Biology subjects

Guo, H.

Publications and source records attributed to Guo, H..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Climate and soil nutrients drive global variations in community-level root nutrient acquisition strategies

The root economics space (RES) provides a framework for understanding species-level belowground strategies, but niche differentiation and environmental filtering may cause community-level root trait coordination to diverge from species-level patterns. Here, we compiled fine-root trait data measured directly from bulk soil samples across 302 plant communities worldwide to examine community-level root trait coordination and its climatic and edaphic drivers. Analyses based on a subset of communities with complete RES traits revealed two major dimensions of variation that were partly consistent with, but not identical to, the classical species-level RES framework. A collaboration-related axis, mainly defined by root diameter and specific root length, was associated with soil pH, with near-neutral soils linked to trait combinations consistent with more "do-it-yourself" nutrient acquisition and acidic soils associated with patterns suggesting greater reliance on mycorrhizal "outsourcing" pathways. A second fast-slow axis, characterized by root tissue density, root nitrogen concentration and root diameter, was associated with precipitation and temperature gradients, with drier environments linked to more conservative trait syndromes and humid, cooler environments associated with more acquisitive strategies. Root nutrient traits also showed ecosystem-specific patterns: in forests, root nitrogen tended to decrease whereas root phosphorus increased along soil nutrient gradients, while in grasslands, root nitrogen increased with soil total nitrogen. Overall, community-level fine-root traits retained key structural elements of the RES framework while exhibiting context-dependent deviations from species-level expectations. These findings highlight how environmental gradients shape belowground trait organization across communities and improve our understanding of plant nutrient-acquisition strategies at large spatial scales.

ecology↗

bioRxiv2025

Nitrogen deposition reshapes plant nutrient acquisition strategies: a meta-analysis within the root economics space

Global nitrogen (N) deposition has fundamentally reshaped plant nutrient acquisition by altering mechanistic trade-offs between root exploration-exploitation strategies and mycorrhizal symbiosis. Through a meta-analysis of 135 studies spanning 153 sites, we demonstrate that N deposition stimulates root exploration (+84.6% root length density) and exploitation (+13.2% nitrogen content and +8.5% root biomass) while suppressing mycorrhizal dependence (-32.8% biomass, -18.73% colonized root length, -7.55% hyphal length), indicating a systemic shift toward root-autonomous nutrient acquisition. Divergent responses emerged between plant lifeforms: woody plants prioritize exploitation (+13.2% nitrogen content) over exploration capacity (-7.9% root length density), whereas herbaceous species exhibit synergistic enhancement of both strategies (+88% root length density, +13.2% nitrogen content and +71.3% root biomass). In contrast to N-only effects, Combined nitrogen and phosphorus additions reversed mycorrhizal suppression (+41.9% biomass), highlighting their persistent role in phosphorus acquisition under elevated nutrient conditions. The root economics space framework demonstrates predictive power, with plants possessing lower specific root length (SRL) and higher nitrogen content exhibiting stronger positive responses to N deposition, while those possessing higher SRL and lower nitrogen content showed reduced investment in root systems. These trait-mediated thresholds in carbon-nutrient tradeoffs refine our capacity to model belowground ecological responses to anthropogenic nitrogen perturbation, establishing a mechanistic basis for projecting ecosystem trajectories under global change.

plant biology↗

bioRxiv2025

Association Between Dietary Vitamin B1 and the Risk of Endometriosis: A Cross-Sectional Study Based on NHANES 2003-2006

Endometriosis is a chronic gynecological condition influenced by inflammation and oxidative stress. Dietary vitamin B1 plays a role in reducing oxidative stress, which may influence endometriosis risk. However, limited research explores this association. ObjectiveTo investigate the association between dietary vitamin B1 intake and the risk of endometriosis, using NHANES 2003-2006 data. Vitamins B2 and B6 are included as reference comparisons. MethodsData from 2,462 participants in NHANES 2003-2006 were analyzed. Logistic regression models were used to examine the association between vitamin B1 intake and endometriosis risk, with adjustments for covariates. Subgroup analyses and restricted cubic spline (RCS) regressions were applied to assess non-linear relationships. Vitamins B2 and B6 served as reference nutrients for comparison. ResultsVitamin B1: Higher intake of dietary vitamin B1 was significantly associated with reduced risk of endometriosis (OR = 0.76, 95% CI: 0.58- 0.99, P = 0.044 in Model 4). Vitamin B2 and B6: No significant associations were observed (P > 0.05). RCS regression demonstrated a non-linear relationship for vitamin B1, with a protective effect observed at intake levels > 1.84 mg/day. ConclusionHigher dietary vitamin B1 intake is associated with a reduced risk of endometriosis. While B2 and B6 showed no significant associations, their trends provide additional insight for future research.

