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View article: The coming era of proteomics-driven precision medicine
The coming era of proteomics-driven precision medicine Open
The concept of ‘proteomics-driven precision medicine’ highlighted in 2019 emphasized the potential of proteomics to transform precision medicine by offering deeper insights into dynamic biological processes. Since then, this field has seen…
View article: Towards Unmanned Proteomics Data Generation: A Fully Automated Sample-to-Data System for Proteomic Experiments
Towards Unmanned Proteomics Data Generation: A Fully Automated Sample-to-Data System for Proteomic Experiments Open
Summary The π-HuB project requires proteomic measurements of millions of low-input samples that are challenging with current technology. Here, we introduce a pilot π-HuB data factory that features a fully automated sample-to-data system to…
View article: Plasma proteomics identifies S100A8/A9 as a novel biomarker and therapeutic target for fulminant myocarditis
Plasma proteomics identifies S100A8/A9 as a novel biomarker and therapeutic target for fulminant myocarditis Open
ClinicalTrials.gov NCT03268642.
View article: Panoramic spatial enhanced resolution proteomics (PSERP) reveals tumor architecture and heterogeneity in gliomas
Panoramic spatial enhanced resolution proteomics (PSERP) reveals tumor architecture and heterogeneity in gliomas Open
The spatial proteomic profiling of complex tissues is essential for investigating cellular function in physiological and pathological states. However, the imbalance among resolution, protein coverage, and expense precludes their systematic…
View article: ZnCl<sub>2</sub> Precipitation-Assisted Sample Preparation for Proteomic Analysis
ZnCl<sub>2</sub> Precipitation-Assisted Sample Preparation for Proteomic Analysis Open
This manuscript details protocols for the ZnCl2 precipitation-assisted sample preparation (ZASP) for proteomic analysis. By inducing protein precipitation with ZASP precipitation buffer (ZPB, final concentration of ZnCl2
View article: Automating Exploratory Proteomics Research via Language Models
Automating Exploratory Proteomics Research via Language Models Open
With the development of artificial intelligence, its contribution to science is evolving from simulating a complex problem to automating entire research processes and producing novel discoveries. Achieving this advancement requires both sp…
View article: A stroke organoids-multiomics platform to study injury mechanism and drug response
A stroke organoids-multiomics platform to study injury mechanism and drug response Open
Stroke is one of the top causes of death and disability worldwide, and its pathogenesis and mechanism have not been fully elucidated. Several agents have shown protective effects against stroke in animal models; however, few studies have s…
View article: ZASP: A Highly Compatible and Sensitive ZnCl2 Precipitation-Assisted Sample Preparation Method for Proteomic Analysis
ZASP: A Highly Compatible and Sensitive ZnCl2 Precipitation-Assisted Sample Preparation Method for Proteomic Analysis Open
Universal sample preparation for proteomic analysis that enables unbiased protein manipulation, flexible reagent use, and low protein loss is required to ensure the highest sensitivity of downstream liquid chromatography-mass spectrometry …
View article: ZNF8 Orchestrates with Smad3 to Promote Lung Metastasis by Recruiting SMYD3 in Breast Cancer
ZNF8 Orchestrates with Smad3 to Promote Lung Metastasis by Recruiting SMYD3 in Breast Cancer Open
Most deaths in breast cancer patients are attributed to metastasis, and lung metastasis is associated with a particularly poor prognosis; therefore it is imperative to identify potential target for intervention. The transforming growth fac…
View article: NRDE2 deficiency impairs homologous recombination repair and sensitizes hepatocellular carcinoma to PARP inhibitors
NRDE2 deficiency impairs homologous recombination repair and sensitizes hepatocellular carcinoma to PARP inhibitors Open
To identify novel susceptibility genes for hepatocellular carcinoma (HCC), we performed a rare-variant association study in Chinese populations consisting of 2,750 cases and 4,153 controls. We identified four HCC-associated genes, includin…
View article: Introducing π-HelixNovo for practical large-scale de novo peptide sequencing
Introducing π-HelixNovo for practical large-scale de novo peptide sequencing Open
