I don't know much about circRNAs so excuse my naiveness - I wonder if it could be used for gene replacement therapy in the future? Something like, if there is a stop codon somewhere in the middle of a gene, the small piece of circRNA, contains the correct version of that stop codon and is introduced into the cell. Next thing you know, that stop codon is by passed, as the transcription or translation machinery builds an entire good sequence using the DNA and the good code circRNA. Also, since they are resistant to degradation, they might be good shuttle vehicles for tiny 'good copy' exons.
I am not an expert in gene therapy, but I think getting the transcription or translation machinery to read the "good" copy instead of the stop codon would be the challenge there.
circRNA have so much value already as a way to diagnose disease — we're excited about just that powerful capability! Our understanding of circRNAs is just beginning, and it'll be interesting to see what other applications for them are invented.
While we have no immediate plans to hire out west, we are changing rapidly and that certainly could change in the future.
We'll be offering our test to patients through doctors and hospitals — imagine going for your annual checkup, and our test is ordered along with all of the other routine blood tests. This is the fastest route for us to be able to get our test onto the market and making a impact on people's lives.
I really think that with heart failure, we need the biomarker equivalent of somatic pre-cancerous DNA changes in cancer. But we also need (to steal from the psychiatrists), better endophenotyping, because many different aberrant states lead to very similar clinical syndromes of "heart failure".
A group, perhaps yours or in concert with yours, could both define the disease subsets based on biomarkers and then diagnose/prognose/inform treatment. Surely the same is true for other diseases, this is just one high-impact example.
We're developing tests around a recently discovered type of RNA called circular RNA. Tissue-specific circular RNAs are present in blood, and so that's how it's possible to use a blood test instead of having to go to tissue like you would with traditional mRNA-seq.
I don't quite understand how just using circ. RNAs would give you better predictions. From the little I've read about circ. RNAs is that they can form from normal RNAs and possibly function in sequestering regulatory small-RNAs.
So you can detect circ. RNA that come from specific tissues and partition those reads out as expression for those tissues? What kind of coverage do you need to do that? Are mRNA circularization rates consistent among different genes?
Hi daemonk,
Jon Armstrong from Cofactor Genomics here. You hit on some excellent points.
So you can detect circ. RNA that come from specific tissues and partition those reads out as expression for those tissues?
In reality, we are detecting circRNA that arises or predominates during a specific disease state and then partition those reads out as a signal for the disease state. On a related note, the circRNA molecule resists degradation much more than linear RNA molecules, leading to a longer half-life and less variability in signal from tissue, plasma, and exosomes.
What kind of coverage do you need to do that?
Currently, 100's of million of reads need to be generated to just detect the highest expressed circRNAs. We have a patent pending circRNA enrichment technology (supported by a large NIH phase II grant) that increases the ratio of circRNA in the total RNA pool by logs, thus one could sequence logs less reads for the same level of detection. The coverage cutoff for detection can be "tuned" for assay sensitivity.
Are mRNA circularization rates consistent among different genes?
CircRNAs do not seem to be translated into proteins and probably perform multiple regulatory functions. Also, the level of a linear form does not correlate with the level of the circular form for the same gene. As with linear mRNA production, which is not consistent from gene to gene or tissue to tissue, we observe the same phenomenon with circRNA.
Finally a topic on hackernews that I am getting my PhD in..! Anyway, do you have any data indicating what percentage of circRNA is "free" in the plasma versus inside of other entities like platelets or extracellular vesicles (exosomes)?
The work with these molecules is early enough, that to my knowledge, there are no studies of this type that are published. And, in fact one could pose the same question for linear mRNA and ncRNA in exosomes (or ESVs). Most of the studies are on miRNA in ESVs, however we have done considerably work internally on characterizing long- mRNA and ncRNA in exosomes. These vesicles are fascinating!
Circular RNAs are really "hot" these days. But, one should keep in mind that the amount of virtually all circular RNAs is lower in cancer (compared to non-cancerous adjacent normal tissue), thus they are not very promising as biomarkers. Also, their biological role is unclear. We did comprehensive literature review on this topic and found nothing truly convincing.
That some circRNAs are lower in cancer than in normal tissue is a reliably detectable difference and is precisely what makes them an excellent biomarker.
I am aware of this study. Funny, how they show expression in deltaCT to make it appear higher in cancer ;). But regardless, the marker has a specificity of 0.62 - really that excellent? Such a high false-positive rate does not belong anywhere near a patient sample.
Our goal is to add additional markers to current candidates using our enrichment tech. It helps to remember that up until the ILMN/Solexa machine came online around 2005-6, we could not reliably detect (statistically) MAFs in heterogenous tumor samples below about 20% on the 454 platform (depending on how much cash you threw at the sample). Point is, our enrichment platform allows a deep dive into signals that have yet to be identified as reliable and low variance biomarkers.
Are there some key publications you could point us at? I've been out of the bioimformatics game for a couple of years and I'm always curious to see where the state of the art is at.
I'm curious why you are going through doctors and not direct to consumers at the begging? I understand FDA might force you to limit your marketing claims, however you now need to convince both physicians and consumers of the benefits of these tests. No? Where as I would imagine there will be enough early-adopters in the consumer space who'd be happy to pay for a test like this.
You can later move to the physicians space and assuringly get insurance companies cover the costs, when you have been more stablished.
Would love to learn more about your thinking and strategy here.
It's the fastest way for us to get this powerful diagnosis technology on the market and helping people.
We believe that our RNA test can become a routine part of a doctor's visit, both as an early indicator of disease and — if there is disease — as a means to monitor the effectiveness of treatment.