cancer biology↗

bioRxiv2025

Spatial Total RNA Sequencing of Formalin-Fixed Paraffin Embedded Tissues by spRandom-seq

Current oligo(dT) primers-based spatial transcriptomic methods are limited to fresh or fresh-frozen samples due to the low efficiency of oligo(dT) primers in capturing RNAs in degraded or microbial samples. Here, we have developed a random primer-based spatial total RNA sequencing (spRandom-seq) technology for simultaneously capturing whole host and microbial RNAs in formalin-fixed paraffin-embedded (FFPE) tissues. spRandom-seq eliminated 3 or 5 gene-body biases and outperformed oligo(dT)-based 10X Visium with an 8-fold higher capturing rate for lncRNA and other non-polyadenylated RNA biotypes, including miRNA, snRNA and miscRNA. In the clinical FFPE sections of breast cancer, we revealed the inherent heterogeneity within the tumor region. We also simultaneously captured host and microbial RNAs in Klebsiella pneumoniae-infected sections. Totally, spRandom-seq provided a versatile tool for both clinical pathology and infection biology with established spatial platforms, ensuring ease of operation and large-scale applications.

genomics↗

bioRxiv2025

In vivo targeted gene delivery using Adenovirus-antibody molecular glue conjugates

Safe and efficient nucleic acid delivery to targeted cell populations remains a significant unmet need in the fields of cell and gene therapy. Towards this end, we pursued Adenoviral vectors genetically modified with the "DogTag" molecular glue peptide, which forms a spontaneous covalent bond with its partner protein, "DogCatcher". Genetic fusion of DogCatcher to single-domain or single-chain antibodies allowed covalent tethering of the antibody at defined locales on the vector capsid. This modification allowed simple, effective and exclusive targeting of the vector to cells bound by the linked antibody. This dramatically enhanced gene transfer into primary B and T cells in vitro and in vivo in mice. These studies form the basis of a novel method for targeting Adenovirus that is functional in stringent in vivo contexts and can be combined with additional well characterized Adenovirus modifications towards applications in cell engineering, gene therapy, vaccines, oncolytics, and others.

bioengineering↗

bioRxiv2025

OPTN protects retinal ganglion cells and ameliorates neuroinflammation in optic neuropathies

Optineurin (OPTN) is a crucial component of the homeostatic pathway, playing a pivotal role in regulating a number of essential signaling pathways including NF-{kappa}B, interferon, autophagy, and vesicular trafficking. The dysfunction of OPTN has been implicated in the pathogenesis of several diseases, such as primary open angle glaucoma (POAG), amyotrophic lateral sclerosis (ALS), frontotemporal lobar dementia, and Pagets disease of bone. Interestingly, mutations in OPTN are implicated as gain-of-function in glaucoma pathology and loss-of-function in ALS. However, the role of loss-of-function OPTN in glaucoma pathology remains unclear. Here, we demonstrate that OPTN dysfunction contributes to chronic neuroinflammation, leading to sustained RGC death, which may represent a shared pathological mechanism in both normal tension glaucoma (NTG) and high-tension glaucoma (HTG). Retinal conditioned OPTN knockout contributes to short-term astrogliosis and long-term microglia activation, with the propagation of microglia activation spreading to the optic nerve. Moreover, OPTN loss of function does not further exacerbate RGC death in the ocular hypertension mouse model induced by viscobead injection. Combined with the downregulation of OPTN in glaucoma patients, we have revealed an IOP-independent mechanism of glaucoma pathogenesis. Furthermore, we found that OPTN-driven NPY upregulation may suppress the CHOP-associated neurodegeneration. Our findings reveal a neuroprotective role for the OPTN-NPY signaling pathway, and its dysfunction promotes RGC loss in glaucoma pathology. The OPTN-NPY-mediated neuroinflammatory pathway provides a potential therapy for IOP-resistant glaucoma and highlights a druggable target for CHOP-associated neurodegeneration.