De novo peptide sequencing is a promising approach for novel peptide discovery, highlighting the performance improvements for the state-of-the-art models. The quality of mass spectra often varies due to unexpected missing of certain ions, …
View article: From PROTAC to TPD: Advances and Opportunities in Targeted Protein Degradation
From PROTAC to TPD: Advances and Opportunities in Targeted Protein Degradation Open
PROTAC is a rapidly developing engineering technology for targeted protein degradation using the ubiquitin–proteasome system, which has promising applications for inflammatory diseases, neurodegenerative diseases, and malignant tumors. Thi…
View article: Myeloid cell-expressed MNDA enhances M2 polarization to facilitate the metastasis of hepatocellular carcinoma
Myeloid cell-expressed MNDA enhances M2 polarization to facilitate the metastasis of hepatocellular carcinoma Open
Stable infiltration of myeloid cells, especially tumor-associated M2 macrophages, acts as one of the essential features of the tumor immune microenvironment by promoting the malignant progression of hepatocellular carcinoma (HCC). However,…
View article: Repopulating Kupffer cells originate directly from hematopoietic stem cells
Repopulating Kupffer cells originate directly from hematopoietic stem cells Open
Background Kupffer cells (KCs) originate from yolk-sac progenitors before birth. Throughout adulthood, they self-maintain independently from the input of circulating monocytes (MOs) at a steady state and are replenished within 2 weeks afte…
View article: RNF149 Promotes HCC Progression through Its E3 Ubiquitin Ligase Activity
RNF149 Promotes HCC Progression through Its E3 Ubiquitin Ligase Activity Open
Hepatocellular carcinoma (HCC) accounts for over 80% of cases among liver cancer, with high incidence and poor prognosis. Thus, it is of valuable clinical significance for discovery of potential biomarkers and drug targets for HCC. In this…
View article: CDS-DB, an omnibus for patient-derived gene expression signatures induced by cancer treatment
CDS-DB, an omnibus for patient-derived gene expression signatures induced by cancer treatment Open
Patient-derived gene expression signatures induced by cancer treatment, obtained from paired pre- and post-treatment clinical transcriptomes, can help reveal drug mechanisms of action (MOAs) in cancer patients and understand the molecular …
View article: Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics
Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics Open
Background Quantitative proteomics is an indispensable tool in life science research. However, there is a lack of reference materials for evaluating the reproducibility of label-free liquid chromatography-tandem mass spectrometry (LC–MS/MS…
View article: Digital image analysis allows objective stratification of patients with silent <scp>PIT1</scp>‐lineage pituitary neuroendocrine tumors
Digital image analysis allows objective stratification of patients with silent <span>PIT1</span>‐lineage pituitary neuroendocrine tumors Open
Studies describing the clinical presentation and prognosis of patients with silent PIT1 (pituitary specific transcription factor)‐lineage pituitary neuroendocrine tumors (PitNETs) are rare. We identified patients with positive PIT1 tumor s…
View article: Nomogram predicting overall survival after surgical resection for retroperitoneal leiomyosarcoma patients
Nomogram predicting overall survival after surgical resection for retroperitoneal leiomyosarcoma patients Open
Background Surgery is the best way to cure the retroperitoneal leiomyosarcoma (RLMS), and there is currently no prediction model on RLMS after surgical resection. The objective of this study was to develop a nomogram to predict the overall…
View article: Introducing<i>π</i>-HelixNovo for practical large-scale de novo peptide sequencing
Introducing<i>π</i>-HelixNovo for practical large-scale de novo peptide sequencing Open
De novo peptide sequencing is a promising approach for novel peptide discovery. We use a novel concept of complementary spectra to enhance ion information and propose a de novo sequencing model π -HelixNovo based on Transformer architectur…
View article: Aberrant LYZ expression in tumor cells serves as the potential biomarker and target for HCC and promotes tumor progression via csGRP78
Aberrant LYZ expression in tumor cells serves as the potential biomarker and target for HCC and promotes tumor progression via csGRP78 Open
