4 ms·

I've been working on this area for quite long, and I think it's just a matter of time it becomes huge. Right now, a major roadblock is that single-cell RNA-seq,

by nextos 4y ago

I've been working on this area for quite long, and I think it's just a matter of time it becomes huge. Right now, a major roadblock is that single-cell RNA-seq, which may also give paired TCR alpha and beta chain data, is too expensive compared to bulk TCR-seq. The latter has limited resolution and more technical variability. However, Microsoft Research has a preprint that employs bulk TCR-seq where they are able to detect Lyme, which is particularly difficult to do using antibody assays and often mistaken for multiple sclerosis: https://www.medrxiv.org/content/10.1101/2021.07.30.21261353v2 https://www.medrxiv.org/content/10.1101/2021.07.30.21261353v... AFAIK, there are a few startups in stealth mode and non-stealth mode collecting big repertoire datasets. In those datasets, one can even measure the effects of vaccinations that occurred decades ago.

panabee 4y ago
what's the approximate cost difference between scRNA-seq and bulk TCR-seq? does the cost curve suggest that scRNA-seq costs will reach cost parity with bulk TCR-seq, or become more practical, within X years? conversely, do you see a way for bulk TCR-seq to overcome issues with resolution and variability? from the outside, it seems like sequencing is such a fundamental piece of understanding the human body yet technology seems incredibly limiting. it's amazing what scientists have discovered so far. imagine what happens if we can help people observe cells more affordably and more accurately.
- jostmey 4y ago
  Bulk TCR sequencing cost around $500 to $1000 and captures under a million T cells. scRNA Seq costs around $10,000 and captures under ten thousand T cells. The price of sequencing is falling exponentially so my numbers can be out of date
  - nextos 4y ago
    These figures are approximately right. We've been able to bring the cost of single-cell RNA-seq + TCR-seq runs down to $3000 by doing targeted gene expression, which requires less reads. Besides, some newer microfluidics platforms are able to yield more cells, close to 2e4. I would say that the major limiting factor is the microfluidics platform. Ideally, we would require something that has a yield within the same order of magnitude of bulk methods. To address this limitation, one can e.g. pre-sort activated cells. Otherwise, the number of receptors is typically not enough to be able to observe meaningful statistical patterns.
    - gww 4y ago
      Parse biosciences and companies have developed methods to perform TCR sequencing without the microfluidics and it will be interesting to see how well it performs. These methods are all based on permeabilizing the cell and keeping it intact instead of encapsulating the in a droplet and then lysing it.
genomer 4y ago
Microsoft Research was a partner in the joint collaboration. Pretty sure this was the research that culminated in the T-Detect Lyme product that Adaptive Biotech launched last year (definitely some Adaptive representation in the publication). https://investors.adaptivebiotech.com/news-releases/news-release-details/adaptive-biotechnologies-launches-t-detecttm-lyme-new-t-cell https://investors.adaptivebiotech.com/news-releases/news-rel...
m463 4y ago
I wonder if low-hanging fruit is just "immune system health". train on healthy vs unhealthy immune systems and give a status bar. I've read that healthy individuals don't get cancer because their body nips it in the bud. Why couldn't we just figure out if people are pre-cancer (susceptible), like pre-diabetes?
- genomer 4y ago
  Age is probably the biggest influence on a "healthy" immune system. I haven't kept up with recent research, but if memory serves the immune repertoire (diversity of T and B cell receptors) decreases essentially linearly with age. Here's some supporting research from a quick search. https://journals.aai.org/jimmunol/article/192/6/2689/1552 https://journals.aai.org/jimmunol/article/192/6/2689/1552 Edit: some fun but possibly pontificating tangents This seems to be part of the reason why vaccines have had relatively poorer efficacy in elderly populations. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901832/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901832/ https://www.nature.com/articles/s41586-021-03739-1 https://www.nature.com/articles/s41586-021-03739-1 I'm hopeful that cancer and immune profiling will be able to be used in tandem to (1) identify cancer early and (2) identify gaps in the immune repertoire to facilitate (3) design of antibodies that specifically target the cancer.
  - nextos 4y ago
    There's a huge variability in the age of thymic involution. Some people have a relatively active thymus at age 50 or 60, whereas in others it has switched off by age 25 or 30. For those not familiar with immunology, the thymus is what populates your immune system with brand new T cells equipped with freshly selected T cell receptors. This suggests interesting anti-aging opportunities, such as artificial thymi to repopulate your immune system and keep a healthy and diverse repertoire.
    - panabee 4y ago
      unrelated but spurred by this comment, have you seen studies exploring correlations between covid infection/severity and tonsils? a cursory google search yielded nothing.
jeffybefffy519 4y ago
May I ask, what are your qualifications and how did you get a job in this field?

