24 results on '"Yanyan Li"'
Search Results
2. Large exchange-driven intrinsic circular dichroism of a chiral 2D hybrid perovskite
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Shunran Li, Xian Xu, Conrad A. Kocoj, Chenyu Zhou, Yanyan Li, Du Chen, Joseph A. Bennett, Sunhao Liu, Lina Quan, Suchismita Sarker, Mingzhao Liu, Diana Y. Qiu, and Peijun Guo
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Science - Abstract
Abstract In two-dimensional chiral metal-halide perovskites, chiral organic spacers endow structural and optical chirality to the metal-halide sublattice, enabling exquisite control of light, charge, and electron spin. The chiroptical properties of metal-halide perovskites have been measured by transmissive circular dichroism spectroscopy, which necessitates thin-film samples. Here, by developing a reflection-based approach, we characterize the intrinsic, circular polarization-dependent complex refractive index for a prototypical two-dimensional chiral lead-bromide perovskite and report large circular dichroism for single crystals. Comparison with ab initio theory reveals the large circular dichroism arises from the inorganic sublattice rather than the chiral ligand and is an excitonic phenomenon driven by electron-hole exchange interactions, which breaks the degeneracy of transitions between Rashba-Dresselhaus-split bands, resulting in a Cotton effect. Our study suggests that previous data for spin-coated films largely underestimate the optical chirality and provides quantitative insights into the intrinsic optical properties of chiral perovskites for chiroptical and spintronic applications.
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- 2024
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3. Molecular basis of TMPRSS2 recognition by Paeniclostridium sordellii hemorrhagic toxin
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Ruoyu Zhou, Liuqing He, Jiahao Zhang, Xiaofeng Zhang, Yanyan Li, Xiechao Zhan, and Liang Tao
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Science - Abstract
Abstract Hemorrhagic toxin (TcsH) is a major virulence factor produced by Paeniclostridium sordellii, which is a non-negligible threat to women undergoing childbirth or abortions. Recently, Transmembrane Serine Protease 2 (TMPRSS2) was identified as a host receptor of TcsH. Here, we show the cryo-EM structures of the TcsH-TMPRSS2 complex and uncover that TcsH binds to the serine protease domain (SPD) of TMPRSS2 through the CROP unit-VI. This receptor binding mode is unique among LCTs. Five top surface loops of TMPRSS2SPD, which also determine the protease substrate specificity, constitute the structural determinants recognized by TcsH. The binding of TcsH inhibits the proteolytic activity of TMPRSS2, whereas its implication in disease manifestations remains unclear. We further show that mutations selectively disrupting TMPRSS2-binding reduce TcsH toxicity in the intestinal epithelium of the female mice. These findings together shed light on the distinct molecular basis of TcsH-TMPRSS2 interactions, which expands our knowledge of host recognition mechanisms employed by LCTs and provides novel targets for developing therapeutics against P. sordellii infections.
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- 2024
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4. Structural dynamics of the CROPs domain control stability and toxicity of Paeniclostridium sordellii lethal toxin
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Yao Zhou, Xiechao Zhan, Jianhua Luo, Diyin Li, Ruoyu Zhou, Jiahao Zhang, Zhenrui Pan, Yuanyuan Zhang, Tianhui Jia, Xiaofeng Zhang, Yanyan Li, and Liang Tao
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Science - Abstract
Abstract Paeniclostridium sordellii lethal toxin (TcsL) is a potent exotoxin that causes lethal toxic shock syndrome associated with fulminant bacterial infections. TcsL belongs to the large clostridial toxin (LCT) family. Here, we report that TcsL with varied lengths of combined repetitive oligopeptides (CROPs) deleted show increased autoproteolysis as well as higher cytotoxicity. We next present cryo-EM structures of full-length TcsL, at neutral (pH 7.4) and acidic (pH 5.0) conditions. The TcsL at neutral pH exhibits in the open conformation, which resembles reported TcdB structures. Low pH induces the conformational change of partial TcsL to the closed form. Two intracellular interfaces are observed in the closed conformation, which possibly locks the cysteine protease domain and hinders the binding of the host receptor. Our findings provide insights into the structure and function of TcsL and reveal mechanisms for CROPs-mediated modulation of autoproteolysis and cytotoxicity, which could be common across the LCT family.
