Publications by authors named "YaFeng Shen"

Article Synopsis
  • This study focuses on the regulation of phosphate (Pi) export in human cells, specifically through a protein called XPR1, which is the only known Pi exporter.
  • Researchers used cryo-electron microscopy to visualize XPR1 in different shapes, uncovering a pathway for Pi to leave the cell and identifying two specific sites where inositol pyrophosphates (PP-IPs) activate this process.
  • By combining structural and electrical studies, the findings show how XPR1 changes shape between open and closed states, highlighting the role of its various domains in the activation process.
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Article Synopsis
  • - Collagen processing is essential for its proper function, and disruptions can cause disorders like osteogenesis imperfecta (OI), which affects tissue development and structure.
  • - Researchers studied the structure of a complex involving prolyl 3-hydroxylase 1 (P3H1), peptidyl-prolyl cis-trans isomerase B (PPIB), and cartilage-associated protein (CRTAP) using cryo-electron microscopy, revealing a unique mechanism involving multiple binding sites.
  • - The study found that mutations and inhibitors can shift the balance between different complex states, offering new insights into the mechanisms behind collagen processing and associated diseases.
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Anion exchanger 3 (AE3) is pivotal in regulating intracellular pH across excitable tissues, yet its structural intricacies and functional dynamics remain underexplored compared to other anion exchangers. This study unveils the structural insights into human AE3, including the cryo-electron microscopy structures for AE3 transmembrane domains (TMD) and a chimera combining AE3 N-terminal domain (NTD) with AE2 TMD (hAE32). Our analyzes reveal a substrate binding site, an NTD-TMD interlock mechanism, and a preference for an outward-facing conformation.

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Sphingomyelin (SM) has key roles in modulating mammalian membrane properties and serves as an important pool for bioactive molecules. SM biosynthesis is mediated by the sphingomyelin synthase (SMS) family, comprising SMS1, SMS2 and SMS-related (SMSr) members. Although SMS1 and SMS2 exhibit SMS activity, SMSr possesses ceramide phosphoethanolamine synthase activity.

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Lipid droplets (LDs) are dynamic lipid storage organelles that can sense and respond to changes in systemic energy balance. The size and number of LDs are controlled by complex and delicate mechanisms, among which, whether and which SNARE proteins mediate LD fusion, and the mechanisms governing this process remain poorly understood. Here we identified a SNARE complex, syntaxin 18 (STX18)-SNAP23-SEC22B, that is recruited to LDs to mediate LD fusion.

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Endoplasmic reticulum-associated degradation (ERAD) maintains protein homeostasis by retrieving misfolded proteins from the endoplasmic reticulum (ER) lumen into the cytosol for degradation. The retrotranslocation of misfolded proteins across the ER membrane is an energy-consuming process, with the detailed transportation mechanism still needing clarification. We determined the cryo-EM structures of the hetero-decameric complex formed by the Derlin-1 tetramer and the p97 hexamer.

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Hypophosphatasia (HPP) is a metabolic bone disease that manifests as developmental abnormalities in bone and dental tissues. HPP patients exhibit hypo-mineralization and osteopenia due to the deficiency or malfunction of tissue non-specific alkaline phosphatase (TNAP), which catalyzes the hydrolysis of phosphate-containing molecules outside the cells, promoting the deposition of hydroxyapatite in the extracellular matrix. Despite the identification of hundreds of pathogenic TNAP mutations, the detailed molecular pathology of HPP remains unclear.

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The cell maintains its intracellular pH in a narrow physiological range and disrupting the pH-homeostasis could cause dysfunctional metabolic states. Anion exchanger 2 (AE2) works at high cellular pH to catalyze the exchange between the intracellular HCO and extracellular Cl, thereby maintaining the pH-homeostasis. Here, we determine the cryo-EM structures of human AE2 in five major operating states and one transitional hybrid state.

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Pyruvate carboxylase (PC) catalyzes the two-step carboxylation of pyruvate to produce oxaloacetate, playing a key role in the maintenance of metabolic homeostasis in cells. Given its involvement in multiple diseases, PC has been regarded as a potential therapeutic target for obesity, diabetes, and cancer. Albeit acetyl-CoA has been recognized as the allosteric regulator of PC for over 60 years, the underlying mechanism of how acetyl-CoA induces PC activation remains enigmatic.

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Mutations of PSEN1 have been reported in dilated cardiomyopathy pedigrees. Understanding the effects and mechanisms of PSEN1 in cardiomyocytes might have important implications for treatment of heart diseases. Here, we showed that PSEN1 was downregulated in ischemia-induced failing hearts.

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As the major component of cell membranes, phosphatidylcholine (PC) is synthesized de novo in the Kennedy pathway and then undergoes extensive deacylation-reacylation remodeling via Lands' cycle. The re-acylation is catalyzed by lysophosphatidylcholine acyltransferase (LPCAT) and among the four LPCAT members in human, the LPCAT3 preferentially introduces polyunsaturated acyl onto the sn-2 position of lysophosphatidylcholine, thereby modulating the membrane fluidity and membrane protein functions therein. Combining the x-ray crystallography and the cryo-electron microscopy, we determined the structures of LPCAT3 in apo-, acyl donor-bound, and acyl receptor-bound states.

