About

Hao Yuan Kueh is an Associate Professor in the Department of Bioengineering at the University of Washington. His research focuses on understanding how immune cells control fate decisions during their development from stem cells and in response to pathogens. His lab employs live-cell imaging to make quantitative measurements of the dynamic behavior of gene and molecule circuits within single cells. These studies are complemented by biochemical, genetic, and modeling approaches to define the molecular basis of these circuits and to elucidate their underlying design principles. The overarching goal of his work is to understand the principles of decision making in mammalian cells and to apply this knowledge to engineer immune cells for disease fighting.

Research topics

• Biology
• Artificial Intelligence
• Genetics
• Cell biology
• Computer Science
• Biochemistry
• Computer network
• Computational biology
• Mathematics

Selected publications

• Design of solubly expressed miniaturized SMART MHCs

  Proceedings of the National Academy of Sciences · 2026-01-02 · 2 citations

  articleOpen access

  The precise recognition of specific peptide–major histocompatibility complex (pMHC) complexes by T cell receptors (TCRs) plays a key role in infectious disease, cancer, and autoimmunity. A critical step in many immunobiological studies is the identification of T cells expressing TCRs specific to a given pMHC antigen. However, the intrinsic instability of empty class-I MHCs limits their soluble expression in Escherichia coli and makes it very difficult to characterize even a small fraction of possible pMHC/TCR interactions. To overcome this limitation, we designed small proteins which buttress the peptide binding groove of class I MHCs, replacing β2-microglobulin (β2m) and the heavy chain α3 domain, and enable soluble and partially soluble expression in E. coli of H-2D b and A*02:01, respectively. We demonstrate that these soluble, monomeric, antigen-receptive, truncated (SMART) MHCs retain both peptide- and TCR-binding specificity and that peptide-bound structures of both allomorphs are similar to their full-length, native counterparts. With extension to the majority of HLA alleles, SMART MHCs should be broadly useful for probing the T cell repertoire in approaches ranging from yeast display to T cell staining.

  PublisherDOI

• Design of a potent interleukin-21 mimic for cancer immunotherapy

  Science Immunology · 2025-09-26 · 3 citations

  articleOpen access

  Long-standing goals of cancer immunotherapy are to activate cytotoxic antitumor T cells across a range of affinities for tumor antigens while suppressing regulatory T cells. Computational protein design has enabled the precise tailoring of proteins to meet specific needs. Here, we report a de novo designed IL-21 mimic, 21h10, with high stability and signaling potency in humans and mice. In murine and ex vivo human organotypic tumor models, 21h10 showed robust antitumor activity, with more prolonged signaling and stronger antitumor activity than native IL-21. 21h10 induced pancreatitis that could be mitigated by TNF blockade without compromising antitumor efficacy. Although antidrug antibodies to 21h10 formed, they were not neutralizing. 21h10 induced highly cytotoxic T cells with a range of affinities, robustly expanding intratumoral low-affinity cytotoxic T cells and driving high expression of IFN-γ and granzyme B compared with native IL-21, while increasing the frequency of IFN-γ + T helper 1 cells and reducing regulatory T cells. The full human-mouse cross-reactivity, high stability and potency, and low-affinity antitumor responses support the translational potential of 21h10.

  PublisherOA PDFDOI

• Proofreading and single-molecule sensitivity in T cell receptor signaling by condensate nucleation

  Proceedings of the National Academy of Sciences · 2025-05-30 · 6 citations

  articleOpen accessSenior authorCorresponding

  T cells display the remarkable ability to detect single foreign peptides displayed on target cells, while ignoring highly abundant self-peptides. This selectivity has been explained by kinetic proofreading in the T cell receptor (TCR) signaling pathway, which prevents responses to short-lived binding events regardless of their abundance. However, the biochemical mechanisms that drive kinetic proofreading have remained unclear. Here, using computational modeling, we show that these key signaling properties of the TCR pathway can emerge from the dynamics of linker for activation of T cells (LAT) phosphorylation, diffusion, and condensation following TCR-peptide major histocompatibility complex (pMHC) binding. In this model, time delays in LAT condensate nucleation underlie kinetic proofreading, enabling selective signaling responses to high-affinity pMHC ligands. The cooperativity in the nucleation and growth of LAT condensates also provides a mechanism to amplify weak signals from single high-affinity peptides and for condensates to grow with increasing antigen numbers. In contrast to other models, condensate-nucleation proofreading predicts a dependence of signal strength on pMHC spacing at fixed number, a prediction we validated experimentally using a protein scaffold to present pMHCs at defined intervals. Our results suggest that nucleation-condensation proofreading underlies the remarkable antigen detection capabilities of the TCR signaling pathway.