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- 2023
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5. Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat
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Hao Zhang, Zhiyuan Jin, Fa Cui, Long Zhao, Xiaoyu Zhang, Jinchao Chen, Jing Zhang, Yanyan Li, Yongpeng Li, Yanxiao Niu, Wenli Zhang, Caixia Gao, Xiangdong Fu, Yiping Tong, Lei Wang, Hong-Qing Ling, Junming Li, and Jun Xiao
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Science - Abstract
Abstract The breeding of crops with improved nitrogen use efficiency (NUE) is crucial for sustainable agriculture, but the involvement of epigenetic modifications remains unexplored. Here, we analyze the chromatin landscapes of two wheat cultivars (KN9204 and J411) that differ in NUE under varied nitrogen conditions. The expression of nitrogen metabolism genes is closely linked to variation in histone modification instead of differences in DNA sequence. Epigenetic modifications exhibit clear cultivar-specificity, which likely contributes to distinct agronomic traits. Additionally, low nitrogen (LN) induces H3K27ac and H3K27me3 to significantly enhance root growth in KN9204, while remarkably inducing NRT2 in J411. Evidence from histone deacetylase inhibitor treatment and transgenic plants with loss function of H3K27me3 methyltransferase shows that changes in epigenetic modifications could alter the strategy preference for root development or nitrogen uptake in response to LN. Here, we show the importance of epigenetic regulation in mediating cultivar-specific adaptation to LN in wheat.
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- 2023
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6. The leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes
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Shifu Aggarwal, Elaine Huang, Hackwon Do, Nishanth Makthal, Yanyan Li, Eric Bapteste, Philippe Lopez, Charles Bernard, and Muthiah Kumaraswami
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Science - Abstract
Abstract The human pathogen Streptococcus pyogenes secretes a short peptide (leaderless communication peptide, LCP) that mediates intercellular communication and controls bacterial virulence through interaction with its receptor, RopB. Here, we show that LCP and RopB homologues are present in other Firmicutes. We experimentally validate that LCPs with distinct peptide communication codes act as bacterial intercellular signals and regulate gene expression in Streptococcus salivarius, Streptococcus porcinus, Enterococcus malodoratus and Limosilactobacillus reuteri. Our results indicate that LCPs are more widespread than previously thought, and their characterization may uncover new signaling mechanisms and roles in coordinating diverse bacterial traits.
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- 2023
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7. Characterization of genome-wide STR variation in 6487 human genomes
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Yirong Shi, Yiwei Niu, Peng Zhang, Huaxia Luo, Shuai Liu, Sijia Zhang, Jiajia Wang, Yanyan Li, Xinyue Liu, Tingrui Song, Tao Xu, and Shunmin He
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Science - Abstract
Abstract Short tandem repeats (STRs) are abundant and highly mutagenic in the human genome. Many STR loci have been associated with a range of human genetic disorders. However, most population-scale studies on STR variation in humans have focused on European ancestry cohorts or are limited by sequencing depth. Here, we depicted a comprehensive map of 366,013 polymorphic STRs (pSTRs) constructed from 6487 deeply sequenced genomes, comprising 3983 Chinese samples (~31.5x, NyuWa) and 2504 samples from the 1000 Genomes Project (~33.3x, 1KGP). We found that STR mutations were affected by motif length, chromosome context and epigenetic features. We identified 3273 and 1117 pSTRs whose repeat numbers were associated with gene expression and 3′UTR alternative polyadenylation, respectively. We also implemented population analysis, investigated population differentiated signatures, and genotyped 60 known disease-causing STRs. Overall, this study further extends the scale of STR variation in humans and propels our understanding of the semantics of STRs.
