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Garcia, K. C.

Publications and source records attributed to Garcia, K. C..

At least 19 recordsLinked to original sources

MHC restriction is structurally encoded by the T cell receptor germline

MHC restriction -- the requirement for {beta} T cell receptors (TCRs) to recognize Major Histocompatibility Complex (MHC) molecules when presenting peptide antigens -- is a pillar of adaptive immunity. Here, we provide direct structural evidence for TCR germline-encoded recognition of MHC molecules irrespective of antigenic peptide. We engineered "germline-like" TCRs to eliminate CDR3 specificity for peptide, and a molecular clamping strategy to trap ultra-low-affinity complexes with peptide-MHC for cryo-EM. We find that germline-like TCR/pMHC docking modes are identical to wild-type T cell receptors with intact CDR3 loops, across distinct peptide antigens and MHC alleles. Analysis of human TCR repertoires reveals enrichment of specific V genes and V-V{beta} pairing patterns associated with HLA-A*02 contexts. Thus, the TCR germline encodes the blueprint for MHC restriction, providing a sequence-based framework that could inform computational and AI-driven prediction of TCR specificity.

immunology↗

A Cytokine Receptor Signaling Atlas Reveals How STAT Mosaics Fine-Tune T Cell Function

The extent to which JAK/STAT cytokine signaling is functionally redundant or selective remains debated. Here we engineered a double orthogonal IL-2/IL-2R{beta}/{gamma}c ternary system enabling programmable, interference-free activation of each of the 36 mammalian cytokine receptors, and their downstream six STATs, in T cells. At the membrane-proximal level, comprehensive phospho-signaling profiling revealed that while each receptor activates a dominant STAT, unique STAT activation fingerprints derived from combinatorial biases fine-tune nuanced T cell fates. At the membrane-distal level, single-cell transcriptomic atlas of all cytokine receptors confirmed that these STAT mosaics sensitively specify non-redundant transcriptional programs. STAT5-dominant receptors drove proliferative expansion at the expense of stemness; STAT3-driven programs instructed a continuum from stem cell memory to terminal effector states with preserved cytotoxic capacity and mediated superior curative antitumor responses; while other STATs specified highly restricted phenotypes. These findings decode a STAT signaling vocabulary that defines the intrinsic functional bandwidth of natural cytokines.

immunology↗

All-by-All Cytokine Receptor Pairing Network Unlocks Coding of Non-Natural T Cell States

Cytokine receptor pairing rules, set by evolution, confine JAK-STAT signaling to a narrow region of a far larger combinatorial space. Of more than 1,200 pairings theoretically possible among the [~]36 JAK-associated human cytokine receptors, only [~]30-40 exist in nature. Using a double-orthogonal platform, we enforced pairings across the full all-by-all receptor matrix and resolved a fine-grained STAT atlas richer than the natural repertoire. Selected non-natural pairings generated emergent T cell states unpredictable from either parental receptor, with pairing orientation encoding signaling specificity. A synthetic IL-21R>IL-2R{beta} pairing, but not its reciprocal, drove a cytotoxic Tc17-like state, whereas natural IL-9R/{gamma}c drove a Tc1 fate despite similar STAT activation, showing that rebalancing quantitative STAT combinatorics can modulate T cell fate. Recombining IL-31R, not expressed in T cells, with STAT-biased receptor partners generated diverse states, several with superior antitumor efficacy. These findings define a non-natural pairing code for engineering synthetic T cell fates.

immunology↗

Functional Pairing of TCR-peptide-MHC Interactomes by Single-cell Clonal Expansion

T cell antigen-specific immunity depends on pairwise interactions between T cell receptors and peptide-MHC, yet isolating the TCR-pMHC pairs that drive productive engagement remains a major obstacle for antigen-specific therapeutics and for decoding TCR specificity. We overcome this by co-encoding TCR and pMHC in a single founder cell, then clonally expanding it inside a semi-permeable capsule so that genetically identical daughter cells engage in trans. T cell activation, rather than binding affinity, is used to sort cells with functional pairs, and a single PCR on the clone's linked genomic library captures both partners. This platform, LINC-seq, recovered known cognate pairs from pooled libraries at up to 95% accuracy and performed simultaneous, library-on-library deep mutational scanning of both partners. Wild-type clonotypes ranked among the top-enriched sequences in complex mixtures, and the screens resolved co-evolutionary epistasis and cross-reactivity rules inaccessible to one-sided mutagenesis. The approach generalizes to any receptor-ligand pair whose trans-engagement drives a reporter.

immunology↗

IL-23 Licenses Pathogenic Th17 Transdifferentiation via STAT4-dependent Upregulation of IL-12Rβ2