neuroscience↗

bioRxiv2024

Silicon-rhodamine-enabled Identification (SeeID) for Near-Infrared Light Controlled Proximity Labeling In Vitro and In Vivo

Advancement in fluorescence imaging techniques enables the study of protein dynamics and localization with unprecedented spatiotemporal resolution. However, current imaging tools are unable to elucidate dynamic protein interactomes underlying imaging observations. In contrast, proteomics tools such as proximity labeling enable the analysis of protein interactomes at a single time point but lack information about protein dynamics. We herein developed Silicon-rhodamine-enabled Identification (SeeID) for near-infrared light controlled proximity labeling that could bridge the gap between imaging and proximity labeling. SeeID was benchmarked through characterization of various organelle-specific proteomes and the KRAS protein interactome. The fluorogenic nature of SiR allows for intracellular proximity labeling with high subcellular specificity. Leveraging SiR as both a fluorophore and a photocatalyst, we developed a protocol that allows the study of dynamic protein interactomes of Parkin during mitophagy. We discovered the association of the proteasome complex with Parkin at early time points, indicating the involvement of the ubiquitin-proteasome system for protein degradation in the early phase of mitophagy. In addition, by virtue of the deep tissue penetration of near-infrared light, we achieved spatiotemporally controlled proximity labeling in vivo across the mouse brain cortex with a labeling depth of [~]2 mm using an off-the-shelf 660 nm LED light set-up.

molecular biology↗

bioRxiv2024

PRMT1-Mediated Metabolic Reprogramming Promotes Leukemogenesis

Copious expression of protein arginine methyltransferase 1 (PRMT1) is associated with poor survival in many types of cancers, including acute myeloid leukemia. We observed that a specific acute megakaryocytic leukemia (AMKL) cell line (6133) derived from RBM15-MKL1 knock-in mice exhibited heterogeneity in Prmt1 expression levels. Interestingly, only a subpopulation of 6133 cells expressing high levels of Prmt1 caused leukemia when transplanted into congenic mice. The PRMT1 inhibitor, MS023, effectively cured this PRMT1-driven leukemia. Seahorse analysis revealed that PRMT1 increased the extracellular acidification rate (ECAR) and decreased the oxygen consumption rate (OCR). Consistently, PRMT1 accelerated glucose consumption and led to the accumulation of lactic acid in the leukemia cells. The metabolomic analysis supported that PRMT1 stimulated the intracellular accumulation of lipids, which was further validated by FACS analysis with BODIPY 493/503. In line with fatty acid accumulation, PRMT1 downregulated the protein level of CPT1A, which is involved in the rate-limiting step of fatty acid oxidation. Furthermore, administering the glucose analogue 2-deoxy-glucose (2-DG) delayed AMKL progression and promoted cell differentiation. Ectopic expression of Cpt1a rescued the proliferation of 6133 cells ectopically expressing PRMT1 in the glucose-minus medium. In conclusion, PRMT1 upregulates glycolysis and downregulates fatty acid oxidation to enhance the proliferation capability of AMKL cells. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/628174v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1ae96borg.highwire.dtl.DTLVardef@d27916org.highwire.dtl.DTLVardef@ba63corg.highwire.dtl.DTLVardef@cee9af_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Interfamily co-transfer of sensor and helper NLRs extends immune receptor functionality between angiosperms

Plant nucleotide-binding, leucine-rich repeat (NLR) immune receptors recognize pathogen effectors and activate defense. NLR genes can be non-functional in distantly related plants (restricted taxonomic functionality, RTF). Here, we enable Solanaceae NLR gene function in rice, soybean and Arabidopsis by co-delivering sensor NLR genes with their cognate NRC-type helper NLRs. In soybean protoplasts and in Arabidopsis plants, Solanum americanum Rpi-amr1, Rpi-amr3 and pepper Bs2 sensor NLRs confer cognate effector responsiveness if co-expressed with NRC helper NLRs. Rice carrying pepper Bs2 and NRCs recognizes the conserved effector, AvrBs2, and resists an important pathogen, Xanthomonas oryzae pv. oryzicola for which no resistance gene is available in rice. Rice lines carrying sensor and helper NLR genes otherwise resemble wild-type, with unaltered basal resistance or field fitness. Thus, interfamily co-transfer of sensor and helper NLRs can broaden utility of sensor NLRs, extending the tools available to control diseases of rice, soybean, Brassicas and other crops.