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- 2023
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8. Predicting response to immunotherapy in gastric cancer via multi-dimensional analyses of the tumour immune microenvironment
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Yang Chen, Keren Jia, Yu Sun, Cheng Zhang, Yilin Li, Li Zhang, Zifan Chen, Jiangdong Zhang, Yajie Hu, Jiajia Yuan, Xingwang Zhao, Yanyan Li, Jifang Gong, Bin Dong, Xiaotian Zhang, Jian Li, and Lin Shen
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Science - Abstract
Predictive methods for gastric cancer to try and differentiate between potential treatment response are required. Here the authors use a multiplexed immunohistochemistry method to propose the proximity of tumour infiltrating immune cells as an indicator of likely therapeutic response.
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- 2022
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9. Paeniclostridium sordellii hemorrhagic toxin targets TMPRSS2 to induce colonic epithelial lesions
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Xingxing Li, Liuqing He, Jianhua Luo, Yangling Zheng, Yao Zhou, Danyang Li, Yuanyuan Zhang, Zhenrui Pan, Yanyan Li, and Liang Tao
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Science - Abstract
Paeniclostridium sordellii is an opportunistic pathogen that can occur and be fatal in women undergoing abortion or childbirth. The pathogenesis of a hemorrhagic toxin, TcsH, produced by this bacteria, remains unknown. Here, authors carry out genome-wide screens to identify pathologically relevant host factors of TcsH.
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- 2022
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10. Multiplexed nanomaterial-assisted laser desorption/ionization for pan-cancer diagnosis and classification
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Hua Zhang, Lin Zhao, Jingjing Jiang, Jie Zheng, Li Yang, Yanyan Li, Jian Zhou, Tianshu Liu, Jianmin Xu, Wenhui Lou, Weige Yang, Lijie Tan, Weiren Liu, Yiyi Yu, Meiling Ji, Yaolin Xu, Yan Lu, Xiaomu Li, Zhen Liu, Rong Tian, Cheng Hu, Shumang Zhang, Qinsheng Hu, Yangdong Deng, Hao Ying, Sheng Zhong, Xingdong Zhang, Yunbing Wang, Hua Wang, Jingwei Bai, Xiaoying Li, and Xiangfeng Duan
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Science - Abstract
As cancer is increasingly considered a metabolic disorder, it is postulated that serum metabolite profiling can be a viable approach for detecting the presence of cancer. Here, the authors report a machine learning model using mass spectrometry-based liquid biopsy data for pan-cancer screening and classification.
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- 2022
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11. Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins
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Stuti Sharma, Ruoyu Zhou, Li Wan, Shan Feng, KangKang Song, Chen Xu, Yanyan Li, and Maofu Liao
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Science - Abstract
In Gram-negative bacteria, lipoproteins are transported from the inner membrane (IM) to the outer membrane (OM) by the ATP-binding cassette (ABC) transporter LolCDE. Here the authors present cryo-EM structures of nanodisc-embedded LolCDE in different states, providing mechanistic insight into the transport mechanism.
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- 2021
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12. A proteomic landscape of diffuse-type gastric cancer
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Sai Ge, Xia Xia, Chen Ding, Bei Zhen, Quan Zhou, Jinwen Feng, Jiajia Yuan, Rui Chen, Yumei Li, Zhongqi Ge, Jiafu Ji, Lianhai Zhang, Jiayuan Wang, Zhongwu Li, Yumei Lai, Ying Hu, Yanyan Li, Yilin Li, Jing Gao, Lin Chen, Jianming Xu, Chunchao Zhang, Sung Yun Jung, Jong Min Choi, Antrix Jain, Mingwei Liu, Lei Song, Wanlin Liu, Gaigai Guo, Tongqing Gong, Yin Huang, Yang Qiu, Wenwen Huang, Tieliu Shi, Weimin Zhu, Yi Wang, Fuchu He, Lin Shen, and Jun Qin
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Science - Abstract
Diffuse-type gastric cancer (DGC) accounts for 30% of gastric cancers and has few treatment options. Here the authors present a mutation and proteome dataset for 84 patients, identifying three major classes of DGC and indicating potential targets for therapy.
