Jingjia Liu

All Publications

• Targeting peptide antigens using a multiallelic MHC I-binding system. Nature biotechnology Du, H., Mallik, L., Hwang, D., Sun, Y., Kaku, C., Hoces, D., Sun, S. M., Ghinnagow, R., Carro, S. D., Phan, H. A., Gupta, S., Blackson, W., Lee, H., Choe, C. A., Dersh, D., Liu, J., Bell, B., Yang, H., Papadaki, G. F., Young, M. C., Zhou, E., El Nesr, G., Goli, K. D., Eisenlohr, L. C., Minn, A. J., Hernandez-Lopez, R. A., Jardine, J. G., Sgourakis, N. G., Huang, P. S. 2024

  Abstract

  Identifying highly specific T cell receptors (TCRs) or antibodies against epitopic peptides presented by class I major histocompatibility complex (MHC I) proteins remains a bottleneck in the development of targeted therapeutics. Here, we introduce targeted recognition of antigen-MHC complex reporter for MHC I (TRACeR-I), a generalizable platform for targeting peptides on polymorphic HLA-A*, HLA-B* and HLA-C* allotypes while overcoming the cross-reactivity challenges of TCRs. Our TRACeR-MHC I co-crystal structure reveals a unique antigen recognition mechanism, with TRACeR forming extensive contacts across the entire peptide length to confer single-residue specificity at the accessible positions. We demonstrate rapid screening of TRACeR-I against a panel of disease-relevant HLAs with peptides derived from human viruses (human immunodeficiency virus, Epstein-Barr virus and severe acute respiratory syndrome coronavirus 2), and oncoproteins (Kirsten rat sarcoma virus, paired-like homeobox 2b and New York esophageal squamous cell carcinoma 1). TRACeR-based bispecific T cell engagers and chimeric antigen receptor T cells exhibit on-target killing of tumor cells with high efficacy in the low nanomolar range. Our platform empowers the development of broadly applicable MHC I-targeting molecules for research, diagnostic and therapeutic applications.

  View details for DOI 10.1038/s41587-024-02505-8

  View details for PubMedID 39672954

  View details for PubMedCentralID 8363505

• A general system for targeting MHC class II-antigen complex via a single adaptable loop. Nature biotechnology Du, H., Liu, J., Jude, K. M., Yang, X., Li, Y., Bell, B., Yang, H., Kassardjian, A., Blackson, W., Mobedi, A., Parekh, U., Parra Sperberg, R. A., Julien, J. P., Mellins, E. D., Garcia, K. C., Huang, P. S. 2024

  Abstract

  Major histocompatibility complex class II (MHCII) bound to a peptide antigen mediates interactions between CD4+ T cells and antigen-presenting cells. Targeting peptide-MHCII with T cell antigen receptors (TCRs) and TCR-like antibodies has shown promise for autoimmune diseases and microbiome tolerance. To develop a general targeting approach, we introduce targeted recognition of antigen-MHC complex reporter for MHCII (TRACeR-II) for the rapid development of peptide-specific MHCII binders. TRACeR-II binders have a small helical bundle scaffold and use a single loop to recognize peptide-MHCII, which offers versatility and enables structural modeling of the interactions to target MHCII antigens. We demonstrate rapid generation of TRACeR-II binders to multiple molecules with affinities in the low-nanomolar to low-micromolar range, comparable to best-in-class TCRs and antibodies. Through computational protein design, we created specific binding sequences in silico from only the sequence of a severe acute respiratory syndrome coronavirus 2 peptide. TRACeR-II provides a straightforward approach to target antigen-MHCII without relying on combinatorial selection on complementarity-determining region loops.

  View details for DOI 10.1038/s41587-024-02466-y

  View details for PubMedID 39672953

  View details for PubMedCentralID 6977962

• Fully synthetic platform to rapidly generate tetravalent bispecific nanobody-based immunoglobulins. Proceedings of the National Academy of Sciences of the United States of America Misson Mindrebo, L., Liu, H., Ozorowski, G., Tran, Q., Woehl, J., Khalek, I., Smith, J. M., Barman, S., Zhao, F., Keating, C., Limbo, O., Verma, M., Liu, J., Stanfield, R. L., Zhu, X., Turner, H. L., Sok, D., Huang, P. S., Burton, D. R., Ward, A. B., Wilson, I. A., Jardine, J. G. 2023; 120 (24): e2216612120

  Abstract

  Nanobodies bind a target antigen with a kinetic profile similar to a conventional antibody, but exist as a single heavy chain domain that can be readily multimerized to engage antigen via multiple interactions. Presently, most nanobodies are produced by immunizing camelids; however, platforms for animal-free production are growing in popularity. Here, we describe the development of a fully synthetic nanobody library based on an engineered human VH3-23 variable gene and a multispecific antibody-like format designed for biparatopic target engagement. To validate our library, we selected nanobodies against the SARS-CoV-2 receptor-binding domain and employed an on-yeast epitope binning strategy to rapidly map the specificities of the selected nanobodies. We then generated antibody-like molecules by replacing the VH and VL domains of a conventional antibody with two different nanobodies, designed as a molecular clamp to engage the receptor-binding domain biparatopically. The resulting bispecific tetra-nanobody immunoglobulins neutralized diverse SARS-CoV-2 variants with potencies similar to antibodies isolated from convalescent donors. Subsequent biochemical analyses confirmed the accuracy of the on-yeast epitope binning and structures of both individual nanobodies, and a tetra-nanobody immunoglobulin revealed that the intended mode of interaction had been achieved. This overall workflow is applicable to nearly any protein target and provides a blueprint for a modular workflow for the development of multispecific molecules.

  View details for DOI 10.1073/pnas.2216612120

  View details for PubMedID 37276407

• De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design. Biodesign research Chu, A. E., Fernandez, D., Liu, J., Eguchi, R. R., Huang, P. S. 2022; 2022: 9842315

  Abstract

  The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrel fold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel protein has been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the fold remains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold) symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbone sampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequence design protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences are highly stable and fold to the designed barrel curvature as determined by a 2.1 Å resolution crystal structure. The designs show robustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in the hydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diverse hydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major step towards the de novo design of functional TIM barrels.

  View details for DOI 10.34133/2022/9842315

  View details for PubMedID 37850141

  View details for PubMedCentralID PMC10521652