Cell Bio 2025 Poster: Validating an evolutionary platform for therapeutic discovery using diverse organisms

A NOTE ON SHARING WITH US! Part of our mission is to share as much useful research as we can. If you choose to share a protocol or other useful information with us after viewing this poster, please understand that we may act upon this knowledge and share it when we publish our work. We publish quickly on an independent platform, so this may happen soon after you share, and we cannot wait for you to publish elsewhere. If you decide to share anyway, yay! That's what science is all about. If your input is useful, we will include you as a contributor to the publication and explain that your role was in providing "Critical Feedback," likely with an additional description of what you shared. tl,dr —If you're not ready for everyone to know about something, please refrain from sharing it with us. Prachee Avasthi • Supervision, conceptualization Audrey Bell • Visualization Brae M Bigge • Supervision, conceptualization, investigation, visualization Christoher Bulow • Supervision, critical feedback Keith Cheveralls • Software, validation Tara Essock-Burns • Investigation, formal analysis, critical feedback Behnom Farboud • Investigation, formal analysis, methodology, conceptualization Megan L Hochstrasser • Editing Evan Kiefl • Software, formal analysis, validation, conceptualization Ryan Lane • Software, formal analysis, critical feedback Cameron Dale MacQuarrie • Investigation, formal analysis, methodology, conceptualization Austin Patton • Software Helen Vander Wende • Investigation, methodology, conceptualization Emily C.P. Weiss • Investigation, methodology, conceptualization Ryan York • Supervision, conceptualization 1. Avasthi P, McGeever E, Patton AH, York R et al. (2024). Leveraging evolution to identify novel organismal models of human biology.https://doi.org/10.57844/arcadia-33b4-4dc5 2. Bell A, Hochstrasser ML, Roth R, Wright G. (2025). A free, open-access library of high-quality organism illustrations for science communication. https://doi.org/10.57844/arcadia-4gbv-pzkv 3. Chou A, Patton AH, Sun DA. (2025). A framework for modeling human monogenic diseases by deploying organism selection.https://doi.org/10.57844/arcadia-ugg5-emyd 4. Kim, DU., Hayles, J., Kim, D.et al.(2010). Analysis of a genome-wide set of gene deletions in the fission yeastSchizosaccharomyces pombe. https://doi.org/10.1038/nbt.1628 5. Li X, Patena W, et al.(2019) DOI: https://doi.org/10.1038/s41588-019-0370-6Thomas Hayeset al. (2024) Simulating 500 million years of evolution with a language model. https://doi.org/10.1126/science.ads0018 6. Winzeler EA, Shoemaker DD, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. https://doi.org/0.1126/science.285.5429.901. The problem: At Arcadia Science, we’re leveraging evolution to accelerate the discovery and testing of therapeutics by integrating target identification, organism selection, and biologics design in a single connected platform. Here, we’re validating that platform technology using scalable and informative cell and organismal experiments. The project: As an early test case, we aimed to do a full loop of the platform, identifying therapeutically relevant targets, pairing them with the best organisms to study them, utilizing our in-house technologies to identify phenotypes, and then introducing designed variants. This poster walks you through our full loop project. The goal: By testing our predictions in living systems, this pipeline establishes a closed loop between computational design and experimental validation. More broadly, it demonstrates how cell biology can be used to build rigorous, multi-system strategies for biological validation, enabling efficient mining of the tree of life for the design and development of effective therapeutics. The method: Designability (size, function, etc.) Therapeutic relevance Adenosine deaminase 1 (ADA1) NH2 OH Palmitoyl-protein thioesterase 1 (PPT1) Palmitate Arylsulfatase G (ARSG) S Ubiquitin-conjugating enzyme E2 A (UBE2A) Ub 0 1 2 3 4 5 6 Trait distance to human 0 500 1000 1500 2000 2500 3000 Cophenetic Distance to Human C. reinhardtii PPT1 is highly conserved in relation to other PPT proteins 0 1 2 3 4 5 6 Trait distance to human 0 500 1000 1500 2000 2500 3000 Cophenetic Distance to Human 0 500 1000 1500 2000 2500 3000 Cophenetic Distance to Human 