Cells can communicate with one another to coordinate essential processes such as development, growth, and repair through the release of signaling intermediates. One class of signaling intermediates are extracellular vesicles (EVs) that contain nucleic acids and proteins that mediate cell-cell communication. In cancer, the cargo of these EVs is altered in order to promote tumor progression, improving the ability to proliferate, invade, metastasize, and develop drug resistance, among other cancer characteristics. While most EVs range in diameter from 50 nanometers to one micron, there has been an increasing interest in smaller particles that might also be released from cells and contribute to cancer. Only recently has technology evolved enough to detect these previously undiscernible nanoparticles. Qin Zhang, PhD, Robert Coffey, MD, and colleagues were motivated by previous advances in the lab regarding the role of EVs in cancer to determine if smaller particles existed with similar functions. Dr. Coffey and his team discovered a new nanoparticle, termed the supermere, with functional relevance not only to cancer but to many other diseases, resulting in a publication at the end of 2021 in Nature Cell Biology (Zhang Q et al. 2021).
EVs can be isolated from a biofluid or cell culture media by spinning (centrifuging) at high speeds to separate the vesicles and other high density non-vesicular components from the surrounding liquid. This solid pellet can then be subjected to density gradient centrifugation, allowing for vesicles to reach their buoyant density, while non-vesicular components settle in the higher density fractions. Qin Zhang in the Coffey lab proposed that the supernatant after pelleting vesicles might contain other nanoparticles important to cancer. By conducting a longer spin, Zhang isolated a nanoparticle, called the exomere, previously identified and described by the Lyden group through use of a non-centrifugation-based procedure called asymmetric flow field-flow fractionation (AF4) that isolates particles of different sizes (Zhang H et al. 2018). While working to characterize these exomere nanoparticles, Zhang and colleagues discovered that they can induce epidermal growth factor (EGFR) signaling when carrying the EGFR ligand amphiregulin as cargo, as detailed in Cell Reports (Zhang Q et al. 2019). Changes in EGFR signaling are a hallmark of some kinds of cancer, including colorectal cancer, a focus of studies in the Coffey lab.
With this finding as a basis, Zhang conducted a higher speed spin for a longer period of time using the supernatant of exomeres to discover yet another nanoparticle, the supermere, which is the subject of the lab’s most recent publication. A careful examination of exomeres, supermeres, and EVs by the Coffey lab revealed that all three particles are distinct in their composition and functional properties. While EVs have a lipid bilayer, supermeres were found to have minimal lipid content, but were enriched in RNA and RNA-binding proteins. Not only were supermeres smaller than exomeres and EVs, they also had higher uptake into a variety of organs when injected into mice, hinting that both cargo and size might contribute to the overall biodistribution of these particles. One surprising finding was the substantial uptake of supermeres in the brain as compared to EVs and exomeres. For decades, researchers have been devising ways for therapeutics to cross the blood-brain barrier. Now supermeres are a new candidate to act as a vehicle for therapeutic delivery.
When comparing the protein content of exomeres, supermeres, small EVs (sEVs), and other non-vesicular material, the researchers discovered that they all had distinct profiles with clinical relevance. The most abundant protein packaged into supermeres was TGFBi, which the researchers found to be prognostic in colorectal cancer (CRC) patients. Patients with high levels of TGFBi had decreased overall survival and progression-free survival rate. In fact, TGFBi was present at higher levels in all the nanoparticle classes isolated from the blood plasma of cancer patients as compared to healthy controls, suggesting that a liquid biopsy focused on TGFBi levels might be helpful for detection and monitoring of colorectal cancer. Supermeres were also enriched in proteins associated with the pathogenesis of Alzheimer’s, such as the amyloid precursor protein (APP).
Along with distinct proteomic profiles, supermeres also had differences in expression of small RNAs. Supermeres contained more small RNA than all the other fractions combined. Supermeres were enriched in small nuclear RNAs (snRNAs) while tRNAs, key intermediates of protein synthesis, were less abundant when compared to cells, sEVs, and exomeres. One of the most abundant small RNAs in supermeres was miR-1246, which was found to be upregulated in cancerous compared to healthy tissue. Supermeres were also enriched in RNA-binding proteins such as Ago2, again particularly in the diseased tissue.
Beyond simply characterizing the nanoparticle and EV classes, the researchers endeavored to find functional properties of supermeres. One aspect that distinguishes cancer cells from normal cells is an increase in glucose uptake without full utilization of the citric acid cycle to produce energy, which results in a buildup of lactate, called the Warburg effect. Adding supermeres to CRC cells increased their secretion of lactate, suggesting that supermeres can alter tumor metabolism. Also, supermeres from drug-resistant CRC cell lines were found to transfer that drug resistance when added to drug-sensitive cells. If tumor cells secrete supermeres into the tumor microenvironment, thereby shifting nearby cells towards a cancerous phenotype, then targeting these supermeres could reduce tumor growth and spread. Besides the arena of cancer, supermeres were also found to affect the liver. Injection of supermeres into mice led to a reduction in liver lipids and glycogen, which can contribute to a variety of liver diseases.
While there is still much to learn about supermeres, such as how they are made and released by cells, the Coffey lab has made important strides in characterizing this new nanoparticle. Their discovery that much of the cargo previously believed to be in other particles such as small extracellular vesicles are actually in exomeres and supermeres has prompted other researchers in the field to investigate and understand the complexity and potential heterogeneity of these nanoparticle classes.
Zhang Q et al. Supermeres are functional extracellular nanoparticles replete with disease biomarkers and therapeutic targets. Nat Cell Biol (2021) 23: 1240-1254. doi: 10.1186/10.1038/s41556-021-00805-8 PMID: 34887515.
Zhang H et al. Identification of distinct nanoparticles and subsets of extracellular vesicles by asymmetric flow field-flow fractionation. Nat Cell Biol (2018) 20: 332-343. doi: 10.1038/s41556-018-0040-4 PMID: 29459780.
Complementary commentaries in the Journal of Extracellular Biology produced by the Coffey lab (Jeppesen DK et al. 2022) and a collaboration among Juan Pablo Tosar, Alfonso Cayota, and Kenneth Witwer (Tosar JP et al. 2022) discuss the potential heterogeneity of nanoparticle classes. You can follow their scientific exchange during an #EVclub online journal club to learn more (video link).
Jeppesen DK, Zhang Q, Franklin JL & Coffey RJ. Are supermeres a distinct nanoparticle? J Extracellular Bio (2022) 1: e44. doi: 10.1002/jex2.44.
Tosar JP, Cayota A, Witwer K. Exomeres and supermeres: Monolithic or diverse? J Extracellular Bio (2022) 1: e45. doi: 10.1002/jex2.45.