Beijing Proteome Research Center

Innate immune responses must be coordinated with the cellular metabolic state. The intracellular pattern recognition receptor NOD1 detects bacterial peptidoglycans and initiates signaling from cellular membranes, a process regulated by ZDHHC5-mediated palmitoylation. Using biochemical analyses and immune-competent cell models, we show that AMP-activated protein kinase (AMPK) integrates metabolic cues into NOD1 signaling by regulating ZDHHC5. AMPK phosphorylates ZDHHC5 at Ser296 and Ser380, weakens its association with Golga7B, and promotes its displacement from the plasma membrane, thereby reducing NOD1 palmitoylation, membrane localization, and downstream signaling. Conversely, stimulation with the NOD1 agonist C12-iE-DAP suppresses AMPK activity, stabilizing ZDHHC5 at the membrane and sustaining NOD1 activation. These findings define a reciprocal regulatory circuit linking metabolic stress sensing and innate immune signaling, and illustrate how metabolic pathways govern the spatial control of pattern recognition receptors in innate immunity.

The Editors would like to alert the readers that concerns have been raised regarding similarities between different images in this article.Specifically, the 0 h, SPK-1 assay in Figure 2c appears to overlap with the 0 h, SPK Antagonist miR-543 assay in Figure 2 g; the p-JNK and p-Jun panels in the top row of Figure 6 h appear to overlap partially.

Ionizing radiation (IR) causes severe vascular damage, yet the dynamic functional states and regulatory mechanisms of vascular endothelial cells (VECs) after irradiation remain poorly understood. To elucidate the underlying processes, we analyzed single-cell RNA sequencing data from mouse dorsal skin collected at multiple post-irradiation (p.i.) time points using trajectory inference, pathway enrichment, transcription factor activity inference, and cell-cell communication analyses. Our results showed that VECs exhibited marked temporal dynamics after irradiation, transitioning from early-stage stress responses to middle-stage angiogenic remodeling and late-stage restoration of homeostasis. A transient Gpihbp1+ capillary endothelial subpopulation (capVEC2) emerged predominantly during the middle stage (2-3 days p.i.) and was enriched for angiogenesis- and migration-related programs. Enhanced Sp1 regulatory activity was associated with its pro-angiogenic phenotype. At 2 days p.i., capVEC2 engaged in pro-angiogenic and pro-repair signaling with keratinocytes, whereas by 3 days p.i. these interactions shifted toward immune surveillance and tissue homeostasis, accompanied by increased pro-inflammatory and pro-apoptotic signaling and a decline in capVEC2 abundance. Collectively, our findings identify a radiation-induced, transient functional endothelial subpopulation that is associated with vascular-epidermal communication during skin repair post irradiation.

The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past five years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape (https://metaproteomics.org/). We outline the Initiative's organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities.

Inhibition of endothelial cell (EC) death is essential for normal angiogenesis. The E3 ubiquitin ligase HOIP, the catalytic subunit of the linear ubiquitin chain assembly complex (LUBAC), is particularly important for EC survival during embryogenesis. The stability of HOIP is critical for LUBAC function. However, the mechanisms underlying the regulation of HOIP stability are largely unknown. Here, we uncovered a novel role of G protein pathway suppressor 2 (GPS2) in regulating EC survival and embryonic vascularization via control of HOIP stability. EC-specific GPS2 deletion mice (Gps2ECKO) are embryonic lethal at embryonic day 16.5 (E16.5) due to defective vascularization. Deficiency of GPS2 in ECs results in aberrant TNFR1-mediated cell death. TNFR1 deletion in Gps2ECKO mice restores normal vascularization and rescues embryonic lethality. At the molecular level, GPS2 binds to the NZF domain of HOIP and inhibits K48-linked polyubiquitination of HOIP at K579, K737, and K988 residues. GPS2 prevents HOIP proteasomal degradation and thus maintains LUBAC stability and activity. GPS2 deficiency in ECs leads to HOIP degradation and LUBAC instability, which in turn attenuates TNF-induced NF-κB activation and exacerbates the formation of the cell-death-inducing complex-II, ultimately increasing EC death. Overall, our data demonstrate that GPS2 is required for maintaining vascular integrity during embryogenesis by inhibiting TNFR1-mediated EC death via stabilizing HOIP.