Th17 cells exhibit substantial developmental plasticity, transdifferentiating into pathogenic, interferon-{gamma} (IFN-{gamma})-producing Th1-like effectors during chronic autoimmune inflammation. While both IL-23 and IL-12 are implicated in this process, how these structurally related cytokines coordinate to drive transdifferentiation remains unresolved. Here, we show that IL-23 acts as a developmental licensor rather than a terminal trigger, priming Th17 cells for transdifferentiation upon subsequent IL-12 encounter. IL-23 signals through STAT4 to upregulate the IL-12-specific receptor subunit IL-12R{beta}2, lowering the signalling threshold for IL-12. This licensing can be conferred at both early and late stages of Th17 development and produces a temporal logic in which IL-23-mediated STAT4 signaling functionally arms Th17 cells to terminally transdifferentiate in response to IL-12. Using Stat4 conditional knockouts and a structure-based IL-23 mutein that selectively abolishes IL-23-driven STAT4 signaling while preserving STAT3-dependent lineage maintenance, we genetically establish the IL-23-STAT4-IL-12R{beta}2 axis as a discrete licensing module. Furthermore, using the adoptive Th17 transfer colitis model, we show that host-derived IL-23 and IL-12 are required for Th17-driven colitis, and the inflamed colonic environment reconstitutes transdifferentiation capacity in classically "non-pathogenic" Th17 cells. These findings reframe the pathogenic dichotomy of Th17 cells as one of cumulative cytokine exposure rather than fixed cellular fate, and reveal a stepwise architecture of Th17 plasticity in which IL-23 licensing and IL-12 triggering operate as functionally distinct events. Significance StatementTh17 cells protect mucosal barriers but can convert into pathogenic, IFN-{gamma}-producing effectors that drive inflammatory bowel disease (IBD). Although IL-23 is essential for this conversion, the underlying molecular mechanism remains elusive. We show that IL-23 does not directly trigger transdifferentiation but instead licenses Th17 cells for this conversion, during both early and late stages of their development. By signaling through STAT4, IL-23 upregulates the IL-12-specific receptor subunit IL-12R{beta}2 on Th17 cells, rendering them responsive to subsequent IL-12 exposure. Our findings reframe the classical "pathogenic" versus "non-pathogenic" Th17 distinction and provide a mechanistic basis for the clinical efficacy of IL-23-targeted therapies in IBD.

immunology↗

Acetyl-CoA Synthetase 1 Regulates Global Histone Propionylation and Metabolic Stress Responses

Cells and organisms are often exposed to various metabolic environments that require adaptive responses for survival. One common way cells adapt to fluctuating nutrient environments is through regulated transcription of metabolic genes. Intermediary metabolites, such as acetyl-CoA, produced by metabolic pathways, serve as cofactors for histone post-translational modifications, which in turn regulate gene expression. However, increasing evidence shows that non-acetyl acyl-CoAs, such as propionyl-CoA, participate in gene regulation during metabolic stress. In this report, we find that histone propionylation functions as a global response to glucose starvation. Furthermore, we find that Acetyl-CoA Synthetase 1 (Acs1) binds chromatin and is the primary enzyme responsible for generating propionyl-CoA in the nucleus. Together, our findings reveal that Acs1-mediated histone propionylation constitutes a novel pathway for metabolic adaptation, linking nutrient availability to chromatin modification.

molecular biology↗

Systematic mapping of emergent transcriptional states in interacting single-cell dyads by Cell-Cell-seq

Cell-cell interactions drive rapid and heterogeneous changes in gene expression, yet most transcriptomic methods either dissociate cells, losing pair identity and interaction timing, or infer communication indirectly from ligand-receptor co-expression. Here we present Cell-Cell-seq, a scalable workflow for profiling defined cell pairs ("dyads") with single-cell transcriptomic resolution. Cell-Cell-seq uses cavity-containing hydrogel microparticles (Nanovials) to confine two cells, synchronize contact onset, protect fragile conjugates during handling and sorting, and interface directly with droplet-based RNA sequencing. Using antigen-matched prostate tumor cells and engineered T cells as a model system, Cell-Cell-seq captured thousands of tumor-T cell dyads and revealed broad functional and transcriptional heterogeneity across interactions. Dyads unmasked transient activation programs that were obscured in standard well-plate co-culture, consistent with asynchronous contact in bulk assays. To distinguish interaction-induced programs from the composite nature of dyad transcriptomes, we developed a pseudo-mixing framework that generates in silico pseudo-dyads to construct an empirical null distribution under "no interaction," enabling statistically robust identification of emergent genes and partner-resolved attribution of responses. Dyad-resolved analysis further revealed coordinated cross-cell programs, including coupled chemokine expression consistent with bidirectional paracrine signaling and inverse coupling between tumor immunoregulatory programs and T cell activation. Finally, we introduce ccRepair to correct compositional dilution in mixed transcriptomes, improving interpretability while preserving genuine cross-cell coordination. Together, Cell-Cell-seq provides a generalizable platform for dissecting immune synapse biology and mapping interaction-dependent programs across heterogeneous cell populations, with applications in profiling tumor-immune communication and functionally screening immunotherapies.

