Biology subjects

Yuan, S.

Publications and source records attributed to Yuan, S..

At least 19 recordsLinked to original sources

bioRxiv2026

GLOM TGITO: multiscale protein modelling and multiview landscape-guided sequence discovery

Motivation: Offline protein design must seek high-activity variants while retaining support for their predicted performance. The challenge is to explore multiple promising regions without confining the search to average-performing sequences. We test whether multiscale representations and local evidence can guide this search. Results: GLOM-TGITO links a global-local fluorescence predictor to multiview landscape-guided optimization. Across 31,434 measured ppluGFP2 sequences, GLOM achieved random/depth-holdout RMSEs of 0.170/0.247 versus 0.247/0.324 for the strongest SaProt-650M controls. Averaged across three training seeds, 96.3%/97.3% of prediction-ranked Top 100 test variants were measured bright (log10 fluorescence >=4.2). Search from 900 peak regions yielded 2,594 distinct candidate sequences. The selected Top 100 showed 2.9-8.2% lower mean representation deviation than four comparator pipelines; 38 versus 11-16 met joint novelty-reliability filters. Deviation identified measured test errors >0.1 (AUROC 0.773). The first molecular-dynamics run of the selected Top 30 identified smaller surface hydrophobic patches in 20 candidates relative to their starts, with representative variants showing more persistent chromophore contacts or narrower torsional fluctuations.

bioinformatics↗

bioRxiv2026

The bacterial antiphage protein Tiamat is an ATPase and DNase whose homologs are found across the tree of life

Bacteria and archaea encode hundreds of antiviral defense systems, some with homologs found in eukaryotic innate immunity. GHL ATPases like plant MORCs and prokaryotic Tiamat defend against viruses and phage, though their architecture and biochemical activities have remained unclear. Searching thousands of proteomes, we find Tiamat is rare in prokaryotes yet enriched across eukaryotes, including green plants, aquatic chordates, sponges, placozoans, and water molds. We resolve the central DUF3684 and flanking region into three predicted folds (TPR-like repeats, an uncharacterized conserved fold, and an inactive metalloprotease-like fold) that occupy the substrate-binding position of other GHL proteins. We show that purified Bacillus cereus Tiamat hydrolyzes ATP, inefficiently nicks duplex DNA, and cleaves single-stranded DNA site-specifically. We identify Tiamat-like proteins whose C-terminal nuclease is often swapped for helicases, peptidases, or other effectors. Additionally, we show Tiamat genes neighbor helicases, DNA methyltransferases, and nucleases, suggesting some Tiamats degrade foreign nucleic acid within a multi-component complex. Eukaryotic Tiamat homologs like the close Arabidopsis homolog NO VEIN and the distant human homolog SACSIN have acquired critical non-defense roles, leaving open whether these homologs remain antiviral or have been exapted.

biochemistry↗

bioRxiv2026

A Dynamically Regulated Designed IL-2 for Tumor-localized Signaling

Cytokines mediate cell-cell communication to coordinate immune responses and hold clinical promise as immunotherapies. While natural cytokines are exquisitely regulated by immune cells, engineered cytokines have not yet matched this sophisticated regulation, limiting clinical efficacy and safety. IL-2 is an important cytokine involved in antitumor response, but its production is disrupted in the immune-suppressive tumor microenvironment. Here we designed a regulated IL-2 module, OUTSMART designed IL-2 (dIL-2), that functions robustly in solid tumors and reduces systemic activity that could trigger toxicity: we computationally redesigned IL-2 to have a novel topology that increases stability, preserves native IL-2R{beta}{gamma} interfaces, ablates IL-2R binding, and delivers IL-2 signaling to CD8+ immune-effector cells. This designed cytokine is genetically regulated by a T cell activation-responsive promoter, allowing dynamic production from chimeric antigen receptor (CAR) T cells. Like wild type IL-2, OUTSMART dIL-2 drives T cell proliferation and enhances effector function. Unlike wild type IL-2, it preferentially stimulates CD8+ T cells and Natural Killer (NK) cells, avoids T regulatory cells, and stimulates CAR-T proliferation while preserving stemness, achieving durable tumor elimination in two solid tumor animal models. These design principles can be applied to create other dynamically-regulated cytokine systems that address mechanisms of complex disease.

synthetic biology↗

bioRxiv2026

A Rationally Designed Transgene Drives CAR T Functional Persistence and Durable Regression of Solid Tumors