The formation of foamy macrophages is often considered a pathological hallmark of atherosclerosis, but the underlying mechanisms remain elusive. Herein, we demonstrated that the transcription factor TFEC could upregulate the expression of Glycoprotein non-metastatic melanoma protein B (GPNMB) in atherosclerotic plaque foamy macrophages. Circulating levels of soluble GPNMB correlated positively with atherosclerotic severity. Moreover, mice with systemic Gpnmb-mutation or myeloid-specific Gpnmb knockout exhibited a reduced atherosclerotic burden. Live-cell imaging revealed that GPNMB-positive vesicles were involved in lipoprotein internalization and transport within macrophages and facilitated lipid droplet formation. In Gpnmb-mutant macrophages, impaired lipid droplet formation from internalized lipoproteins, combined with enhanced lipid β-oxidation and lysosomal lipolysis, led to reduced macrophage foaming. Notably, mice treated with siRNA-loaded lipid nanoparticles targeting Gpnmb in lesional foamy macrophages showed alleviation of atherosclerotic burden. Overall, our findings elucidate the intracellular lipoprotein processing in macrophages and suggest GPNMB as a potential therapeutic target for atherosclerosis.

Abstract The increasing scale and complexity of proteomics data demand robust, scalable, and interpretable quality control (QC) frameworks to ensure data reliability and reproducibility. Here, we present pmultiqc, an open-source Python package that standardizes and generates web-based QC reports across multiple proteomics data analysis platforms. Built on top of the widely adopted MultiQC framework, pmultiqc offers specialized modules tailored to mass spectrometry workflows, with full initial support for quantms, DIA-NN, MaxQuant/MaxDIA, and mzIdentML/mzML-based pipelines. The package computes a wide range of QC metrics, including raw intensity distributions, identification rates, retention time consistency, and missing value patterns, and presents them in interactive, publication-ready reports. By leveraging sample metadata in the SDRF format, pmultiqc enables metadata-aware QC and introduces, for the first time in proteomics, QC reports and metrics guided by standardized sample metadata. Its modular architecture allows easy extension to new workflows and formats. Alongside comprehensive documentation and examples for running pmultiqc locally or integrated into existing workflows, we offer a cloud-based service that enables users to generate QC reports from their own data or public PRIDE datasets.

ABSTRACTGasdermin (GSDM)-mediated pyroptosis has been extensively visualized in vitro and linked to multiple physiological and pathological processes. However, the in vivo phenotype and clinical outcome of pyroptosis remain undetermined. Here, we sought to profile in vivo pyroptosis using lipid-nanoparticle (LNP)-encapsulated mRNA encoding the pore-forming N-terminal of GSDMD (GSDMDNT). Upon intravenous (IV) injection, robust expression of GSDMDNT led to acute liver damage, systemic inflammation and sudden death, both in mice and non-human primates, which could be reversed by the GSDMD inhibitor disulfiram or glucocorticoids. Imaging techniques revealed that GSDMDNT targeted both plasma membrane and intracellular membranous organelles, causing membrane rupture and organelle swelling, as well as the formation of intracellular membranous vacuoles. Furthermore, heterologous expression of other GSDM members also caused pyroptosis, both in vitro and in vivo, with varying magnitude. These findings provide insights into the dynamic characteristics of pyroptotic organ injury-related diseases and offer the basis for developing GSDM-based therapeutics.

Hepatocellular carcinoma (HCC) constitutes approximately 90% of liver cancers, yet its early detection remains challenging due to the low sensitivity of current diagnostic methods and the difficulty in identifying minimal cancer cells within the body. This study employed a patient-derived xenograft (PDX) mouse model to screen for biomarkers, leveraging its advantage of low background interference compared to human serum exosome studies. Using a novel microextraction technique, exosomes were isolated from just one microliter of serum from HCC PDX mice, followed by proteomic profiling. Analysis revealed that serum exosomal proteins from PDX mice were enriched in cancer-related pathways. The exosomal proteome not only distinguished PDX mice from controls but also differentiated between individual PDX groups, supporting its use as a tumor-specific identifier (tumor ID) and a noninvasive tool for monitoring tumors. Bioinformatics identified a panel of serum exosomal protein biomarkers predictive of HCC patient outcomes, which were validated via targeted proteomics and array-based high-throughput detection. These upregulated biomarkers in HCC patients positively correlate with disease severity and poor prognosis, underscoring their clinical potential.