bioengineering↗

Antibody Fc receptor CD16a mediates natural killer cell activation via mechanotransduction of piconewton forces

Natural Killer(NK) cells eliminate target cells through antibody-dependent cell-mediated cytotoxicity(ADCC), initiated by CD16a(Fc{gamma}RIIIa) recognizing the Fc region of antibodies bound to the target cell surface. While the recognition is considered to be driven by CD16a-Fc binding avidity, it fails to explain why Fc multimers inhibit ADCC rather than trigger it. Here, we reveal that CD16a transduces piconewton forces, and acts as a mechanosensor to facilitate NK activation. We demonstrate that CD16a force and the actin foci formation associated with it are essential for the phosphorylation of mechanosensitive adaptor Cas-L and signaling adaptor LAT, reshaping NK cell cytoskeletal dynamics and signaling. Our findings show that NK activation is an intricate process that integrates both biochemical and biophysical information, and provides new mechanistic insight for immunoengineering.

biophysics↗

Selective Immune Silencing by Targeted TGF-β Agonists

Depletion of pathogenic T and B cells is a pillar of therapies for autoimmune, inflammatory, and transplantation-related immunological diseases. However, adverse events, safety concerns in immunocompromised patients, and disease relapse limit clinical utility. Here, we exploit the immunosuppressive properties of a transforming growth factor beta (TGF-{beta}) mimic repurposed from helminths for cell type-specific therapeutic silencing, as a new approach to complement existing therapies. Mouse CD4 and CD8 T cell-targeted TGF-{beta} agonists selectively and potently silence antigen-specific T cell responses in OVA-immunized mice by suppressing pro-inflammatory effector, cytotoxic, and T follicular helper programs, while skewing cells toward a quiescent state biased toward regulatory and type 17 T cell phenotypes. Similarly, human CD4 and CD8 T cell-targeted TGF-{beta} agonists precisely and effectively suppress live-attenuated influenza vaccine (LAIV)-induced T cell activation and expansion in human spleen organoids. Correspondingly, CD4 T cell-targeted TGF-{beta} agonist effectively ameliorated disease activity and promoted disease remission in CD4 T cell-driven models of autoimmune neuroinflammation and allergic airway inflammation, demonstrating efficacy in both prophylactic and established inflammatory settings. Moreover, both CD4 and CD8 T cell-targeted TGF-{beta} agonists ameliorated disease activity in graft-versus-host disease. Additionally, a human CD19 B cell-targeted TGF-{beta} agonist robustly inhibits germinal center B cell-to-plasmablast maturation and antibody responses in LAIV-stimulated human spleen organoids. These early-stage results suggest that cell-selective TGF-{beta} agonism merits further investigation as a versatile therapeutic approach for the precise silencing of pathogenic adaptive immune responses.

immunology↗

Structural basis of stepwise G protein activation by a viral chemokine receptor

G protein-coupled receptors (GPCRs) govern diverse cellular responses and are crucial drug targets. However, the sequence of structural events from G protein recognition to GDP release has remained elusive. Here, we leveraged the viral chemokine GPCR US28 to capture multiple activation states of the US28-Gq complex. Using cryo-electron microscopy and an engineered chemokine superagonist, we determined three distinct complex structures, capturing a GDP-bound Encounter state, the nucleotide-free Canonical state, and a putative intermediate bridging the two states, the Transition-to-Canonical state. These structures, along with simulations and functional data, provide high-resolution snapshots of a plausible G protein activation trajectory and support a stepwise conformational model for G protein activation. This activation cascade closely parallels mechanisms proposed for human GPCRs, suggesting a conserved GPCR signaling mechanism.

biophysics↗

Bispecific T cell engagers control solid tumors through clonal replacement and IL2-driven effector differentiation of CD8 T-cells