The eradication of solid tumors by chimeric antigen receptor (CAR) T cells requires dynamic therapies capable of outlasting an immune suppressive tumor microenvironment (TME). However, biological barriers--including rapid exhaustion, poor expansion, and loss of stem-like memory--quickly neutralize these therapies. Because single-technology interventions often introduce unacceptable tradeoffs between efficacy and safety, durable remission demands a paradigm where multiple engineered solutions work in concert. To holistically address these mechanisms, we rationally designed a single-vector transgene that intrinsically drives CAR T functional persistence. The platform integrates four synergistic technologies: a high-avidity mesothelin (MSLN)-targeting CAR optimized to resist shed decoy antigens, a T-cell activation-responsive promoter (OUTLAST OP1) resisting exhaustion, a CD8-targeted designed IL-2 cytokine (OUTSMART dIL-2) driving intratumoral CAR-T expansion, and an EGFRopt safety switch. In lung and ovarian cancer models, this rational integration was required to drive antigen-dependent T cell expansion and eradicate established tumors at extremely low CAR T doses. Furthermore, engineered cells established a self-renewing pool of stem-like memory T cells capable of rejecting tumor rechallenge months later. Ultimately, this work demonstrates that intrinsic T cell dysfunction and extrinsic tumor-derived barriers can be simultaneously overcome by integrating synergistic technologies.

synthetic biology↗

bioRxiv2026

Active control modulates memory-related activity during encoding and encoding-retrieval similarity

Self-directed learning allows learners to actively control their learning experience and has been shown to enhance memory compared with matched yoked learning. However, it remains unclear when and how active control modulates memory-related neural activity during learning and retrieval. We recorded electroencephalography (EEG) while participants encoded objects under active and yoked learning conditions and again during a delayed recognition test approximately 24 h later. We examined event-related potential (ERP) activity across earlier processing windows, including pre-stimulus slow potentials and early N2 activity, and later processing windows, including P300, late slow-wave, and post-stimulus slow-potential activity. We also examined encoding-retrieval similarity (ERS) between neural patterns during encoding and retrieval. Behaviorally, active control improved delayed recognition, with the advantage selectively expressed in detailed recognition. In the ERP analyses, earlier processing windows showed memory-related effects, with pre-stimulus slow-potential and N2 activity differentiating subsequently remembered from forgotten items, but were not modulated by active control. By contrast, active control modulated later memory-related ERP activity, with remembered-forgotten differences expressed during late stimulus-related and immediate post-stimulus processing only in the active condition. ERS showed a similar active-control modulation: memory-related encoding-retrieval pattern similarity was evident under active learning, but not under yoked learning, with this effect involving relatively late encoding and retrieval windows. Together, these findings support a constructive-processing account, suggesting that memory formation under active control depends more strongly on rich, detailed encoding representations that can be reinstated during retrieval.

neuroscience↗

bioRxiv2026

A small molecule inhibitor of CD28 costimulation restrains pathogenic T-cell responses in inflammatory bowel disease

CD28 costimulation contributes to pathogenic T cell responses in inflammatory bowel disease (IBD), but current B7-directed blockade also limits CTLA-4 signaling. Using a sensitive NanoBiT split-luciferase screening platform, we identified and optimized CA-23, a small molecule antagonist that directly binds human and mouse CD28 without measurable binding to CD80, CD86, or CTLA-4. CA-23 inhibited CD28-B7 engagement and CD28-dependent T cell activation without agonist activity in human whole blood and peripheral blood mononuclear cells. CA-23 achieved exposure in the colon and mesenteric lymph nodes and reduced disease severity, histologic injury, and pathogenic Th1 and Th17 responses in a T cell transfer model of colitis. In PBMCs from donors with ulcerative colitis or Crohns disease, CA-23 suppressed inflammatory cytokine production and T cell activation to a degree matching or exceeding Abatacept. In human intestinal epithelial-PBMC co-cultures, CA-23 preserved Treg suppressive activity and epithelial barrier integrity, whereas Abatacept reduced Treg function. CA-23 did not alter CD80 or CD86 expression on autologous antigen-presenting cells and showed no substantial off-target activity in the tested selectivity panel. These findings support direct CD28 antagonism as a mechanistically differentiated alternative to B7-directed co-stimulation blockade for suppressing pathogenic T cell responses in preclinical models of IBD. One Sentence SummaryA CD28-selective small molecule blocks pathogenic T cell activation and preserves Treg function unlike Abatacept in IBD models.