plant biology↗

bioRxiv2024

Identification and genomic characterization of a novel bisegmented coronavirus in the lesser panda

Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses and are renowned for their capacity to infect a diverse range of animals, including humans. In this study, we report the identification and characterization of a novel bisegmented coronavirus, designated LpCoV, from a dead lesser panda, which exhibited severe clinical manifestations and lesions in multiple organs. The LpCoV represents the first documented coronavirus with a unique bisegmented genome while maintaining the typical coronavirus morphology. One genomic segment encodes the ORF1ab polyprotein, while the other segment encodes the spike and nucleocapsid proteins, notably lacking the envelope (E) and membrane (M) genes. The pairwise patristic distances of the five concatenated domains in the replicase region (3CLpro, NiRAN, RdRP, ZBD, and HEL1) between LpCoV and -{delta} coronaviruses range from 1.19 to 1.70. Based on the classification criteria established by the International Committee on Taxonomy of Viruses (ICTV), LpCoV is proposed to constitute a new genus within the Coronaviridae family. An epidemiological investigation identified five LpCoV-like viruses in lesser pandas from two different provinces (Sichuan and Jiangsu) indicating the long-term circulation and expansion of bisegmented coronaviruses in wildlife. These findings highlight the imperative for comprehensive viral surveillance in wildlife, which is essential for understanding and mitigating the risk of animal diseases and zoonotic spillover.

microbiology↗

bioRxiv2024

Risk factors, prognostic factors, and nomograms for distant metastasis in patients with triple-negative breast cancer: a population-based study

BackgroundTriple-negative breast cancer (TNBC) is associated with a poor prognosis, higher invasiveness compared to other breast cancer variants, and limited treatment options. Due to the lack of conventional treatment methods, TNBC patients are prone to distant metastasis. The purpose of this study is to evaluate the clinical and pathological characteristics of TNBC patients, predict the impact of risk factors on their prognosis, and establish a predictive model to assist doctors in treating TNBC patients and improving their outcomes. MethodsWe conducted a retrospective study on patients with TNBC from 2010 to 2015 in the Surveillance, Epidemiology, and End Results (SEER) database. We gathered tumor characteristics and treatment data from these patients. Univariate and multivariate logistic regression analyses were employed to identify independent risk factors for distant metastasis in TNBC patients, while univariate and multivariate Cox proportional hazards regression analyses were utilized to determine independent prognostic factors for TNBC patients with distant metastasis. Based on these factors, a new nomogram was constructed, and patients were categorized into high and low-risk groups using the nomogram scores. The prognosis of the patients was analyzed using Kaplan-Meier (K-M) survival analysis. ResultsThis study enrolled a total of 16,959 patients with TNBC, among whom 730 (4.3%) had distant metastasis at the time of diagnosis. Independent risk factors for distant metastasis in TNBC patients encompass being married, having an invasive lobular carcinoma (ILC) pathology, advanced T stage, advanced N stage, no radiotherapy, no surgery, and tumor size exceeding 50mm. The area under the curve (AUCs) for the training set and validation set were 0.892 and 0.907, respectively. The independent prognostic factors for patients with distant metastasis were being unmarried (P < 0.001), not undergoing surgery (P < 0.001), and not receiving chemotherapy (P < 0.001). The AUCs for the training set at 12, 36, and 60 months were 0.751, 0.709, and 0.691, respectively, while the AUCs for the validation set at 12, 36, and 60 months were 0.690, 0.690, and 0.732, respectively. The AUCs for the extended test set at 12, 36, and 60 months were 0.741, 0.727, and 0.718 respectively. The results of the calibration curve, decision curve analysis (DCA), and K-M survival curve confirm that both nomograms can accurately predict the occurrence of distant metastasis and prognosis in TNBC patients. ConclusionWe constructed two nomograms to predict distant metastasis risk in TNBC patients and prognosis in patients with distant metastasis. Our findings suggest that they could serve as effective predictive tools and may assist in clinical decision-making.

cancer biology↗

bioRxiv2024

PAM-flexible adenine base editing rescues hearing loss in a humanized MPZL2 mouse model harboring an East Asian founder mutation