Bispecific T cell engagers (TCEs) often exhibit limited efficacy in solid tumors, in part due to immunosuppressive cues in the tumor microenvironment and low expression of targetable tumor antigens. Therapeutic strategies to improve TCE target sensitivity and enhance T cell effector functions therefore have significant translational potential. Here, we engineered TCEs that induce T cell activation in vitro against the low-abundance target antigens, TRP2/Kb and DLL3. Despite in vitro activity in these models, TCE monotherapy showed limited control of tumor growth in immunocompetent mice. Leveraging this in vivo model of TCE treatment failure, we discovered that co-treatment with TCE and a CD25-biased Interleukin-2 (IL2) rescues anti-tumor activity. Further, multimodal single-cell transcriptomic and immune repertoire analyses revealed that TCE-IL2 combination therapy controlled tumors by recruiting and activating new CD8+ T cells into the tumor microenvironment. These findings demonstrate that TCE-mediated anti-tumor responses function through a CD8+ T cell clonal replacement mechanism that can be augmented by cytokine therapy. One Sentence SummaryCombining TCE therapy with IL-2 enhances TCE efficacy in aggressive small-cell lung cancer and melanoma models with low target antigen density through T cell clonal replacement and CD8+ effector T cell differentiation.

cancer biology↗

Targeting peptide-MHC complexes with designed T cell receptors and antibodies

Class I major histocompatibility complexes (MHCs), expressed on the surface of all nucleated cells, present peptides derived from intracellular proteins for surveillance by T cells. The precise recognition of foreign or mutated peptide-MHC (pMHC) complexes by T cell receptors (TCRs) is central to immune defense against pathogens and tumors. Although patient-derived TCRs specific for cancer-associated antigens have been used to engineer tumor-targeting therapies, their reactivity toward self- or near-self antigens may be constrained by negative selection in the thymus. Here, we introduce a structure-based deep learning framework, ADAPT (Antigen-receptor Design Against Peptide-MHC Targets), for the design of TCRs and antibodies that bind to pMHC targets of interest. We evaluate the ADAPT pipeline by designing and characterizing TCRs and antibodies against a diverse panel of pMHCs. Cryogenic electron microscopy structures of two designed antibodies bound to their respective pMHC targets demonstrate atomic-level accuracy at the recognition interface, supporting the robustness of our structure-based approach. Computationally designed TCRs and antibodies targeting pMHC complexes could enable a broad range of therapeutic applications, from cancer immunotherapy to autoimmune disease treatment, and insights gained from TCR-pMHC design should advance predictive understanding of TCR specificity with implications for basic immunology and clinical diagnostics.

immunology↗

Type I interferon signaling instills divergent metastatic phenotypes and immunotherapy responses

Metastatic colonization of distant tissues is responsible for most cancer deaths, yet while this colonization is typically preceded by lymph node (LN) metastasis, the clonal and functional relationships between metastases in these tissues remain unclear. Reconstruction of metastatic phylogenies in mouse models and patients suggests that LN and distant organ metastases are often seeded by independent clones, yet no genetic alterations have bene found to account for this divergent seeding. Here, we discover opposing roles for interferon signaling in metastasis to LNs and distant organs. We uncover that exposure to leukocyte-derived type I interferon promotes LN metastasis while impairing spread to distant organs by inducing interferon-stimulated gene (ISG) expression. Further, while LN metastases have previously been demonstrated to disrupt anti-tumor immunity, we find that ISG expression induced during LN metastasis sensitizes tumors to immune checkpoint blockade (ICB). By mimicking the phenotype of LN metastases through delivery of type I interferon, ICB refractory primary tumors and distant metastases can be sensitized to ICB. Collectively, these findings demonstrate that the immune system conditions tumors for LN metastasis through type I interferon secretion while impairing distant spread and that this axis can be exploited to render immunotherapy resistant tumors sensitive to immune checkpoint blockade therapy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/677123v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@197cf34org.highwire.dtl.DTLVardef@1a466eborg.highwire.dtl.DTLVardef@60ead7org.highwire.dtl.DTLVardef@d9ce93_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

cancer biology↗

Receptor-tethered orthogonal IL-2 enhances regulatory T cell therapy

Regulatory T cell (Treg) therapy is an emerging platform for controlling immune overactivation. Efficacy of Treg therapy is limited by the poor persistence of infused Tregs due to insufficient IL-2, which is essential for Treg survival and function. IL-2 activates many immune cells besides Tregs, imposing a challenge for the selective provision of IL-2 to infused Tregs. In this study, we found infusions of orthogonal (ortho) IL-2 failed to enhance Tregs engineered with a corresponding orthoIL-2 receptor (IL-2R) in a mouse model of autoimmune diabetes. We then developed a receptor-tethered orthoIL-2 by optimizing the combination of IL-2, IL-2R, and the linker connecting them to achieve autocrine signaling selectively in engineered Tregs. Tregs expressing the tethered orthoIL-2 showed autocrine IL-2 signaling in vitro, enhanced CD25, CTLA-4, and Foxp3 expression, persisted without exogenous IL-2 in vivo, and prevented autoimmune diabetes using as few as 2,000 Tregs. Knocking the tethered orthoIL-2 construct into the Foxp3 locus enabled Treg-specific expression, with the additional benefit of positively reinforcing tethered orthoIL-2 expression through the activation of the Foxp3 gene by enhanced IL-2 signaling. Together, these results illustrate a safe and effective cell-engineering solution for overcoming Tregs dependency on exogenous IL-2, thereby achieving superior therapeutic efficacy.