pharmacology and toxicology↗

bioRxiv2026

MG2Act: A Mechanism-Inspired Sequential Attention Framework for Molecular Glue Degradation Prediction

Molecular glue degraders act by inducing productive proximity between an E3 ligase and a substrate protein. For most characterized degradative glues, a small molecule first engages the E3, conditions its substrate-recognition surface, and only then enables recruitment of a compatible neo-substrate. This directionality is rarely encoded explicitly in computational models, which typically fuse molecule, E3 and target representations simultaneously. We present MG2Act, a structure-independent framework that translates this two-step logic into sequential cross-attention, using CRBN-mediated degradation as the most data-rich representative system. Starting from a curated continuous-valued benchmark of 1,207 pairs across 47 targets, a refined subset of 1,159 pairs was selected to train MG2Act after excluding rare targets. On identical processed data, MG2Act consistently outperforms machine learning baselines, robustly generalizes under strict redundancy-filtering, and responds coherently to mechanism-based perturbations. Prospective screening and zero-shot target-conditioned prioritization identified nanomolar degraders of IKZF1, CK1 and CDK4, including the non-classical IMiD-core CDK4 degrader SWC-202.

bioinformatics↗

bioRxiv2026

Protein design to broadly reprogram engineered T cell function

The efficacy of engineered T cell therapies in solid tumors remains limited by T cell dysfunction, driven by complex processes that cannot be easily manipulated via genetic knockouts or overexpression of individual genes. Protein design can create new biological functions that can rewire these consequential cell fate decisions. Here, we introduce OUTLAST Regulators, designed proteins that reprogram critical T cell signaling pathways to enhance functional persistence. These proteins are capable of regulating diverse groups of proteins such as the NR4A family of pro-exhaustion transcription factors, E3 ligases Cbl-b and c-Cbl, and SOCS family proteins. Our designs markedly improve CAR-T and TCR-T performance in vitro and in vivo in stringent solid tumor preclinical models. OUTLAST Regulators are implemented as compact genetic modules compatible with standard viral vectors and cell therapy manufacturing processes, creating a powerful platform for programming new functions into enhanced cell and gene therapies.

synthetic biology↗

bioRxiv2026

A Quartet of Native Orai Channel Isoforms Orchestrates Graded NFAT Activation and Transcription

The Ca{superscript 2} release-activated Ca{superscript 2} (CRAC) channel mediates store-operated calcium entry (SOCE), a ubiquitous pathway essential for many cell types, including immune cells. Three Orai (Orai1/2/3) proteins constitute the plasma membrane pore-forming units of CRAC channels that are activated by the endoplasmic reticulum (ER) Ca2+-sensing STIM1/2 proteins when ER Ca2+ stores are depleted. Orai1/2/3 are differentially expressed across primary cells with discernible differences in their structures and biophysical properties. Further, Orai1 has two alternatively translated isoforms: long mammalian-specific Orai1 and the 63-residue shorter Orai1{beta}, which is evolutionarily older and conserved across vertebrates. Whether Orai1/1{beta}/2/3 produce unique cytosolic Ca{superscript 2} signatures that bias transcriptional responses through effectors like NFAT is unclear. Here, we used HEK293 cells engineered to express one native Orai isoform and show that all Orai isoforms couple to NFAT1/4 induction. The magnitude of NFAT1/4 induction for each Orai isoform matches that of SOCE, with the following profile: Orai1{beta}>Orai1>>Orai2>Orai3. Near-native re-expression of either Orai1 or Orai1{beta} in primary murine Orai1-/- CD4 T cells restored SOCE, NFAT activation, cytokine production and promoted near identical transcriptional responses enriched for immune activation pathways. An analysis of genetic and clinical data of human individuals showed that homozygous null mutations selectively abolishing Orai1 are not associated with disease resembling CRAC channelopathy. Primary T cells from individuals homozygous or heterozygous for an Orai1 null mutation showed enhanced, rather than impaired, SOCE and NFAT induction. Our data indicate that NFAT activation and transcriptional outputs are primarily driven by the graded strength of SOCE mediated by each isoform of the Orai quartet.

cell biology↗

bioRxiv2026

Ancient pyroptotic machinery via GSDMA/B cleavage by LPS-activated caspase-1 in cartilaginous fish

