Note: this post is still a rough draft but I think this idea is important enough to publish it anyway. I intend to revise it in the future. Also if you are a biologist who wants to collaborate with me on this project, or a philanthropist who wants to provide funding, please email me: metacelsus at protonmail dot com
Gwern Branwen, Carl Shulman,and others have written about the concept of iterated embryo selection (IES). The idea of IES is to:
Take some embryos,
derive embryonic stem cell lines from them,
genotype the cells and select the best ones according to a polygenic score,
differentiate the stem cells to gametes,
generate a new population of embryos and repeat.
IES would allow a much more rapid improvement in genotype than would be possible under normal selective breeding.
But there may be a faster and better way to do this (and it might even be easier)!
The idea: iterated meiotic selection
Here is my proposal:
Take a diploid cell line (probably ESC or iPSC or PGCLC)
This does not require in vitro gametogenesis technology, since the final generation of an embryo could be performed by somatic cell nuclear transfer into a donor oocyte.
In addition to enabling iterated selection, this would also allow “genetic crosses” for human cells. Genetic crosses are very useful for model organisms (e.g. crossing Cre/lox mouse lines to generate tissue-specific knockouts) and they would be similarly useful for human cell lines.
Technological challenges and prospects
The key piece of missing technology is a way to induce meiosis in a diploid cell line to generate haploid lines. Other pieces (such as culturing haploid human stem cells, or electrofusion of cells) are already in place. Therefore, meiosis is all you need.
Now, inducing meiosis won’t be easy. Meiosis normally takes place only during gametogenesis and it is unclear whether it is possible to activate meiosis separately. But I think that it has a good chance of being achievable, and might even be easier than in vitro gametogenesis (because it’s easier to screen for a haploid cell than for a viable gamete).
I will approach this problem by:
Performing a literature search and computational analysis to identify proteins involved in meiosis.
Constructing a barcoded transposon library for inducible expression of these proteins.
Integrating the library into iPSC lines with reporters for meiosis-specific proteins (e.g. REC8)2
Inducing expression and sorting reporter-positive cells. Haploid cells could also be sorted by staining for DNA content, although this has a smaller dynamic range than fluorescent reporters.
Sequencing barcodes to identify the top factors.
Validating the top factors by expressing them individually or in small combinations.
This overall approach has worked before to generate a variety of cell types (including granulosa cells and oogonia)3 and I think it has a decent chance of success on this problem.4
Footnotes:
1 Note that these would have to be female (X-bearing) since the X chromosome contains essential genes.
2 REC8 is a meiosis-specific cohesin. I actually already made a REC8 reporter line as part of my gametogenesis project.
4 It may not be feasible to induce meiosis directly from iPSCs. However, I think that this has a high chance of working in iPSC-derived oogonia or spermatogonia, although these are more difficult to culture.
Cool! Is it known how to sequence the haploid cell? Can you get a haploid cell to divide so you can feed it into PCR or something? (I'm a layperson w.r.t. biology.) I just recently had an idea about sequencing sperm by looking at their meiotic cousins and would be interested in talking in general about this topic; email at gmail, address tsvibtcontact.
https://tsvibt.blogspot.com/2022/06/non-destructively-sequencing-gametes-by.html
Yes, you can let them divide and then use the usual (destructive) sequencing.
And also yes, sequencing meiotic cousins of sperm (or polar bodies, in the case of eggs) is a promising concept. Unfortunately primary spermatocytes won't do meiosis if you isolate them; the environment of the seminiferous tubules is very important. So you would have to be able to track them within the tubules in an organ culture system.
Polar body biopsies for eggs are much more feasible (I have done them, although I haven't sequenced the polar bodies). Unfortunately the efficacy of selection is limited by the number of eggs.
Cross-posted from my Substack.
Note: this post is still a rough draft but I think this idea is important enough to publish it anyway. I intend to revise it in the future. Also if you are a biologist who wants to collaborate with me on this project, or a philanthropist who wants to provide funding, please email me: metacelsus at protonmail dot com
Gwern Branwen, Carl Shulman, and others have written about the concept of iterated embryo selection (IES). The idea of IES is to:
IES would allow a much more rapid improvement in genotype than would be possible under normal selective breeding.
But there may be a faster and better way to do this (and it might even be easier)!
The idea: iterated meiotic selection
Here is my proposal:
This would have several advantages.
In addition to enabling iterated selection, this would also allow “genetic crosses” for human cells. Genetic crosses are very useful for model organisms (e.g. crossing Cre/lox mouse lines to generate tissue-specific knockouts) and they would be similarly useful for human cell lines.
Technological challenges and prospects
The key piece of missing technology is a way to induce meiosis in a diploid cell line to generate haploid lines. Other pieces (such as culturing haploid human stem cells, or electrofusion of cells) are already in place. Therefore, meiosis is all you need.
Now, inducing meiosis won’t be easy. Meiosis normally takes place only during gametogenesis and it is unclear whether it is possible to activate meiosis separately. But I think that it has a good chance of being achievable, and might even be easier than in vitro gametogenesis (because it’s easier to screen for a haploid cell than for a viable gamete).
I will approach this problem by:
Footnotes:
1 Note that these would have to be female (X-bearing) since the X chromosome contains essential genes.
2 REC8 is a meiosis-specific cohesin. I actually already made a REC8 reporter line as part of my gametogenesis project.
3 Preprints to be released shortly.
4 It may not be feasible to induce meiosis directly from iPSCs. However, I think that this has a high chance of working in iPSC-derived oogonia or spermatogonia, although these are more difficult to culture.