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Endoplasmic reticulum-associated degradation (ERAD) is a process directing misfolded proteins from the ER lumen and membrane to the degradation machinery in the cytosol. A key step in ERAD is the translocation of ER proteins to the cytosol. Derlins are essential for protein translocation in ERAD, but the mechanism remains unclear.

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Genetically engineered T cells expressing a chimeric antigen receptor (CAR) are rapidly emerging a promising new treatment for haematological and non-haematological malignancies. CAR-T therapy can induce rapid and durable clinical responses but is associated with unique acute toxicities. Moreover, CAR-T cells are vulnerable to immunosuppressive mechanisms.

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Chronic PKA phosphorylation of ryanodine receptor 2 (RyR2) has been shown to increase diastolic sarcoplasmic reticulum (SR) Ca leakage and lead to cardiac dysfunction. We hypothesize that intracellular gene delivery of an RyR2-targeting phosphorylation site-specific nanobody could preserve the contractility of the failing myocardium. In the present study, we acquired RyR2-specific nanobodies from a phage display library that were variable domains of heavy chain-only antibodies.

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Purpose: Both EGFR and PI3K-Akt signaling pathways have been used as therapeutically actionable targets, but resistance is frequently reported. In this report, we show that enrichment of the cancer stem cell (CSC) subsets and dysregulation of Notch signaling underlie the challenges to therapy and describe the development of bispecific antibodies targeting both HER and Notch signaling.

Experimental Design: We utilized cell-based models to study Notch signaling in drug-induced CSC expansion.

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Post-ischaemic heart failure is a major cause of death worldwide. Reperfusion of infarcted heart tissue after myocardial infarction has been an important medical intervention to improve outcomes. However, disturbances in Ca and redox homeostasis at the cellular level caused by ischaemia/reperfusion remain major clinical challenges.

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Article Synopsis
  • Different types of carbon materials were used to make special catalysts with Palladium (Pd) for chemical reactions.
  • The tests showed that more surface features on the carbon materials helped make smaller Pd particles and changed how they acted chemically.
  • The Pd/AC-N catalyst, made with carbon treated with nitric acid, worked best in a reaction to produce a substance called dibenzylbiotinmethylester, thanks to extra oxygen groups on the carbon support improving the process.
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Recently, PSEN1 has been reported to have mutations in dilated cardiomyopathy pedigrees. However, the function and mechanism of PSEN1 in cardiomyopathy remains unresolved. Here, we established four types of genetically modified mice to determine the function of PSEN1 in cardiac development and pathology.

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HER2, a ligand-free tyrosine kinase receptor of the HER family, is frequently overexpressed in breast cancer. The anti-HER2 antibody trastuzumab has shown significant clinical benefits in metastatic breast cancer. Despite the effectiveness of trastuzumab, its efficacy remains variable and often modest.

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Epidermal growth factor receptor (EGFR) blockade and radiation are efficacious in the treatment of cancer, but resistance is commonly reported. Studies have suggested that dysregulation of Notch signaling and enrichment of the cancer stem cell population underlie these treatment challenges. Our data show that dual targeting of EGFR and Notch2/3 receptors with antibody CT16 not only inhibited signaling mediated by these receptors but also showed a strong anti-stem cell effect both in vitro and in vivo.

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Recent studies have shown that some members of the tripartite motif-containing protein (TRIM) family serve as important regulators of tumorigenesis. However, the biological role of TRIM14 in osteosarcoma remains to be established. In this study, we showed that TRIM14 is upregulated in human osteosarcoma specimens and cell lines, and correlated with osteosarcoma progression and shorter patient survival times.

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Article Synopsis
  • Cetuximab is a medicine that helps treat a type of cancer, but sometimes cancer cells can become resistant to it.
  • Researchers discovered why some cancer cells resist cetuximab by studying specific signals in those cells that help them survive.
  • They found new ways to make cetuximab work better, including a special treatment called VIPs, which can help stop the cancer from coming back.
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A series of well-dispersed carbon supported Pd catalysts were prepared by a simple and effective method under mild conditions. The functionalized carbon supported Pd catalyst (Pd/AC-H) demonstrated a enhanced performance to original carbon supported Pd catalyst (Pd/AC) in the probe reaction hydrogenation of 3,4-(1',3'-Dibenzyl-2'-oxoimidazolido)-2-(4-carboxybutylidene)thiophane to dibenzylbiotinmethylester. The results of various characterization techniques revealed that the improvement of Pd dispersion on Pd/AC-H catalyst surface could be associated to the presence of abundant oxygen-containing groups available for anchorage.

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  • Researchers investigated the T-Tubule/SR junction in skeletal muscle, which is crucial for Ca(2+) release during muscle contraction, focusing on the roles of integral proteins DHPR and RyR1.
  • Using electron tomography, the study revealed that DHPR and RyR1 are closely positioned and interact directly, supporting the mechanism of Ca(2+) release.
  • The findings highlight electron tomography as a valuable tool for analyzing the complex architecture of membrane proteins and their interactions in muscle cells.
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  • Gold nanoparticles, especially gold nanorods, are being studied in medicine because they have special properties.
  • In this study, scientists found that gold nanorods could be taken in by A549 cells and caused damage to the cells' membranes after just 4 hours.
  • The damage led to less cell health and more harmful substances being released, showing that higher amounts of gold nanorods were more toxic to the cells due to stress caused by reactive oxygen species.
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