Gasdermins are pore-forming effectors that mediate pyroptosis, an inflammatory form of programmed cell death characterized by membrane permeabilization and the release of intracellular contents. Phylogenetically, gasdermin members can be broadly divided into two major branches, the GSDME/PJVK branch and the GSDMA/B/C/D branch. Whereas the GSDME mediated pyroptosis was traced back to metazoans, the functional origins of GSDMA/B/C/D branch remain poorly understood. As a basal representative of the GSDMA-D lineage in cartilaginous fish, Callorhinchus milii GSDMA/B (CmiGSDMA/B) provides essential information for the ancestral state of this branch. Here, we functionally characterized CmiGSDMA/B and identified CmiCASP1 as its upstream protease. Mechanistically, Lipopolysaccharide (LPS) activates CmiCASP1 via its CARD domain, leading to cleavage of CmiGSDMA/B into two functionally distinct products, N241 and N288. N241 binds cell membrane to drive pyroptosis, whereas N288 suppresses N241-triggered cell death. Interestingly, N241 exhibits bactericidal activity against Gram-negative bacteria in vitro, suggesting that antimicrobial activity may have been an early feature of the GSDMA-D lineage. Collectively, these findings provide insight into a non-canonical, LPS-responsive, caspase-driven pyroptosis pathway in cartilaginous fish and reveal the dual-fragment antagonistic regulation within this branch.

evolutionary biology↗

bioRxiv2026

ANCHOR: haplotype-aware allelic and isoform inference from single-cell long-read RNA sequencing with de novo variant calling

Long-read RNA sequencing enables haplotype- and isoform-resolved allelic analysis of transcriptomes, yet extending this capability to single cells and distinct cell types remains computationally challenging due to sparse coverage, sequencing errors, incomplete variant information, and reference-biased transcript assignment. Here we present ANCHOR, a haplotype-aware framework for single-cell long-read RNA sequencing that performs de novo expressed-variant discovery, molecule-level haplotype assignment and isoform-resolved allelic quantification. ANCHOR combines a signed-graph variant caller, pair hidden Markov modelling and beta-binomial UMI aggregation to infer parental allele counts for genes and splice-resolved isoforms, without requiring a pre-existing phased genotype or deep learning. In human single-cell long-read RNA benchmarks, ANCHOR improved variant-calling performance over tested long-read RNA callers at single-cell and low-to-moderate coverage, and its beta-binomial model reduced depth-driven false positives in allele-specific expression testing. Applied to newly generated single-cell long-read RNA-seq data from reciprocal mouse crosses during gastrulation, ANCHOR resolved cell-type- and isoform-specific parent-of-origin imprinting and identified an antagonistic maternally biased Sgce isoform. ANCHOR provides a general framework for allele-and isoform-resolved analysis of diploid single-cell long-read transcriptomes.

bioinformatics↗

bioRxiv2026

Tracing the Evolutionary Origin of Interferon to Basal Chordates and Unveiling Its Antiviral Functionality in Jawless Vertebrates

Interferons (IFNs) are essential mediators of antiviral defense in vertebrates, having gradually replaced the RNA interference (RNAi) antiviral mechanism that predominates in invertebrates and plants. To date, IFNs have been identified exclusively in jawed vertebrates, leaving the origin of IFN-based antiviral mechanisms largely mysterious. In this study, by conducting a genome-wide screening of IFN homologs accross various species, we successfully identified seveal IFN homologs from agnatha and lancelet, but not other invertebrates. Notably, both agnatha and lancelet IFN homologs have ability to induce a set of interferon-stimulated genes (ISGs)-like genes, thus tracing the origin of IFN to basal chordate. Using VSV infected peripheral blood mononuclear cells (PBMCs) of Japanese lampreys, we found that lamprey IFNs have antiviral functionality by inducing the expression of hundreds of ISGs through interacting with a heterodimeric complex composed of CRFB7 and CRFB14. In addition to robustly mediating antiviral responses in monocytes, lamprey IFNs exert their effects on variable lymphocyte receptor B (VLRB)+ cells by remodeling the cytokine/chemokine networks to orchestrate antiviral innate and adaptive immunity. Furthermore, cross-species functional comparison of Dicer revealed that changes in residues essential for dsRNA processing occurred concurrently with the evolution of the IFN system. Collectively, these findings uncover the evolutionary origin of IFN and underscore its ancient roles in antiviral response and immune regulation, especially in the takeover of the RNAi antiviral mechanism during the early evolution of vertebrates. Significance StatementInterferons (IFNs) represent a hallmark of vertebrate antiviral immunity, yet their origin has remained elusive. Here, we reported bona fide IFN ligands and cognate receptors in both lamprey and lancelet, two key species placed at the transition from invertebrates to vertebrates. Using the VSV infection model, we further demonstrated the roles of lamprey IFN in antiviral defense and immune regulation. We also found that substitutions in residues essential for Dicer mediated dsRNA processing coincided with the emergence of the IFN system. Collectively, our findings provide key insights into the evolutionary origin of IFN-based immunity and its gradual replacement of RNAi as the dominant antiviral strategy in vertebrates.