0 1 2 3 4 5 6 Trait distance to human 0 1 2 3 4 5 6 Trait distance to human 0 500 1000 1500 2000 2500 3000 Cophenetic Distance to Human DMSO (n=289) Nile Red (n=239) DMSO (n=303) Nile Red (n=450) 0.0 2.5 5.0 7.5 10.0 12.5 15.0 17.5 Fluorescence Intensity, AU Background Subtracted wild-type ∆ppt1 Here, we focus on C. reinhardtii, which has an increase in Nile Red-visualized lipid bodies. Significance between samples was evaluated using a Kruskal-Sallis H test. Cells were also larger and had deceased chlorophyll fluorescence. In addition, S. pombe mutants have increase cell area and length. C. elegans mutants are dumpy and have decreased brood sized and reduced motility. wild-type ∆arsg 0 50 100 150 Major axis length ∆arsg WT 0 1000 2000 3000 Area ∆arsg WT In S. pombe, cells lacking ARSG are larger than wild-type, potentially indicating a division issue. We observed this in the majority of our S. pombe mutants, including PPT1, UBE2A, and ADA1 mutants as well. C. elegans lacking ARSG are small, have an accumulation of gut granules, and have reduced viability and motility. In C. elegans, cells lacking UBE2A cells have severe morphological phenotypes. Instead of clear fertilized eggs and a gut, they have tumors. Additionally, they have reduced brood size and reduced motility, among other things. Also, S. pombe and S. cerevisiae cells with mutated UBE2A are larger than wild-type, and in S. cerevisiae cells lacking UBE2A are UV and temperature sensitive. In C. reinhardtii, cells are larger, have increased starch accumulation, and decreased chlorophyll fluorescence. EV WT E215A GV_107 E1_65 E1_67 E2_83 Empty vector Human wild-type ADA1 Catalytically dead variant Variant generated with novel model Variant generated with ESM2 (method 1) Variant generated with ESM2 (method 1) Variant generated with ESM2 (method 2) Constructs tested 0% 5% 10% 15% 20% 25% 30% 18.9% 28.1% 18.4% 20.0% 30.2% 16.7% 22.1% EV WT E215A GV_107 E1_65 E1_67 E2_83 Volume (% change) We transformed cells with variants designed with ESM and other methods, induced expression, and analyzed phenotypes including changes in morphology and lipid accumulation. We found that upon induction, cells with functional ADA1, include E_65, increased in cell volume. ADA1 was also evaluated in C. reinhardtii and S. pombe. EV WT E215A E1_65 Induced Uninduced Distance plot showing the overall distance between species on the x-axis the trait distance between the human PPT1 and the PPT1 from our models and mouse on the y-axis. In C. reinhardtii, mutants lacking PPT1 accumulate lipid droplets more than wild-type cells S. pombe ARSG is well-conserved but not more than other proteins C. elegans UBE2A is conserved compared to mouse, but not to other models S. cerevisiae ADA1 is more conserved than mouse ADA1 Distance plot showing the overall distance between species on the x-axis the trait distance between the human ADA1 and the ADA1 from our models and mouse on the y-axis. Distance plot showing the overall distance between species on the x-axis the trait distance between the human UBE2A and the UBE2A from our models and mouse on the y-axis. Distance plot showing the overall distance between species on the x-axis the trait distance between the human ADA1 and the ADA1 from our models and mouse on the y-axis. ARSG mutants in S. pombe are longer and larger than wild-type cells C. elegans lacking UBE2A have severe morphological defects Novel designed ADA1 variants are able to rescue size phenotypes observed in S. cerevisiae (an example of the final step of our validation process) Target identification Model selection Technology development Biologics design References Contribu Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) t Contributors (A–Z) Contributors (A–Z) ors Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) Contributors (A–Z) All other published work: research.arcadiascience.com bit.ly/evo-val Download the poster Validating an evolutionary platform for therapeutic discovery using diverse organisms Brae M Bigge Presented by @BiggeBrae 100um Wild-type ∆ube2a Target selection DNASE2 PPT1 ARSG UBE2A ADA1 cgc.umn.edu us.bioneer.com euroscarf.de chlamylibrary.org Mutant procurement Spectroscopy Microscopy Growth Mutant phenotyping MAQTPAFDKP... MAQTPAFDKP... MARTPGFEKP... ESM2 Masking Fill in the blank Variant design Variant rescue Try Zoogle: zoogle.arcadiascience.com Organism pairing