exRNA Research
in Cell Press

Cell Press recently published 18 articles from the ERCC, a capstone to 5 years of research during Stage 1.

Extracellular vesicles (EVs) regulate many processes in the healthy body. They also play a role in cancer, sending signals between cells in the tumor microenvironment. EVs can stimulate tumor cell migration, invasion, blood vessel growth, immune response, and cell survival, as well as metastasis. However, we know little about the cargo of these EVs that play such diverse roles. Analysis of vesicle cargo can shed light on the molecular mechanisms of vesicle biology and be helpful in disease diagnosis and prognosis.

I am lucky to be a member in Jan Lötvall’s lab in Gothenburg, Sweden, which pioneered the field of extracellular vesicles with the early discovery of exosomes shuttling RNA between cells. An exciting collaboration with Yong Song Gho from POSTECH in South Korea led us to develop a new approach to isolate vesicles from human tumor tissues. Using this technology, we were able to isolate and characterize subpopulations of extracellular vesicles from melanoma metastatic tissue. We just published our findings in the Journal of Extracellular Vesicles. Jan Lötvall also discussed them in a recent ERCC webinar.

Finding extracellular vesicles in tumor tissue with TEM

Our first challenge was to find vesicles in metastatic melanoma tumor tissues. Using transmission electron microscopy, we showed that the tumor microenvironment is a complex world composed of different types of cells and structures with vesicles present between them.

TEM of extracellular vesicles in tumor tissue
Transmission electron micrograph of melanoma metastatic tissue showing a large tumor cell and two lymphocytes. Black stain, possibly melanin, is clearly visible inside the melanoma cells, which are recognizable from their characteristic cell membrane. The higher magnification image shows vesicles (red arrows) in the extracellular space.

In this study, we performed a detailed proteomics analysis of EVs isolated from metastatic melanoma tissues from 27 patients. We identified numerous new EV proteins, including potential biomarkers for metastatic melanoma.

Tumor tissue vs. Cell lines

Studying extracellular vesicles in tumor tissues is important, because, compared to cell lines, tumor tissues more closely approximate the situation in vivo. EVs from tumor tissue are more likely to represent the full array of vesicle behaviors and populations in the tumor microenvironment. Furthermore, to develop a non-invasive test for cancer, we must use biofluids such as circulating plasma, where vesicles from all over the body intermingle. A proteomic snapshot of vesicles isolated directly from tumor tissue can help target the search for disease-specific biomarker in that complex mixture. We trust the tools and experiments developed in this work will contribute to our field’s understanding of EV function in complicated tissues such as the metastatic melanoma tumor.

Crescitelli R, Lässer C, Jang SC, Cvjetkovic A, Malmhäll C, Karimi N, Höög J.L, Johansson I, Fuchs J, Thorsell A, Gho YS, R, Olofsson Bagge R, Lötvall J Subpopulations of extracellular vesicles from human metastatic melanoma tissue identified by quantitative proteomics after optimized isolation. Journal of Extracellular Vesicles 9:1, 1722433 doi: 10.1080/20013078.2020.1722433.

This work was supported by the Swedish Research Council (K2014-85X-22504-01-3), the Swedish Heart and Lung Foundation (20120528), the Swedish Cancer Foundation (CAN2014/844), and the Knut och Alice Wallenberg Foundation (Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden).

Flow cytometry (FC) is a powerful method for counting single cells and measuring their molecular components. There is increasing interest in applying flow cytometry to the analysis of extracellular vesicles (EV), but EVs are orders of magnitude smaller than the cells for which FC instruments and protocols were originally designed. To catalyze the development of new instruments and assays for EV flow cytometry, three scientific societies came together to form the EV Flow Cytometry Working Group (evflowcytometry.org):

  • ISEV, the International Society of Extracellular Vesicles
  • ISAC, the International Society for Advancement of Cytometry, and
  • ISTH, the International Society for Thrombosis and Haemostasis.

The working group first performed two standardization studies, distributing standards and samples to EV-FC laboratories worldwide to enable an objective comparison of methods, instruments, controls, and analytical tools. Those initial studies led to the realization that a standard framework for reporting experimental results is essential.

The working group has now published that standard in the Journal of Extracellular Vesicles. It is called MIFlowCyt-EV, the Minimum Information to report for Flow Cytometry studies of Extracellular Vesicles. The MIFlowCyt-EV reporting framework incorporates the existing Minimum Information for Studies of EVs (MISEV) guidelines and Minimum Information about a Flow Cytometry experiment (MIFlowCyt) standard.

The figure above outlines the 7 main categories of information included in the framework. Not all EV-FC experiments will involve all seven areas, but any area touched on by an experiment should follow the MIFlowCyt-EV reporting guidelines.