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- 2018
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13. Highly selective and active CO2 reduction electrocatalysts based on cobalt phthalocyanine/carbon nanotube hybrid structures
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Xing Zhang, Zishan Wu, Xiao Zhang, Liewu Li, Yanyan Li, Haomin Xu, Xiaoxiao Li, Xiaolu Yu, Zisheng Zhang, Yongye Liang, and Hailiang Wang
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Science - Abstract
Electrochemical reduction of carbon dioxide is a sustainable way of producing carbon-neutral fuels. Here, the authors take a combined nanoscale and molecular approach to develop a highly active and selective cobalt phthalocyanine/carbon nanotube hybrid electrocatalyst for carbon dioxide reduction to carbon monoxide.
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- 2017
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14. Author Correction: A proteomic landscape of diffuse-type gastric cancer
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Sai Ge, Xia Xia, Chen Ding, Bei Zhen, Quan Zhou, Jinwen Feng, Jiajia Yuan, Rui Chen, Yumei Li, Zhongqi Ge, Jiafu Ji, Lianhai Zhang, Jiayuan Wang, Zhongwu Li, Yumei Lai, Ying Hu, Yanyan Li, Yilin Li, Jing Gao, Lin Chen, Jianming Xu, Chunchao Zhang, Sung Yun Jung, Jong Min Choi, Antrix Jain, Mingwei Liu, Lei Song, Wanlin Liu, Gaigai Guo, Tongqing Gong, Yin Huang, Yang Qiu, Wenwen Huang, Tieliu Shi, Weimin Zhu, Yi Wang, Fuchu He, Lin Shen, and Jun Qin
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Science - Abstract
The original version of this Article contained an error in the email address of the corresponding author Jun Qin. The correct email is jqin1965@126.com. The error has been corrected in the HTML and PDF versions of the Article.
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- 2018
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15. Predicting response to immunotherapy in gastric cancer via multi-dimensional analyses of the tumour immune microenvironment
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Yang Chen, Keren Jia, Yu Sun, Cheng Zhang, Yilin Li, Li Zhang, Zifan Chen, Jiangdong Zhang, Yajie Hu, Jiajia Yuan, Xingwang Zhao, Yanyan Li, Jifang Gong, Bin Dong, Xiaotian Zhang, Jian Li, and Lin Shen
- Subjects
Multidisciplinary ,Lymphocytes, Tumor-Infiltrating ,Stomach Neoplasms ,Biomarkers, Tumor ,Tumor Microenvironment ,General Physics and Astronomy ,Humans ,General Chemistry ,Immunotherapy ,Immunohistochemistry ,General Biochemistry, Genetics and Molecular Biology ,B7-H1 Antigen - Abstract
A single biomarker is not adequate to identify patients with gastric cancer (GC) who have the potential to benefit from anti-PD-1/PD-L1 therapy, presumably owing to the complexity of the tumour microenvironment. The predictive value of tumour-infiltrating immune cells (TIICs) has not been definitively established with regard to their density and spatial organisation. Here, multiplex immunohistochemistry is used to quantify in situ biomarkers at sub-cellular resolution in 80 patients with GC. To predict the response to immunotherapy, we establish a multi-dimensional TIIC signature by considering the density of CD4+FoxP3−PD-L1+, CD8+PD-1−LAG3−, and CD68+STING+ cells and the spatial organisation of CD8+PD-1+LAG3− T cells. The TIIC signature enables prediction of the response of patients with GC to anti-PD-1/PD-L1 immunotherapy and patient survival. Our findings demonstrate that a multi-dimensional TIIC signature may be relevant for the selection of patients who could benefit the most from anti-PD-1/PD-L1 immunotherapy.
