Biology subjects

Hoi, K. H.

Publications and source records attributed to Hoi, K. H..

4 recordsLinked to original sources

bioRxiv2025

Inferring cellular communication through mapping cells in space using Tangram 2

Cell-to-cell communication (CCC) shapes development, immunity, and disease, yet current spatial transcriptomics (SRT) platforms rarely achieve both single-cell resolution and high-quality transcriptome-wide coverage to accurately characterize CCC in the tissue microenvironment. Tangram2 bridges this gap by integrating single-cell RNA sequencing (scRNA-seq) with SRT to identify genes whose expression changes as a function of neighboring cell types. By accurately mapping cells in tissue space, Tangram2 disentangles interaction-driven transcriptional shifts from intrinsic identity markers, yielding mechanistic CCC maps. Validation across diverse settings--including Slide-tags, co-cultured experiments, human lymph nodes, and simulations--demonstrates high accuracy. Applied to triple-negative breast cancer (TNBC) and cutaneous squamous cell carcinoma (cSCC), Tangram2 recapitulates known biology and uncovers new hypotheses, including various immunosuppressive mechanisms in TNBC and a macrophage-regulatory T-cell circuit associated with survival in cSCC.

genomics↗

bioRxiv2022

Novel Antibody Interfaces Revealed Through Structural Mining

Antibodies are fundamental effectors of humoral immunity, and have become a highly successful class of therapeutics. There is increasing evidence that antibodies utilize transient homotypic interactions to enhance function, and elucidation of such interactions can provide insights into their biology and new opportunities for their optimization as drugs. Yet the transitory nature of weak interactions makes them difficult to investigate. Capitalizing on their rich structural data and high conservation, we have characterized all the ways that antibody Fab regions interact crystallographically. This approach led to the discovery of previously unrealized interfaces between antibodies. While diverse interactions exist, {beta}-sheet dimers and variable-constant elbow dimers are recurrent motifs. Disulfide engineering enabled interactions to be trapped and investigated structurally and functionally, providing experimental validation of the interfaces and illustrating their potential for optimization. This work provides first insight into previously undiscovered oligomeric interactions between antibodies, and enables new opportunities for their biotherapeutic optimization.

biochemistry↗

bioRxiv2019

Heavy Chain CDR 3 and Junctional Length Biases in Human Antibody Repertoires Associated with Heavy and Light Chain Germline Utilization

Antibody variable domain sequence diversity is generated by recombination of germline segments. The third complementarity-determining region of the heavy chain (CDR H3) is the region of highest sequence diversity and is formed by the joining of heavy chain VH, DH and JH germline segments combined with random nucleotide trimming and additions between these segments. We show that CDR H3 length distribution is biased in human antibody repertoires as a function of VH, VL and JH germline segment utilization. Most length biases are apparent in the naive B cell compartment, with a significant bias towards shorter CDR H3 sequences observed in association with a subset of VH and VL germlines in the antigen experienced compartment. Similar biases were not observed in nonproductive heavy chain recombination products, indicating selection of the repertoire during B cell maturation as a major driver of the length biases. Some VH-associated CDR H3 length biases are dependent on utilization of specific JH germline segments in a manner not directly linked to JH segment length in the germline, but are rather associated with selection of differentially trimmed JH segments in the naive compartment. In addition, DH segment and N-region random nucleotide insertion lengths within CDR H3 in the naive compartment were also biased by specific VH/JH germline combinations, indicating a complex set of constraints between germline segments selected during repertoire maturation. Our findings reveal biases in the antibody diversity landscape shaped by VH, VL, and JH germline features with implications for mechanisms of naive and immune repertoire selection.

immunology↗

bioRxiv2019

Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies

Using high-throughput single-cell B-cell receptor sequencing (scBCR-seq) we obtained accurately paired full-length heavy- and light-chain variable domains from thousands of individual B cells in a massively parallel fashion. We sequenced more than 250,000 B cells from rat, mouse and human repertoires to characterize their lineages and expansion. In addition, we immunized rats with chicken ovalbumin and profiled antigen-reactive B cells from lymph nodes of immunized animals. The scBCR-seq data recovered 81% (n = 56/69) of B-cell lineages identified from hybridomas generated from the same set of B cells that were subjected to scBCR-seq. Importantly, scBCR-seq identified an additional 710 candidate lineages that were not recovered as hybridomas. We synthesized, expressed and tested 93 clones from the identified lineages and found that 99% (n = 92/93) of the clones were antigen-reactive. Our results establish scBCR-seq as a powerful tool for antibody discovery.

immunology↗