MIFlowCyt-EV provides a structure for sharing EV-FC results, but it does not mandate the use of specific instruments or protocols, since the field of EV flow cytometry is still rapidly evolving. MIFlowCyt-EV accommodates this evolution, while providing information needed to evaluate and compare different approaches. Consistent reporting of the results of EV flow cytometry studies will improve the ability to quantitatively compare results from different laboratories and support the development of new instruments and assays for improved measurement of EVs.

Welsh JA, et al. MIFlowCyt-EV: a framework for standardized reporting of extracellular vesicle flow cytometry experiments. J Extracell Vesicles (2020) doi: 10.1080/20013078.2020.1713526

Illinois researchers developed a method to detect microRNA cancer markers with single-molecule resolution, a technique that could be used for liquid biopsies.

From left: Taylor Canady, postdoctoral scholar; Andrew Smith, professor of bioengineering; Nantao Li, graduate student; Lucas Smith, postdoctoral scholar; and Brian Cunningham – professor of Electrical and Computer Engineering; director of Micro and Nanotechnology Laboratory.
Photo by L. Brian Stauffer

Thanks to the University of Illinois News Bureau for allowing us to share this article here.

CHAMPAIGN, Ill. — A fast, inexpensive yet sensitive technique to detect cancer markers is bringing researchers closer to a liquid biopsy – a test using a small sample of blood or serum to detect cancer, rather than the invasive tissue sampling routinely used for diagnosis.

Researchers at the University of Illinois developed a method to capture and count cancer-associated microRNAs, or tiny bits of messenger molecules that are exuded from cells and can be detected in blood or serum, with single-molecule resolution. The team published its results in the Proceedings of the National Academy of Science.

“Cancer cells contain gene mutations that enable them to proliferate out of control and to evade the immune system, and some of those mutations turn up in microRNAs,” said study leader Brian Cunningham, an Illinois professor of electrical and computer engineering. Cunningham also directs the Holonyak Micro and Nanotechnology Lab at Illinois.

“There are specific microRNA molecules whose presence and concentration is known to be related to the presence and aggressiveness of specific types of cancer, so they are known as biomarkers that can be the target molecule for a diagnostic test,” he said.

Cunningham’s group developed a technique named Photonic Resonator Absorption Microscopy to capture and count microRNA biomarkers. In collaboration with professor Manish Kohli at the Moffitt Cancer Center in Florida, they tested PRAM on two microRNAs that are known markers for prostate cancer.

They found it was sensitive enough to detect small amounts that would be present in a patient’s serum, yet also selective enough to detect the marker among a cocktail of molecules that also would be present in serum.

“One of the main challenges of biosensing is to maintain sensitivity and selectivity at the same time,” said Nantao Li, a graduate student and co-first author. “You want it to be sensitive enough to detect very small amounts, but you don’t want it to pick up every RNA in the blood. You want this specific sequence to be your target.”

Each dot seen in this PRAM image represents one microRNA that has bound to the sensor.
Image courtesy of Nantao Li


PRAM achieves both qualities by combining a molecular probe and a photonic crystal sensor. The probe very specifically pairs to a designated microRNA and has a protective cap that comes off when it finds and binds to the target biomarker. The exposed end of the probe can then bind to the sensor, producing a signal visible through a microscope.

Each individual probe that binds sends a separate signal that the researchers can count. This means researchers are able to detect much smaller amounts than traditional methods like fluorescence, which need to exceed a certain threshold to emit a measurable signal. Being able to count each biomarker also carries the added benefit of allowing researchers to monitor changes in the concentration of the biomarker over time.

“With PRAM, we squirt a sample into a solution and get a readout within two hours,” said postdoctoral researcher Taylor Canady, a co-first author of the study. “Other technologies that produce single-molecule readouts require extra processing and additional steps, and they require a day or more of waiting. PRAM seems like something that could be much more feasible clinically. In addition, by using an optical signal instead of fluorescence, we could one day build a miniaturized device that doesn’t need a trained laboratory technician.”

The PRAM approach could be adapted to different microRNAs or other biomarkers, the researchers say, and is compatible with existing microscope platforms.

“This approach makes the idea of performing a ‘liquid biopsy’ for low-concentration cancer-related molecules a step closer to reality,” Cunningham said. “This advance demonstrates that it is possible to have an inexpensive and routine method that is sensitive enough to require only a droplet of blood. The results of the test might tell a physician whether a regimen of chemotherapy is working, whether a person’s cancer is developing a new mutation that would make it resistant to a drug, or whether a person who had been previously treated for cancer might be having a remission.”

The Carl R. Woese Institute for Genomic Biology at the U. of I. and the National Institutes of Health supported this work. Illinois chemistry professor Yi Lu and bioengineering professor Andrew Smith were coauthors of the work.

Canady TD, Li N, Smith LD, Lu Y, Kohli M, Smith AM & Cunningham BT. Digital-resolution detection of microRNA with single-base selectivity by photonic resonator absorption microscopy. Proc Natl Acad Sci U S A. (2019) 116:19362-19367. doi: 10.1073/pnas.1904770116 PMID: 31501320