Unlocking the
Mysteries of
Extracellular RNA

Once thought to exist only inside cells, RNA is
known to travel outside of cells and play a role in newly
discovered mechanisms of cell-to-cell communication.

This post originated as a press release from Linköping University.

The waste-management system of the cell appears to play an important role in the spread of Alzheimer’s disease in the brain. A new study, published in the prestigious scientific journal Acta Neuropathologica, has focused on small membrane-covered droplets known as exosomes. It was long believed that the main task of exosomes was to help the cell to get rid of waste products. In simple terms, they were thought of as the cell’s rubbish bags. However, our understanding of exosomes has increased, and we now know that cells throughout the body use exosomes to transmit information. It’s now known that the exosomes can contain both proteins and genetic material, which other cells can absorb.

The Linköping researchers have shown in the new study that exosomes can also transport toxic aggregates of the protein amyloid beta, and in this way spread the disease to new neurons. Aggregated amyloid beta is one of the main findings in the brains of patients with Alzheimer’s disease, the other being aggregates of the protein tau. As time passes, they form ever-increasing deposits in the brain, which coincides with the death of nerve cells. The cognitive functions of a person with Alzheimer’s disease gradually deteriorate as new parts of the brain are affected.

“The spread of the disease follows the way in which parts of the brain are anatomically connected. It seems reasonable to assume that the disease is spread through the connections in the brain, and there has long been speculation about how this spread takes place at the cellular level,” says Martin Hallbeck, associate professor in the Department of Clinical and Experimental Medicine at Linköping University and senior consultant of clinical pathology at Linköping University Hospital.

Cells became diseased
In a collaboration with researchers at Uppsala University, he and his co-workers have investigated exosomes in brain tissue from deceased persons. The research team at Linköping University found more amyloid beta in exosomes from brains affected by Alzheimer’s disease than in healthy controls. Furthermore, the researchers purified exosomes from the brains from people with Alzheimer’s disease, and investigated whether they could be absorbed by cells cultured in the laboratory.

“Interestingly, exosomes from patients were absorbed by cultured neurons, and subsequently passed on to new cells. The cells that absorbed exosomes that contained amyloid beta became diseased,” says Dr. Hallbeck.

The researchers treated the cultured neurons with various substances that prevent exosomes from being formed, released, or absorbed by other cells. They were able to reduce the spread of the aggregated amyloid beta between cells by disrupting the mechanism in these ways. The methods used in these laboratory experiments are not yet suitable for treating patients, but the discovery is important in principle.

“Our study demonstrates that it is possible to influence this pathway, and possibly develop drugs that could prevent the spreading. The findings also open up the possibility of diagnosing Alzheimer’s disease in new ways, by measuring the exosomes,” says Martin Hallbeck.

The research has received financial support from donors that include the Swedish Research Council, the Swedish Alzheimer’s Foundation, and the Swedish Brain Foundation.

Sinha MS, Ansell-Schultz A, Civitelli L, Hildesjö C, Larsson M, Lannfelt L, Ingelsson M & Hallbeck M. Alzheimer disease pathology propagation by exosomes containing toxic amyloid-beta oligomers. Acta Neuropathologica AOP 13 June 2018. doi: 10.1007/s00401-018-1868-1

Translation by George Farrants.

This commentary originally appeared as an Editor’s Choice in Science Translational Medicine. Thanks to STM and Steven Jay for permission to reprint here.

The sci-fi thriller I, Robot tells the story of robots attempting to take over the world based on their interpretation of the three governing laws of their programming. This plan is thwarted with the help of Sonny, a unique robot who can ignore the three laws due to being programmed differently. This movie illustrates how selective programming can be a powerful tool that can be used to turn a subset of a population against the rest. This same concept underlies the strategy of gene-directed enzyme prodrug therapy (GDEPT) for cancer, which involves specific delivery of a gene to cancer cells that allows for subsequent activation of a systemically administered prodrug into a toxic form only in cells where an enzyme encoded by the delivered gene is present. Several GDEPT strategies have advanced to clinical trials; however, the specificity and fidelity of gene delivery are still limiting factors to successful translation.

Toward addressing these limitations, Wang et al. describe the use of modified extracellular vesicles (EVs) for targeted delivery of mRNA to cancer cells overexpressing the HER2 receptor. EVs are nanoscale vesicles secreted by many cell types that have been co-opted for a variety of therapeutic applications. However, targeted delivery using EVs has been challenging, as has encapsulation of large nucleic acid cargo. To address cargo encapsulation, the authors applied a transfection-based approach to successfully load exogenous mRNA encoding for the enzyme HChrR6 into EVs. To address targeting, the authors created a novel chimeric protein consisting of a HER2 antibody fragment to target the receptor on cancer cells and the C1C2 domain of lactadherin, which interacts with the EV membrane. By mixing mRNA-loaded EVs with purified chimeric protein, the EVs were endowed with targeting capability for HER2-overexpressing cancer cells. Delivery of these EVs followed by systemic administration of the prodrug 6-chloro-9-nitro-5-oxo-5H-benzo-(a)-phenoxazine (CNOB) resulted in near complete growth arrest of orthotopically implanted HER2-overexpressing breast tumors in mice.