  PublisherDOI

• Design of solubly expressed miniaturized SMART MHCs

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-14 · 1 citations

  preprintOpen access

  Abstract The precise recognition of specific peptide-MHC (pMHC) complexes by T-cell receptors (TCRs) plays a key role in infectious disease, cancer and autoimmunity. A critical step in many immunobiological studies is the identification of T-cells expressing TCRs specific to a given pMHC antigen. However, the intrinsic instability of empty class-I MHCs limits their soluble expression in Escherichia coli ( E. coli ) and makes it very difficult to characterize even a small fraction of possible pMHC/TCR interactions. To overcome this limitation, we designed small proteins which buttress the peptide binding groove of class I MHCs, replacing β2-microglobulin (β2m) and the heavy chain α3 domain, and enable soluble expression of both H-2D b and A*02:01 in E. coli . We demonstrate that these soluble, monomeric, antigen-receptive, truncated (SMART) MHCs retain both peptide- and TCR-binding specificity, and that peptide-bound structures of both allomorphs are similar to their full-length, native counterparts. With extension to the majority of HLA alleles, SMART MHCs should be broadly useful for probing the T-cell repertoire in approaches ranging from yeast display to T-cell staining. Significance Despite the critical role that TCR/pMHC interactions play in human health, it has remained difficult to produce reagents necessary to study them. Requirements for refolding or sequence optimization limit immunologists’ and biochemists’ ability to characterize diverse pMHC/TCR interactions. Here, we develop a de-novo designed protein domain that stabilizes the H-2D b and A*02:01 class I MHC allomorphs, allowing soluble expression in E. coli without the need for a stabilizing peptide, and improving display on the yeast surface, while maintaining peptide and TCR binding interactions. These features facilitate a wide range of experiments to more fully understand the nature of pMHC/TCR interactions, and pave the way for the development of stabilizing domains for all MHC allomorphs.

  PublisherOA PDFDOI

• An early precursor CD8+ T cell that adapts to acute or chronic viral infection

  Nature · 2025-01-08 · 62 citations

  article
  PublisherDOI

• Early generation of a precursor CD8 T cell that can adapt to acute or chronic viral infection

  Research Square · 2024-02-12 · 1 citations

  preprintOpen access
  PublisherOA PDFDOI

• Reversible, tunable epigenetic silencing of TCF1 generates flexibility in the T cell memory decision

  Immunity · 2024-01-31 · 50 citations

  articleOpen accessSenior authorCorresponding

  The immune system encodes information about the severity of a pathogenic threat in the quantity and type of memory cells it forms. This encoding emerges from lymphocyte decisions to maintain or lose self-renewal and memory potential during a challenge. By tracking CD8+ T cells at the single-cell and clonal lineage level using time-resolved transcriptomics, quantitative live imaging, and an acute infection model, we find that T cells will maintain or lose memory potential early after antigen recognition. However, following pathogen clearance, T cells may regain memory potential if initially lost. Mechanistically, this flexibility is implemented by a stochastic cis-epigenetic switch that tunably and reversibly silences the memory regulator, TCF1, in response to stimulation. Mathematical modeling shows how this flexibility allows memory T cell numbers to scale robustly with pathogen virulence and immune response magnitudes. We propose that flexibility and stochasticity in cellular decisions ensure optimal immune responses against diverse threats.

  PublisherDOI

• What unique insights can modeling approaches capture about the immune system?

  Cell Systems · 2024-12-01 · 4 citations

  article1st authorCorresponding
  PublisherDOI

• Immune cells can adapt to invading pathogens, deciding whether to fight now or prepare for the next battle

  2024-03-08

  articleOpen accessSenior author
  PublisherDOI

• Potent antitumor activity of a designed interleukin-21 mimic

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-07 · 5 citations

  preprintOpen access

  Abstract Long-standing goals of cancer immunotherapy are to activate cytotoxic antitumor T cells across a broad range of affinities while dampening suppressive regulatory T (Treg) cell responses, but current approaches achieve these goals with limited success. Here, we report a de novo IL-21 mimic, 21h10, designed to have augmented stability and high signaling potency in both humans and mice. In multiple animal models and in ex vivo human melanoma patient derived organotypic tumor spheroids (PDOTS), 21h10 showed robust antitumor activity. 21h10 generates significantly prolonged STAT signaling in vivo compared with native IL-21, and has considerably stronger anti-tumor activity. Toxicities associated with systemic administration of 21h10 could be mitigated by TNFα blockade without compromising antitumor efficacy. In the tumor microenvironment, 21h10 induced highly cytotoxic antitumor T cells from clonotypes with a range of affinities for endogenous tumor antigens, robustly expanding low-affinity cytotoxic T cells and driving high expression of interferon-𝛾 (IFN-𝛾) and granzyme B compared to native IL-21, while increasing the frequency of IFN-𝛾 + Th1 cells and reducing that of Foxp3 + Tregs. As 21h10 has full human/mouse cross-reactivity, high stability and potency, and potentiates low-affinity antitumor responses, it has considerable translational potential.

  PublisherOA PDFDOI

Recent grants

• Single-cell analysis of immune cell fate decision making

  NIH · $747k · 2014–2020

• Single cell analysis of hematopoietic cell fate determination

  NIH · $180k · 2014–2016

• A chromatin-based timer controlling T-cell development

  NIH · $1.9M · 2020–2025

Frequent coauthors

• Timothy J. Mitchison

  Harvard University

  22 shared

• Ellen V. Rothenberg

  California Institute of Technology

  18 shared

• William M. Brieher

  University of Illinois Urbana-Champaign

  16 shared

• José M. G. Vilar

  Biofisika

  16 shared

• Stanislas Leibler

  Center for Systems Biology

  16 shared

• Naama Barkai

  Weizmann Institute of Science

  16 shared

• Michael B. Elowitz

  Howard Hughes Medical Institute

  15 shared

• Kenneth K.H. Ng

  Yale University

  12 shared