Biology subjects

Anighoro, A.

Publications and source records attributed to Anighoro, A..

3 recordsLinked to original sources

bioRxiv2026

A DNA foundation model predicts osteoporosis risk genes without proximity bias

Targets supported by human genetic associations are more than twice as likely to progress from clinical development to approval. Genome-wide association studies are the largest source of genetic evidence for disease risk but linking non-coding variants to effector genes remains a significant barrier to identifying causal targets. Current gene-mapping approaches suffer from proximity bias, largely ignoring distal genes. Here we introduce Rosalind, a DNA foundation model fine-tuned on human genetic variation from GTEx, that directly predicts variant-gene regulatory relationships from sequence without relying on nearest-gene heuristics. We demonstrate Rosalinds accuracy through extensive benchmarking, apply it to multiple complex traits to establish broad utility, and provide experimental validation in osteoporosis using a translational osteoblast assay. We demonstrate that genes distal to osteoporosis risk variants were significantly more likely to alter a bone formation phenotype than nearest genes. Together, these results highlight deep learning-based regulatory models as a general and scalable framework for translating novel genetic insights to drug discovery.

genetics↗

bioRxiv2025

PatchDNA: A Flexible and Biologically-Informed Alternative to Tokenization for DNA

AO_SCPLOWBSTRACTC_SCPLOWDNA language models are emerging as powerful tools for representing genomic sequences, with recent progress driven by self-supervised learning. However, performance on downstream tasks is sensitive to tokenization strategies reflecting the complex encodings in DNA, where both regulatory elements and single-nucleotide changes can be functionally significant. Yet existing models are fixed to their initial tokenization strategy; single-nucleotide encodings result in long sequences that challenge transformer architectures, while fixed multi-nucleotide schemes like byte pair encoding struggle with character level modeling. Drawing inspiration from the Byte Latent Transformers combining of bytes into patches, we propose that patching provides a competitive and more efficient alternative to tokenization for DNA sequences. Furthermore, patching eliminates the need for a fixed vocabulary, which offers unique advantages to DNA. Leveraging this, we propose a biologically informed strategy, using evolutionary conservation scores as a guide for patch boundaries. By prioritizing conserved regions, our approach directs computational resources to the most functionally relevant parts of the DNA sequence. We show that models up to an order of magnitude smaller surpass current state-of-the-art performance in existing DNA benchmarks. Importantly, our approach provides the flexibility to change patching without retraining, overcoming a fundamental limitation of current tokenization methods.

genomics↗

bioRxiv2022

Validation of a small molecule inhibitor of PDE6D-RAS interaction with potent anti-leukemic effects

RAS mutations prevalent in high-risk leukemia have been linked to relapse and chemotherapy resistance. Efforts to directly target RAS proteins have been largely unsuccessful. However, since RAS-mediated transformation is dependent on signaling through the RAS-related C3 botulinum toxin substrate (RAC) small GTPase, we hypothesized that targeting RAC may be an effective therapeutic approach in RAS mutated tumors. Here we describe multiple small molecules capable of inhibiting RAC activation in acute lymphoblastic leukemia cell lines. One of these, DW0254, also demonstrates promising anti-leukemic activity in RAS-mutated cells. Using chemical proteomics and biophysical methods, we identified the hydrophobic pocket of phosphodiester 6 subunit delta (PDE6D), a known RAS chaperone, as a target for this compound. Inhibition of RAS localization to the plasma membrane upon DW0254 treatment is associated with RAC inhibition through a phosphatidylinositol-3-kinase/AKT-dependent mechanism. Our findings provide new insights on the importance of PDE6D-mediated transport for RAS-dependent RAC activation and leukemic cell survival.

cancer biology↗