Hepatocellular carcinoma (HCC) takes the predominant malignancy of hepatocytes with bleak outcomes owing to high heterogeneity among patients. Personalized treatments based on molecular profiles will better improve patients’ prognosis. Lys…
View article: Nucleophilic covalent ligand discovery for the cysteine redoxome
Nucleophilic covalent ligand discovery for the cysteine redoxome Open
View article: Proteomic characteristics reveal the signatures and the risks of T1 colorectal cancer metastasis to lymph nodes
Proteomic characteristics reveal the signatures and the risks of T1 colorectal cancer metastasis to lymph nodes Open
The presence of lymph node metastasis (LNM) affects treatment strategy decisions in T1NxM0 colorectal cancer (CRC), but the currently used clinicopathological-based risk stratification cannot predict LNM accurately. In this study, we detec…
View article: Author response: Proteomic characteristics reveal the signatures and the risks of T1 colorectal cancer metastasis to lymph nodes
Author response: Proteomic characteristics reveal the signatures and the risks of T1 colorectal cancer metastasis to lymph nodes Open
Full text Figures and data Side by side Abstract Editor's evaluation eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abs…
View article: Supplementary Methods, Supplementary Figures 1-10, Supplementary Tables 1-17, Supplementary References from Genome-Wide Association Study Identifies a New Locus at 7q21.13 Associated with Hepatitis B Virus–Related Hepatocellular Carcinoma
Supplementary Methods, Supplementary Figures 1-10, Supplementary Tables 1-17, Supplementary References from Genome-Wide Association Study Identifies a New Locus at 7q21.13 Associated with Hepatitis B Virus–Related Hepatocellular Carcinoma Open
Supplementary Figure 1. An overview of the study workflow; Supplementary Figure 2. The principal components analyses (PCA) of samples in the discovery stage and reference samples from the 1000 Genomes Project data. Supplementary Figure 3. …
View article: Data from Genome-Wide Association Study Identifies a New Locus at 7q21.13 Associated with Hepatitis B Virus–Related Hepatocellular Carcinoma
Data from Genome-Wide Association Study Identifies a New Locus at 7q21.13 Associated with Hepatitis B Virus–Related Hepatocellular Carcinoma Open
Purpose: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. In China, chronic hepatitis B virus (HBV) infection remains the major risk factor for HCC. In this study, we performed a genome-wide association st…
View article: Supplementary Methods, Supplementary Figures 1-10, Supplementary Tables 1-17, Supplementary References from Genome-Wide Association Study Identifies a New Locus at 7q21.13 Associated with Hepatitis B Virus–Related Hepatocellular Carcinoma
Supplementary Methods, Supplementary Figures 1-10, Supplementary Tables 1-17, Supplementary References from Genome-Wide Association Study Identifies a New Locus at 7q21.13 Associated with Hepatitis B Virus–Related Hepatocellular Carcinoma Open
Supplementary Figure 1. An overview of the study workflow; Supplementary Figure 2. The principal components analyses (PCA) of samples in the discovery stage and reference samples from the 1000 Genomes Project data. Supplementary Figure 3. …
View article: Data from Genome-Wide Association Study Identifies a New Locus at 7q21.13 Associated with Hepatitis B Virus–Related Hepatocellular Carcinoma
Data from Genome-Wide Association Study Identifies a New Locus at 7q21.13 Associated with Hepatitis B Virus–Related Hepatocellular Carcinoma Open
Purpose: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. In China, chronic hepatitis B virus (HBV) infection remains the major risk factor for HCC. In this study, we performed a genome-wide association st…
View article: Supplementary Figure 5 from LSECtin Expressed on Melanoma Cells Promotes Tumor Progression by Inhibiting Antitumor T-cell Responses
Supplementary Figure 5 from LSECtin Expressed on Melanoma Cells Promotes Tumor Progression by Inhibiting Antitumor T-cell Responses Open
PDF file - 76KB, Supplementary Figure 5 Anti-LSECtin ameliorates B16 melanoma growth.
View article: Supplementary Figure 6 from LSECtin Expressed on Melanoma Cells Promotes Tumor Progression by Inhibiting Antitumor T-cell Responses
Supplementary Figure 6 from LSECtin Expressed on Melanoma Cells Promotes Tumor Progression by Inhibiting Antitumor T-cell Responses Open
PDF file - 90KB, Supplementary Figure 6 Tumor-derived LSECtin stimulates MDSC to express iNOS and promotes MDSC accumulation in spleen, but not in tumor site.