immunology↗

Two parallel lineage-committed progenitors contribute to the developing brain

The hindbrain is a life-sustaining brain region. In one model, a common neural progenitor generates all brain regions. Here our studies of mouse embryos and human pluripotent stem cells (hPSCs) support a different model: two parallel brain progenitors emerge simultaneously during gastrulation, anterior neural ectoderm (forebrain/midbrain progenitor) and posterior neural ectoderm (hindbrain progenitor). Not only are they lineage-committed to respectively form forebrain/midbrain vs. hindbrain in vitro, but they also have diverging chromatin landscapes foreshadowing future forebrain/midbrain vs. hindbrain identities. Leveraging these differences, we differentiated hPSCs into hindbrain rhombomere 5/6-specific motor neurons, hitherto difficult to generate in vitro. We postulate the brain is a composite organ emanating from two lineage-restricted progenitors; these dual progenitors may be evolutionarily conserved across 550 million years from hemichordates to mammals.

developmental biology↗

Intra-Tumoral Treg Ablation Unleashes NK Cell-Mediated Control of CD8 T Cell-Resistant Tumors

Cancer cells frequently lose MHC I to evade CD8+ T cell recognition. While Natural Killer (NK) cells are poised to target MHC I-deficient cancer cells, MHC I loss alone is often insufficient to unleash fully effective NK cell responses. Here we show that selective intra-tumoral (IT) ablation of regulatory T (Treg) cells elicited potent antitumor NK cell responses that controlled MHC I-deficient and even MHC I+ cancers. Tregs controlled the activation, maturation, and anti-tumor cytotoxic activity of NK cells within the tumor microenvironment. Mechanistically, IT Tregs prevented the cDC2-dependent induction of IL-2 production by CD4+ Tconv cells that was necessary for NK cell activation. Systemically administered antibodies that selectively depleted IT Tregs similarly empowered NK- dependent tumor control. These findings expand the breadth of Treg-mediated cancer immunosuppression to encompass antitumor NK cells and suggest that targeting Tregs in tumors can control CD8+ T cell-resistant cancers. One Sentence SummaryIT Treg ablation drives NK cell tumor control via CD4+ Tconv-derived IL-2, eliminating MHC I+/MHC I- cancers without systemic toxicity.

immunology↗

Designed NGF mimetics with reduced nociceptive signatures in neurons

The clinical use of Nerve Growth Factor (NGF) for neuronal regeneration has been hampered by pain sensitization side effects. NGF signals through the receptor tyrosine kinase TrkA and the co-receptor p75NTR; pain sensitization is thought to involve p75NTR. We sought to overcome this limitation by de novo design of a TrkA agonist that does not bind p75NTR. We designed homodimeric TrkA engaging constructs that dimerize TrkA subunits in a variety of geometries, and identified those eliciting the strongest signaling. The resulting designed agonists are able to stimulate transdifferentiated neurons and neuroblastoma cell lines, leading to neurite outgrowth and neuronal differentiation, with considerably reduced transcription of inflammation and pain related genes. These agonists are promising candidates for promoting neuronal regeneration without adverse side effects. HighlightsO_LIDe novo designed TrkA agonists activate MAPK and PI3K-AKT signaling C_LIO_LIRigid fusions allow for highly tunable signaling signatures C_LIO_LITrkA agonists lead to neurite outgrowth in neuroblastoma cells comparable to retinoic acid C_LIO_LIModulation of the TrkA pathway without co-stimulating p75NTR leads to a downregulation of inflammatory and nociceptive signature in neurons. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/648806v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@c48066org.highwire.dtl.DTLVardef@c9c5a7org.highwire.dtl.DTLVardef@cf8ebdorg.highwire.dtl.DTLVardef@a4345a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Design of solubly expressed miniaturized SMART MHCs

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 {beta}2-microglobulin ({beta}2m) and the heavy chain 3 domain, and enable soluble expression of both H-2Db 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. SignificanceDespite 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-2Db 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.

biochemistry↗