Hearing loss is one of the most prevalent sensory disorders, but no commercial biological treatments are currently available. Here, we identified an East Asia-specific founder mutation, the homozygous c.220C>T mutation in MPZL2, that contributes to a significant proportion of hereditary deafness cases in our cohort study. We found that the disease-causing mutation could be targetable by adenine base editors (ABEs) that enable A{middle dot}T-to-G{middle dot}C base corrections without DNA double-strand breaks. To demonstrate this, we developed a humanized mouse model (hMPZL2Q74X/Q74X) that recapitulates human MPZL2 deafness and leads to progressive hearing loss. A PAM-flexible ABE variant with reduced bystander and off-target effects (ABE8eWQ-SpRY:sgRNA3) was packaged in dual adeno-associated viruses (AAVs) and injected into the inner ear of hMPZL2Q74X/Q74X mice and effectively corrected the mutation. This treatment significantly restored hearing function, improved inner ear structural integrity, and reversed altered gene expression. Base editing may hold therapeutic potential for hereditary deafness, including most cases of MPZL2 deafness.

genetics↗

bioRxiv2024

Denoising complex-valued diffusion MR images using a two-step non-local principal component analysis approach

Purposeto propose a two-step non-local principal component analysis (PCA) method and demonstrate its utility for denoising diffusion tensor MRI (DTI) with a few diffusion directions. MethodsA two-step denoising pipeline was implemented to ensure accurate patch selection even with high noise levels and was coupled with data preprocessing for g-factor normalization and phase stabilization before data denoising with a non-local PCA algorithm. At the heart of our proposed pipeline was the use of a data-driven optimal shrinkage algorithm to manipulate the singular values in a way that would optimally estimate the noise-free signal. Our approachs denoising performances were evaluated using simulation and in-vivo human data experiments. The results were compared to those obtained with existing local-PCA-based methods. ResultsIn both simulation and human data experiments, our approach substantially enhanced image quality relative to the noisy counterpart, yielding improved performances for estimation of relevant DTI metrics. It also outperformed existing local-PCA-based methods in reducing noise while preserving anatomic details. It also led to improved whole-brain tractography relative to the noisy counterpart. ConclusionThe proposed denoising method has the utility for improving image quality for DTI with reduced diffusion directions and is believed to benefit many applications especially those aiming to achieve quality parametric mapping using only a few image volumes.

neuroscience↗

bioRxiv2024

Salmonella exploits host- and bacterial-derived β-alanine for replication inside host macrophages

Salmonella is a major foodborne pathogen that can effectively replicate inside host macrophages to establish life-threatening systemic infections. Salmonella must utilize diverse nutrients for growth in nutrient-poor macrophages, but which nutrients are required for intracellular Salmonella growth is largely unknown. Here, we found that either acquisition from the host or de novo synthesis of a nonprotein amino acid, {beta}-alanine, is critical for Salmonella replication inside macrophages. The concentration of {beta}-alanine is decreased in Salmonella-infected macrophages, while the addition of exogenous {beta}-alanine enhances Salmonella replication in macrophages, suggesting that Salmonella can uptake host-derived {beta}-alanine for intracellular growth. Moreover, the expression of panD, the rate-limiting gene required for {beta}-alanine synthesis in Salmonella, is upregulated when Salmonella enters macrophages. Mutation of panD impaired Salmonella replication in macrophages and colonization in the mouse liver and spleen, indicating that de novo synthesis of {beta}-alanine is essential for intracellular Salmonella growth and systemic infection. Additionally, we revealed that {beta}-alanine influences Salmonella intracellular replication and in vivo virulence partially by increasing expression of the zinc transporter genes znuABC, which in turn facilitates the uptake of the essential micronutrient zinc by Salmonella. Taken together, these findings highlight the important role of {beta}-alanine in the intracellular replication and virulence of Salmonella, and panD is a promising target for controlling systemic Salmonella infection.

microbiology↗

bioRxiv2024

ProteinAligner: A Multi-modal Pretraining Framework for Protein Foundation Models