by nextos 4y ago

panabee 4y ago

what's the approximate cost difference between scRNA-seq and bulk TCR-seq? does the cost curve suggest that scRNA-seq costs will reach cost parity with bulk TCR-seq, or become more practical, within X years? conversely, do you see a way for bulk TCR-seq to overcome issues with resolution and variability? from the outside, it seems like sequencing is such a fundamental piece of understanding the human body yet technology seems incredibly limiting. it's amazing what scientists have discovered so far. imagine what happens if we can help people observe cells more affordably and more accurately.

jostmey 4y ago
Bulk TCR sequencing cost around $500 to $1000 and captures under a million T cells. scRNA Seq costs around $10,000 and captures under ten thousand T cells. The price of sequencing is falling exponentially so my numbers can be out of date
- nextos 4y ago
  These figures are approximately right. We've been able to bring the cost of single-cell RNA-seq + TCR-seq runs down to $3000 by doing targeted gene expression, which requires less reads. Besides, some newer microfluidics platforms are able to yield more cells, close to 2e4. I would say that the major limiting factor is the microfluidics platform. Ideally, we would require something that has a yield within the same order of magnitude of bulk methods. To address this limitation, one can e.g. pre-sort activated cells. Otherwise, the number of receptors is typically not enough to be able to observe meaningful statistical patterns.
  - gww 4y ago
    Parse biosciences and companies have developed methods to perform TCR sequencing without the microfluidics and it will be interesting to see how well it performs. These methods are all based on permeabilizing the cell and keeping it intact instead of encapsulating the in a droplet and then lysing it.

genomer 4y ago

Microsoft Research was a partner in the joint collaboration. Pretty sure this was the research that culminated in the T-Detect Lyme product that Adaptive Biotech launched last year (definitely some Adaptive representation in the publication). https://investors.adaptivebiotech.com/news-releases/news-release-details/adaptive-biotechnologies-launches-t-detecttm-lyme-new-t-cell https://investors.adaptivebiotech.com/news-releases/news-rel...

m463 4y ago

I wonder if low-hanging fruit is just "immune system health". train on healthy vs unhealthy immune systems and give a status bar. I've read that healthy individuals don't get cancer because their body nips it in the bud. Why couldn't we just figure out if people are pre-cancer (susceptible), like pre-diabetes?

genomer 4y ago
Age is probably the biggest influence on a "healthy" immune system. I haven't kept up with recent research, but if memory serves the immune repertoire (diversity of T and B cell receptors) decreases essentially linearly with age. Here's some supporting research from a quick search. https://journals.aai.org/jimmunol/article/192/6/2689/1552 https://journals.aai.org/jimmunol/article/192/6/2689/1552 Edit: some fun but possibly pontificating tangents This seems to be part of the reason why vaccines have had relatively poorer efficacy in elderly populations. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901832/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901832/ https://www.nature.com/articles/s41586-021-03739-1 https://www.nature.com/articles/s41586-021-03739-1 I'm hopeful that cancer and immune profiling will be able to be used in tandem to (1) identify cancer early and (2) identify gaps in the immune repertoire to facilitate (3) design of antibodies that specifically target the cancer.
- nextos 4y ago
  There's a huge variability in the age of thymic involution. Some people have a relatively active thymus at age 50 or 60, whereas in others it has switched off by age 25 or 30. For those not familiar with immunology, the thymus is what populates your immune system with brand new T cells equipped with freshly selected T cell receptors. This suggests interesting anti-aging opportunities, such as artificial thymi to repopulate your immune system and keep a healthy and diverse repertoire.
  - panabee 4y ago
    unrelated but spurred by this comment, have you seen studies exploring correlations between covid infection/severity and tonsils? a cursory google search yielded nothing.

jeffybefffy519 4y ago

May I ask, what are your qualifications and how did you get a job in this field?