This report establishes a new and versatile approach for improving GDEPT that could be applied to a wide variety of cancers and other diseases. Significant barriers to translation of this approach remain, most notably the problem of scalability of EV-based approaches. However, the methods and strategy described are likely to have broad utility in further developing both GDEPT and therapeutic EVs.

Highlighted Article
J.-H. Wang, A. V. Forterre, J. Zhao, D. O. Frimannsson, A. Delcayre, T. J. Antes, B. Efron, S. S. Jeffrey, M. D. Pegram, A. C. Matin, Anti-HER2 scFv-directed extracellular vesicle-mediated mRNA-based gene delivery inhibits growth of HER2-positive human breast tumor xenografts by prodrug activation. Mol. Cancer Ther. (2018) 17:1133-1142. PMID:29483213 doi:10.1158/1535-7163.MCT-17-0827

Despite being one of the earliest known classes of non-coding RNA molecules, tranfer RNAs (tRNAs) are still notoriously difficult to study. The challenge is largely due to this molecule’s secondary structure, chemical modifications to its constituent nucleotides (see figure), and the multiplicity of tRNA genes. As the number of non-coding RNA datasets proliferates, it is becoming increasingly important for tRNA genes to be accurately annotated. In a recent study, Thomas Tuschl from Rockefeller University and colleagues tackled this problem by developing a new protocol for sequencing tRNAs. The new method enabled them to assemble an atlas of human tRNAs for other researchers to use in analyzing their non-coding RNA data.

Hydro-tRNA Sequencing
Transfer RNAs have thermodynamically stable secondary and tertiary structures, and their constituent nucleotides are highly modified by RNA editing. Both of these characteristics are problematic for traditional RNA sequencing methods. The key to the Tuschl lab’s protocol, called hydro-tRNA sequencing (hydro-tRNAseq), is a partial alkaline hydrolysis step that breaks the 60-100 nucleotide-long tRNA into smaller fragments with fewer RNA modifications. These fragments, 19-35 nucleotides in size, have weaker secondary structure and fewer RNA modifications per fragment than the parent tRNA.

Applying the method to short RNA extracted from human embryonic kidney (HEK293) cells resulted in an increase in the fraction of reads mapped to tRNA between 2% and 40%, depending on the depth of sequencing. The short fragment length also improved read accuracy per base compared to standard tRNA sequencing.

To develop a thorough and representative reference set of human tRNAs, the HEK293 dataset was subjected to iterative cycles of mapping to existing reference tRNAs followed by manual curation. In each round, all transcripts with an error distance (number of mismatches, insertions, and deletions) of 1-2 from a given tRNA were kept as candidate reference sequences if they could be attributed to a tRNA isoacceptor (i.e. a different tRNA that binds to the same amino acid). If not, assuming that other mismatches were caused by misidentifying a modified base, transcripts with more than 10% mismatches compared to reference were expanded into a set of all possible combinations of RNA modifications and included in the reference pool (see figure). This mapping and selection process was repeated until there were no longer any modified positions left with a mismatch frequency over 10% compared to reference.

Candidate pre-tRNA genes were obtained by mapping the final tRNA reference sequences back to the genome. Altogether, this analysis was able to account for 93% of the 114 million reads in the deepest library of HEK293 cells’ tRNAs.

tRNA Modification Sites

tRNA Modification Sites
The team identified sites of modification from the high frequency of mismatches during mapping caused by read errors there during reverse transcription. Here the reference nucleotide is at ring center, known modification outside the ring, and frequency of each nucleotide read at that site inside the ring.
Source: Cell Reports

The Added Power of SSB PAR-CLIP
Though hydro-tRNAseq greatly improved the reference dataset of human tRNAs, there was still a risk that it alone would miss pre-tRNAs expressed at low levels or processed quickly into mature tRNA. Previous efforts to assay that ephemeral population employed ChIP-seq of POLR3, the polymerase that transcribes all tRNA genes, but doing so assumed that polymerase binding always led to expression and complete processing. The Tuschl lab focused instead on SSB, a protein that binds to the 3′ end of pre-tRNAs, immunoprecipitating tRNAs crosslinked to SSB using a method called PAR-CLIP. As predicted, almost half of the reads from their SSB PAR-CLIP experiments mapped to pre-tRNAs. Combining SSB PAR-CLIP with hydro-tRNAseq allowed the team to better identify mature and pre-tRNAs with improved, accurate, nucleotide-level resolution.

This study supplies the community with several new and useful resources. Hydro-tRNAseq provides a new method to overcome many of the struggles of tRNA sequencing analyses. Combining this method with SSB PAR-CLIP enabled the construction of a comprehensive atlas of pre-tRNAs and mature tRNAs in humans. This methodology can now be applied to study the tRNA complement in other species to further dissect tRNA biology.

Tasos Gogakos T, Brown M, Garzia A, Meyer C, Hafner M, & Tuschl T. Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP. Cell Reports (2017) 20: 1463-1475. doi: 10.1016/j.celrep.2017.07.029