evolutionary biology↗

bioRxiv2026

Inhibition of hexokinase 2 undermines cartilage health and accelerates osteoarthritis

ObjectiveEnhanced glycolysis is a metabolic hallmark of chondrocytes in osteoarthritis (OA); however, the roles of the glycolytic rate-limiting enzyme hexokinase 2 (HK2) in cartilage remain poorly understood. MethodsPharmacological approach (3-bromopyruvate (3-BrPA) treatment) and mice model involving HK2 knockout in Col2a1-expressing chondrocytes are utilized to access the impact of HK2 blockage on cartilage ex vivo and in vivo. The in vivo effects of HK2 inhibition on OA progression were evaluated using a destabilization of the medial meniscus (DMM)-induced OA mouse model, through both intra-articular 3-BrPA administration and chondrocyte HK2 deletion. Additionally, we analyzed published single-cell RNA sequencing (scRNA-seq) datasets from human articular cartilage and integrated these with bulk RNA-seq data from HK2-deficient chondrocytes to characterize HK2 expression features across conditions. ResultsBoth pharmacological inhibition and genetic deletion of HK2 impair cartilage formation ex vivo. Bulk RNA-seq analysis and ex vivo studies demonstrated a promoted ossification-like process due to HK2 ablation in chondrocytes. Through pseudotime analysis of published single-cell RNA sequencing (scRNA-seq) datasets from human articular cartilages, we further identified that HK2 is differentially expressed across conditions, with a feature of a relatively high expression level at terminal stages of chondrocyte differentiation in the context of OA. We next confirmed HK2 deficiency in chondrocytes significantly exacerbated OA progression but having no impact on skeletal development in mice. ConclusionsHK2 plays a critical role in maintaining cartilage health, likely through the regulation of calcification, thereby highlighting the potential risks associated with targeting glycolytic enzymes as a therapeutic strategy for OA.

pathology↗

bioRxiv2026

WTAP-mediated epitranscriptomic program in alveolar macrophages confers prolonged protection against postinfluenza bacterial pneumonia

Secondary bacterial infections remain an intractable problem of seasonal influenza, primarily due to the depletion and defunctionalization of alveolar macrophages (AMs). Here, we described that N6-methyladenosine (m6A), the most prevalent RNA modification in eukaryotes, critically orchestrates trained immunity (TRIM) establishment in AMs. Influenza A virus (IAV)-trained AMs maintained low Wilms tumor 1-associated protein (WTAP) expression and reduced global m6A deposition for over two months. Mechanistically, this IAV-induced m6A decrease promotes TRIM by enhancing the RNA stability of phagocytic and metabolic genes, thereby boosting antibacterial function. Mimicking this m6A reduction pharmacologically or genetically recapitulates the IAV-trained TRIM phenotype, which improves phagocytosis and protects mice from secondary infection. Clinically, elevated WTAP in AMs correlates with impaired phagocytosis and disease severity in COVID-19 and COPD. These findings for the first time unveil how respiratory virus infection shapes AM TRIM via epitranscriptomic reprogramming, and offer prospective strategies for the prevention and treatment of post-viral bacterial complications.

immunology↗

bioRxiv2026

Dual histone methylation reader ZCWPW2 links histone methylation to initiation of meiotic recombination

Meiotic homologous recombination initiates with the formation of programmed DNA double-strand breaks (DSBs) by complexes comprising SPO11 and accessory proteins at discrete sites called recombination hotspots. In mammals, PRDM9-dependent H3K4me3 and H3K36me3 define recombination hotspots, but how these epigenetic characteristics determine the physiological DSB formation remains unknown. Here we show that dual histone methylation reader ZCWPW2 can recognize H3K4me3 and H3K36me3 marks in testis. The binding activity of ZCWPW2 to histone methylation is dependent on PRDM9 function. Moreover, we find the epigenetic writer-reader axis PRDM9-ZCWPW2 is essential for DSB formation at meiotic recombination hotspots, which may be partly explained by the finding that ZCWPW2 can physically interact with HORMAD1, IHO1, MEI4, and REC114. Finally, the absence of ZCWPW2 leads to disrupted chromosomal synapsis and recombination, thereby obstructing meiotic progression. Taken together, our findings provide new insights into how histone modifications and their associated regulatory proteins collectively regulate meiotic homologous recombination initiation.

