Biology subjects

Hill, A. J.

Publications and source records attributed to Hill, A. J..

4 recordsLinked to original sources

bioRxiv2025

Better antibodies engineered with a GLIMPSE of human data

GLIMPSE-1 is a protein language model trained solely on paired human antibody sequences. It captures immunological features and achieves best-in-class performance in humanization benchmarks. We demonstrate the utility of GLIMPSE-1 in humanization; engineering of antibodies for affinity, species cross-reactivity, and key developability parameters; and the creation of highly divergent functional variants with <90% sequence identity to a marketed antibody. Learning exclusively from human antibody data enables GLIMPSE-1 to enhance therapeutics and native antibodies based on patterns in the human repertoire. DisclaimerWhile we provide detailed descriptions of experimental methods and success metrics, certain methodological details of GLIMPSE-1 remain proprietary and/or redacted in this work for commercial considerations. We warmly invite researchers and potential collaborators interested in accessing GLIMPSE-1 to connect with our team via partnerships@infinimmune.com.

bioinformatics↗

bioRxiv2023

Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy

Chemical genetic screens are a powerful tool for exploring how cancer cells response to drugs is shaped by their mutations, yet they lack a molecular view of the contribution of individual genes to the response to exposure. Here, we present sci-Plex-Gene-by-Environment (sci-Plex-GxE), a platform for combined single-cell genetic and chemical screening at scale. We highlight the advantages of large-scale, unbiased screening by defining the contribution of each of 522 human kinases to the response of glioblastoma to different drugs designed to abrogate signaling from the receptor tyrosine kinase pathway. In total, we probed 14,121 gene-by-environment combinations across 1,052,205 single-cell transcriptomes. We identify an expression signature characteristic of compensatory adaptive signaling regulated in a MEK/MAPK-dependent manner. Further analyses aimed at preventing adaptation revealed promising combination therapies, including dual MEK and CDC7/CDK9 or NF-kB inhibitors, as potent means of preventing transcriptional adaptation of glioblastoma to targeted therapy.

genomics↗

bioRxiv2019

Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes

Multi-nucleotide variants (MNVs), defined as two or more nearby variants existing on the same haplotype in an individual, are a clinically and biologically important class of genetic variation. However, existing tools for variant interpretation typically do not accurately classify MNVs, and understanding of their mutational origins remains limited. Here, we systematically survey MNVs in 125,748 whole exomes and 15,708 whole genomes from the Genome Aggregation Database (gnomAD). We identify 1,996,125 MNVs across the genome with constituent variants falling within 2 bp distance of one another, of which 31,510 exist within the same codon, including 405 predicted to result in gain of a nonsense mutation, 1,818 predicted to rescue a nonsense mutation event that would otherwise be caused by one of the constituent variants, and 16,481 additional variants predicted to alter protein sequences. We show that the distribution of MNVs is highly non-uniform across the genome, and that this non-uniformity can be largely explained by a variety of known mutational mechanisms, such as CpG deamination, replication error by polymerase zeta, or polymerase slippage at repeat junctions. We also provide an estimate of the dinucleotide mutation rate caused by polymerase zeta. Finally, we show that differential CpG methylation drives MNV differences across functional categories. Our results demonstrate the importance of incorporating haplotype-aware annotation for accurate functional interpretation of genetic variation, and refine our understanding of genome-wide mutational mechanisms of MNVs.

genomics↗

bioRxiv2018

On the design of CRISPR-based single cell molecular screens

Several groups recently reported coupling CRISPR/Cas9 perturbations and single cell RNA-seq as a potentially powerful approach for forward genetics. Here we demonstrate that vector designs for such screens that rely on cis linkage of guides and distally located barcodes suffer from swapping of intended guide-barcode associations at rates approaching 50% due to template switching during lentivirus production, greatly reducing sensitivity. We optimize a published strategy, CROP-seq, that instead uses a Pol II transcribed copy of the sgRNA sequence itself, doubling the rate at which guides are assigned to cells to 94%. We confirm this strategy performs robustly and further explore experimental best practices for CRISPR/Cas9-based single cell molecular screens.

genomics↗