Protein foundation models, particularly protein language models, have demonstrated strong success in learning meaningful representations of proteins using transformer architectures pretrained on large-scale protein datasets with self-supervised learning. These representations have been highly effective for downstream tasks such as predicting protein functions and properties. However, most current protein foundation models focus on pretraining with amino acid sequences, often neglecting additional modalities like protein structures and related literature, both of which provide valuable insights. To address this gap, we propose a multi-modal pretraining approach that integrates three key modalities - protein sequences, structures, and literature text. In our framework, the protein sequence modality serves as the anchor, with the other two modalities aligned to it, enhancing the models capacity to capture more comprehensive protein information. ProteinAligner out-performed state-of-the-art protein foundation models in predicting protein functions and properties across diverse down-stream tasks.

bioinformatics↗

bioRxiv2024

RIPK1 is essential for Herpes Simplex Virus-triggered ZBP1-dependent necroptosis in human cells

Necroptosis initiated by the host sensor Z-NA Binding Protein-1 (ZBP1) is essential for host defense against a growing number of viruses, including Herpes Simplex Virus-1 (HSV-1). Studies with HSV-1 and other necroptogenic stimuli in murine settings have suggested that ZBP1 triggers necroptosis by directly complexing with the kinase RIPK3. Whether this is also the case in human cells, or whether additional co-factors are needed for ZBP1-mediated necroptosis, is unclear. Here, we show that ZBP1-induced necroptosis in human cells requires RIPK1. We have found that RIPK1 is essential for forming a stable and functional ZBP1-RIPK3 complex in human cells, but is dispensable for the formation of the equivalent murine complex. The RIP Homology Interaction Motif (RHIM) in RIPK3 is responsible for this difference between the two species, because replacing the RHIM in human RIPK3 with the RHIM from murine RIPK3 is sufficient to overcome the requirement for RIPK1 in human cells. These observations describe a critical mechanistic difference between mice and humans in how ZBP1 engages in necroptosis, with important implications for treating human diseases.

cell biology↗

bioRxiv2024

Global Scientific Trends in Organoids from 2004 to 2023: A Data Bibliometric and Visualized Analysis

To conduct a bibliometric analysis of organoids to describe international research trends and visualize current research directions. This cross-sectional bibliometric analysis examined the development of organoid research from 2004 to 2023. The current study used VOS-viewer to assess and analyze 13,174 documents. Literature data were collected on a specific date (Feb 19, 2024) and downloaded in plain text from Web of Science Core Collection. In this paper, 13,174 organoid papers were retrieved from Web of Science Core Collection. There were only 114 organoid studies in 2004, and from 2015 onward, the number of annual publications on this topic began to proliferate, reaching 10,023 from 2019 to 2023, accounting for as much as 76.1% of the total number of published papers. The United States proudly leads the way in both the volume of articles published and the number of citations garnered, standing tall as the undisputed frontrunner. Among the illustrious institutions, Harvard University and the University of Washington are among the most prolific. Hans Clevers has worked with 121 prolific authors and has the most publications. With the use of organoids in cancer modeling, drug screening, and regenerative medicine, organoid technology has attracted much attention in medicine, and the significant increase in the number of published papers and citations signifies the expanding influence and global collaboration in the field of organoid research. This study contributes to our understanding of current trends and potential future advances in the field of organoid research by identifying five distinct clusters in the field.

cancer biology↗

bioRxiv2024

Spatiotemporally-resolved mapping of extracellular proteomes via in vivo-compatible TyroID

Extracellular proteins play pivotal roles in both intracellular signaling and intercellular communications in health and disease. While recent advancements in proximity labeling (PL) methods, such as peroxidase- and photocatalyst-based approaches, have facilitated the resolution of extracellular proteomes, their in vivo compatibility remains limited. Here, we report TyroID, an in vivo-compatible PL method for unbiased mapping of extracellular proteins with high spatiotemporal resolution. TyroID employs plant- and bacteria-derived tyrosinases to produce reactive o-quinone intermediates, enabling the labeling of multiple residues on endogenous proteins with bioorthogonal handles, thereby allowing for their identification via chemical proteomics. We validate TyroIDs specificity by mapping extracellular proteomes and HER2-neighboring proteins using nanobody-directed recombinant tyrosinases. Demonstrating its superiority over other PL methods, TyroID enables in vivo mapping of extracellular proteomes, including mapping HER2-proximal proteins in tumor xenografts, quantifying the turnover of plasma proteins and labeling hippocampal-specific proteomes in live mouse brains. TyroID emerges as a potent tool for investigating protein localization and molecular interactions within living organisms.

biochemistry↗