA)

Sandro Santagata (Brigham and Women’s Hospital, Boston)

Peter Sorger (Harvard Medical School)

Jia-Ren Lin (Harvard Medical School)

NIH Support: National Cancer Institute; National Institute of General Medical Sciences; National Institute of Diabetes and Digestive and Kidney Diseases

New Target for Cancer Immunotherapy: Exosomes

Posted on by Dr. Francis Collins

It was once a central tenet of biology that RNA molecules did their work inside the cell. But it’s now clear that RNA molecules are also active outside the cell, with potentially major implications for our health. To learn more about these unrecognized roles, the NIH Common Fund has launched the Extracellular RNA (exRNA) Communication Program.

This month, members of this research consortium described their latest progress in unraveling the secrets of exRNA in a group of 18 papers in the Cell family of journals. And it’s not just RNA that the consortium is studying, it’s also proteins. Among the many exciting results just published is the serendipitous discovery that proteins carried inside tiny, bubble-like vesicles, called exosomes, may influence a cancer’s response to immunotherapy [1]. The work sheds light on why certain cancers are resistant to immunotherapy and points to new strategies for unleashing the immune system in the fight against cancer.

The new findings center on a type of immunotherapy drugs known as checkpoint inhibitors. They are monoclonal antibodies produced by industry that can boost the immune system’s ability to attack and treat cancer.

One of those antibodies specifically targets a protein, called PD-1, on the surface of certain immune cells. When PD-1 binds a similarly named protein, called PD-L1, on the surface of another cell, the interaction prevents immune cells from attacking. Some tumors seem to have learned this and load up on PD-L1 to evade the immune system.

That’s where checkpoint inhibitors come in. By blocking the interaction between PD-1 and PD-L1, the treatment removes a key check on the immune system, allowing certain immune cells to wake up and attack the tumor.

Checkpoint inhibitors work better in some cancer types than in others. In melanoma, for example, up to about 30 percent of patients respond to checkpoint inhibitor therapy. But in prostate cancer, response rates are in the single digits.

Researchers led by Robert Blelloch, a member of the exRNA consortium and a scientist at the University of California, San Francisco, wanted to know why. He and his team looked for clues in RNA within the cells taken from immunotherapy-resistant prostate cancers.

As published in Cell, the researchers got their first hint of something biologically intriguing in an apparent discrepancy in their data. As they expected from prior work, PD-L1 protein was present in the treatment-resistant cancers. But the PD-L1 messenger RNAs (mRNA), which serve as templates for producing the protein, told an unexpected story. The resistant cancer cells made far more PD-L1 mRNAs than needed to produce the modest levels of PD-L1 proteins detected inside the cells.

Where was the missing PD-L1? Blelloch’s team found it in exosomes. The cancer cells were packaging large quantities of the protein inside exosomes and secreting them out of the cell to other parts of the body.

In additional studies with a mouse model of prostate cancer, the researchers found that those PD-L1-packed exosomes travel through the blood and lymphatic systems to lymph nodes, the sites where immune cells become activated. Once there, PD-L1-laden exosomes put the immune system to sleep, preventing certain key cells from locating and attacking the cancer, including the primary tumor and places where it may have spread.

In important follow up studies, the researchers edited two genes in cancer cells to prevent them from producing exosomes. And, in the absence of exosomes, the cells no longer formed tumors. Importantly, both edited and unedited cells still produced PD-L1, but only those that exported PD-L1 in exosomes disarmed the immune system. Studies in a mouse model of immunotherapy-resistant colorectal cancer yielded similar results.

The new evidence suggests that blocking the release of PD-L1 in exosomes, even temporarily, might allow the immune system to launch a successful and sustained attack against a cancer.

Blelloch notes that many intriguing questions remain. For example, it’s not yet clear why antibodies that target PD-L1 on cancer cells don’t disable PD-L1 found in exosomes. The good news is that the new findings suggest it may be possible to find small molecules that do target PD-L1-packed exosomes, unleashing the immune system against cancers that don’t respond to existing checkpoint inhibitors. In fact, Blelloch’s team is already screening for small molecules that might fit the bill.

Since its launch about five years ago, the exRNA Communication Program has published an impressive 480 peer-reviewed papers, including the latest work in the Cell family of journals. I’d encourage readers to click on some of the other excellent work. I hear that another batch of papers will be published later this year.


[1] Suppression of exosomal PD-L induces systemic anti-tumor immunity and memory. Poggio M, Hu T, Pai CC, Chu B, Belair CD, Chang A, Montabana E, Lang UE, Fu Q, Fong L, Blelloch R. Cell. 2019 Apr 4;177(2):414-427.


Video: Unlocking the Mysteries of RNA Communication (Common Fund/NIH)

Immunotherapy to Treat Cancer (National Cancer Institute/NIH)

Blelloch Lab (University of California, San Francisco)

NIH Support: Common Fund; National Cancer Institute; National Center for Advancing Translational Sciences; National Heart, Lung, and Blood Institute; National Institute on Drug Abuse

Are Some Tumors Just ‘Born to Be Bad’?

Posted on by Dr. Francis Collins

Human Colon Cancer Cells

Caption: Human colon cancer cells.
Credit: National Cancer Institute, NIH

Thanks to improvements in screening technologies and public health outreach, more cancers are being detected early. While that’s life-saving news for many people, it does raise some important questions about the management of small, early-stage tumors. Do some tumors take a long time to smolder in their original location before they spread, or metastasize, while others track to new, distant, and dangerous sites early in their course? Or, as the authors of a new NIH-funded study put it, are certain tumors just “born to be bad”?

To get some answers, these researchers recently used genomic data from 19 human colorectal tumors (malignant and benign) to model tumor development over time [1]. Their computer simulations showed that malignant tumors displayed distinctive spatial patterns of genetic mutations associated with early cell mobility. Cell mobility is a prerequisite for malignancy, and it indicates an elevated risk of tumors invading the surrounding tissue and spreading to other parts of the body. What’s more, the team’s experimental work uncovered evidence of early abnormal cell movement in more than half of the invasive tumors.

Much more remains to be done to validate these findings and extend them to other types of cancer. But the study suggests that spatial mutation patterns may someday prove useful in helping decide whether to pursue aggressive treatment for early-stage cancer or opt for careful monitoring instead.

KRAS Targeted Cancer Strategy Shows Early Promise

Posted on by Dr. Francis Collins

KRAS in active and inactive states

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].

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