July // August 2024 Progress Update
Completing the discovery cycle
The late summer days are long in Northern California, and we’ve been putting the extra daylight hours to good use at NewLimit.
A few highlights from July & August:
+2500 TF sets tested
+20 TF sets that reverse the phenotypic age of T cells
2X acceleration of reprogramming library Build cycles
0 -> 3 hits with preliminary functional effects in primary T cells
+3 functional assays for hepatocyte cell age
+4 team members
People
We had a rapid few months of growth across several key roles. We’re excited for our new colleagues to join the team:
Adam Ferguson is joining us from Ginkgo as a Senior Automation Engineer on our Read team.
Kate Franz is joining us from Verily as a Senior Scientist on our Immunology team.
Catherine O’Hare is joining us from GlaxoSmithKlein as our Head of Operations.
Rowena Suriben is joining us from Kinnate Biopharma as an Associate Director to lead our Metabolism team.
Early functional effects of partial reprogramming
Our Discovery efforts are ultimately all in service of developing medicines that improve the function of old cells and treat disease in patients. For our T cell program, we’ve now discovered dozens of transcription factor (TF) sets that make old cells look young based on our phenotypic screening assays. Until this summer, we had yet to test whether any of these sets make old T cells act young, improving their function to youthful levels.
Our Immunology team has now developed a series of functional assays that can discriminate between young and old T cells. With these assays in hand, we began testing whether partial reprogramming with our top phenotypic hits could improve T cell function on one of these assays in July.
We found preliminary evidence that 3 of the phenotypic hits we tested improved the performance of old T cells in this assay, suggesting that at least this particular function is amenable to reprogramming. These results represent our first complete cycle of phenotypic discovery followed by functional validation, and we’ll be radically increasing the throughput of these validations going forward.
We believe it’s important that our eventual medicines improve T cell function across multiple axes. These results are encouraging, but only the beginning of our validation process that will feed into therapeutic development.
Scaling the data corpus
Alongside our first functional validations, we’ve continued to run our Discovery Engine at a steady clip. We tested another 2500+ TF sets for their effect on cell age in old human T cells across July & August, including our largest screen yet (and the largest in the world that we know of).
From these experiments, we discovered another 20+ TF sets that reverse the phenotypic age of T cells through partial reprogramming. Each of these new hits provides both a direct substrate for our validation assays and contributes to the development of our in silico reprogramming models by adding to our data corpus. With each new screen, we discover additional axes of cell state that are amenable to partial reprogramming.
We hope that these diverse data will allow us to design better experiments in the world of bits, then discover more hits per dollar in the world of atoms in the near future.
Accelerating Discovery Engine screens
Each of our Discovery Engine screens requires us to build a set of nucleic acid reagents to activate TFs in old cells, then detect which TFs are present to enable pooled experiments. This Build process is one of the most labor intensive steps of each screen and increases our turn-around time from one experiment to the next. We’re firm believers that reducing cycle times in our process will allow us to learn and improve that process more rapidly, ultimately yielding more discoveries and downstream assets.
Our Write team has been working for the past quarter to develop a new molecular biology process that cuts our Build time and costs in half. We developed a “two-step” Build process in the early days of NewLimit to ensure high fidelity – almost all of the reagents we start building complete successfully. However, the total amount of effort required was roughly 2X the theoretical minimum. Through a clever series of molecular tricks encoded in base pairs, our team was able to achieve a “one-step” process that preserves nearly the same fidelity as our original version.
In practice, this improvement cuts the turn-around time and the cost of our Build processes by roughly 2X. Through a series of improvements like this, we hope to continually improve the performance of our Engine.
Measuring functional age in human hepatocytes
The clinical evidence that human livers decline in function with age is quite clear, but measuring these defects in human hepatocytes in the laboratory is surprisingly understudied. Our Metabolism team previously developed an assay to discriminate young and old human cells based on their metabolism, and over the past two months we’ve also built a system to discriminate human cells based on their regenerative potential.
Hepatocyte regeneration is an important function that allows the liver to tolerate damage from environmental insults like a Western diet. We’ve found that regeneration declines with age in old mice, and our team developed a clever functional assay to demonstrate that the same is true in human cells.
We transplanted young and old human hepatocytes into humanized liver mice, then measured how well they regenerated. The humanized liver system, originally developed by our SAB member Markus Grompe, allows human cells to engraft in a “sick” mouse liver and slowly regenerate it over time until it’s mostly human. The more regenerative a cell is, the more abundant its progeny will be in the resulting humanized liver.
We found that young human hepatocytes are consistently more regenerative than old human hepatocytes, by a factor of >6X. The performance of human cells in this assay is sufficient to discriminate the age of the donor with strong performance. We can take a reasonable guess at a donor’s birthday based simply on how their hepatocytes perform in our laboratory.
It’s worth emphasizing that this assay is cell-intrinsic and long-term. Even when surrounded by the exact environment over a long time period, old human hepatocytes maintain intrinsic defects relative to their young counterparts. Hepatocyte regeneration is also associated with positive outcomes for liver disease patients, supporting the clinical relevance of this cell function.
Our Metabolism team is now hard at work deploying this new tool to discover rejuvenating factors.
Come join us
NewLimit is always recruiting talented scientists, engineers, and operators. Right now, we have exciting opportunities for a Lipid Nanoparticle Delivery Scientist to build out our delivery technology and for a Machine Learning Scientist to own our in silico phenotyping suite.
Please reach out if you or any colleagues would be a good fit!