cell biology↗

bioRxiv2026

Cyclic Peptides Target CAPON and Modulate Cellular Responses under Alzheimers Disease-Relevant Stress

CAPON (NOS1AP) is an adaptor protein involved in neuronal nitric oxide synthase (nNOS) signaling and has been implicated in Alzheimers disease (AD), excitotoxicity, and tau-associated neurodegeneration. Here, we report the identification of cyclic peptide ligands targeting CAPON using phage display screening of a disulfide-constrained peptide library. Phage enrichment, ELISA validation, microscale thermophoresis (MST), and biolayer interferometry (BLI) identified CAP1 as the lead peptide, exhibiting low micromolar binding affinity toward CAPON. Computational studies further supported stable CAPON-CAP1 interactions through complementary hydrophobic and electrostatic contacts. Functionally, CAP1 attenuated A{beta}42-induced neuronal toxicity, suppressed NMDA-driven nitric oxide production, and reduced pathological tau phosphorylation in neuronal models under AD-relevant stress conditions. In addition, CAP1 demonstrated favorable preliminary pharmacokinetic properties, including good aqueous solubility, plasma stability, and measurable membrane permeability. Collectively, these findings establish the first cyclic peptide ligands targeting CAPON and identify CAP1 as a promising scaffold for modulation of CAPON-dependent neurodegenerative signaling.

pharmacology and toxicology↗

bioRxiv2026

A JNK-interacting protein 1 acts across the midline to mediate synaptic localization of the SARM1 calcium-signaling scaffold protein for asymmetric neuronal fate choice

The Caenorhabditis elegans AWC olfactory neuron pair specifies asymmetric subtypes, AWCOFF and AWCON, through stochastic and coordinated cell signaling events. UNC-104/kinesin-3 (KIF1A) and UNC-116/kinesin-1 motor proteins act in the AWCON cell to regulate the synaptic localization of the TIR-1/SARM1-assembled calcium signaling complex in the AWCOFF cell to promote AWCOFF. However, the molecular mechanism in the AWCON cell that acts non-cell autonomously to control synaptic TIR-1 calcium signaling to promote AWCOFF remains unclear. Here, we show that JIP-1, a conserved c-Jun N-terminal kinase (JNK)-interacting protein 1, mediates the synaptic localization of TIR-1 in the AWC axon to specify the AWCOFF subtype. A jip-1 loss-of-function mutant, identified from an unbiased forward genetic screen, has reduced localization of TIR-1 at synapses in the AWC axon and accumulation of TIR-1 in the AWC cell body. jip-1 mutants significantly enhance the 2AWCON phenotype of a hypomorphic tir-1 mutant. JIP-1, like UNC-104 and UNC-116, mainly acts non-cell autonomously in AWCON to specify the AWCOFF subtype. Our findings provide mechanistic insights into how cell-specific Ca2+ signaling proteins, such as TIR-1, target synaptic regions via intercellular signaling to promote neuronal diversification.

developmental biology↗

bioRxiv2026

Phage Display-Derived Cyclic Peptides Target TREM2 and Modulate Microglial Responses under Amyloid Stress

Triggering receptor expressed on myeloid cells 2 (TREM2) is a key regulator of microglial function and a promising therapeutic target in Alzheimers disease. While current strategies have largely focused on antibody-based agonists, alternative modalities capable of modulating TREM2 signaling remain underexplored. Here, we report the discovery of TREM2-binding cyclic peptides using a disulfide-constrained phage display library. Screening and biophysical validation identified multiple binders, with TREM2-6 and TREM2-12 exhibiting micromolar affinity. Both peptides modulated microglial responses in human iPSC-derived model of amyloid stress and in neuron-microglia co-cultures. Molecular dynamics simulations supported stable peptide-TREM2 interactions, with TREM2-12 displaying a more constrained binding mode. In vitro pharmacokinetic profiling revealed favorable plasma and intestinal stability but limited permeability, consistent with cyclic peptide scaffolds. Together, these findings establish cyclic peptides as a viable modality for targeting TREM2 and provide a foundation for the development of tunable neuroimmune therapeutics. Insert Table of Contents artwork here O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/720287v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@fbe978org.highwire.dtl.DTLVardef@9cd946org.highwire.dtl.DTLVardef@17cb644org.highwire.dtl.DTLVardef@a2669e_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