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- 2021
16. Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins
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Chen Xu, Li Wan, Stuti Sharma, KangKang Song, Shan Feng, Yanyan Li, Maofu Liao, and Ruoyu Zhou
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Protein Conformation ,Science ,Acylation ,Lipoproteins ,General Physics and Astronomy ,ATP-binding cassette transporter ,Peptide ,General Biochemistry, Genetics and Molecular Biology ,Article ,Adenosine Triphosphate ,Escherichia coli ,chemistry.chemical_classification ,Bacterial structural biology ,Multidisciplinary ,Binding Sites ,Chemistry ,Cell Membrane ,Cryoelectron Microscopy ,General Chemistry ,Periplasmic space ,Transmembrane domain ,Protein Transport ,Biochemistry ,Cytoplasm ,Mutation ,Periplasm ,lipids (amino acids, peptides, and proteins) ,ATP-Binding Cassette Transporters ,Bacterial outer membrane ,Hydrophobic and Hydrophilic Interactions ,Lipoprotein ,Cysteine ,Bacterial Outer Membrane Proteins - Abstract
Lipoproteins are important for bacterial growth and antibiotic resistance. These proteins use lipid acyl chains attached to the N-terminal cysteine residue to anchor on the outer surface of cytoplasmic membrane. In Gram-negative bacteria, many lipoproteins are transported to the outer membrane (OM), a process dependent on the ATP-binding cassette (ABC) transporter LolCDE which extracts the OM-targeted lipoproteins from the cytoplasmic membrane. Lipid-anchored proteins pose a unique challenge for transport machinery as they have both hydrophobic lipid moieties and soluble protein component, and the underlying mechanism is poorly understood. Here we determined the cryo-EM structures of nanodisc-embedded LolCDE in the nucleotide-free and nucleotide-bound states at 3.8-Å and 3.5-Å resolution, respectively. The structural analyses, together with biochemical and mutagenesis studies, uncover how LolCDE recognizes its substrate by interacting with the lipid and N-terminal peptide moieties of the lipoprotein, and identify the amide-linked acyl chain as the key element for LolCDE interaction. Upon nucleotide binding, the transmembrane helices and the periplasmic domains of LolCDE undergo large-scale, asymmetric movements, resulting in extrusion of the captured lipoprotein. Comparison of LolCDE and MacB reveals the conserved mechanism of type VII ABC transporters and emphasizes the unique properties of LolCDE as a molecule extruder of triacylated lipoproteins., In Gram-negative bacteria, lipoproteins are transported from the inner membrane (IM) to the outer membrane (OM) by the ATP-binding cassette (ABC) transporter LolCDE. Here the authors present cryo-EM structures of nanodisc-embedded LolCDE in different states, providing mechanistic insight into the transport mechanism.
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- 2021
17. Probing altered receptor specificities of antigenically drifting human H3N2 viruses by chemoenzymatic synthesis, NMR, and modeling
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Luca Unione, Augustinus N. A. Ammerlaan, Gerlof P. Bosman, Elif Uslu, Ruonan Liang, Frederik Broszeit, Roosmarijn van der Woude, Yanyan Liu, Shengzhou Ma, Lin Liu, Marcos Gómez-Redondo, Iris A. Bermejo, Pablo Valverde, Tammo Diercks, Ana Ardá, Robert P. de Vries, and Geert-Jan Boons
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Science - Abstract
Abstract Prototypic receptors for human influenza viruses are N-glycans carrying α2,6-linked sialosides. Due to immune pressure, A/H3N2 influenza viruses have emerged with altered receptor specificities that bind α2,6-linked sialosides presented on extended N-acetyl-lactosamine (LacNAc) chains. Here, binding modes of such drifted hemagglutinin’s (HAs) are examined by chemoenzymatic synthesis of N-glycans having 13C-labeled monosaccharides at strategic positions. The labeled glycans are employed in 2D STD-1H by 13C-HSQC NMR experiments to pinpoint which monosaccharides of the extended LacNAc chain engage with evolutionarily distinct HAs. The NMR data in combination with computation and mutagenesis demonstrate that mutations distal to the receptor binding domain of recent HAs create an extended binding site that accommodates with the extended LacNAc chain. A fluorine containing sialoside is used as NMR probe to derive relative binding affinities and confirms the contribution of the extended LacNAc chain for binding.
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- 2024
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18. Aggresome formation promotes ASK1/JNK signaling activation and stemness maintenance in ovarian cancer
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Yurou Chen, Yulong Qiang, Jiachen Fan, Qian Zheng, Leilei Yan, Guanlan Fan, Xiaofei Song, Nan Zhang, Qiongying Lv, Jiaqiang Xiong, Jingtao Wang, Jing Cao, Yanyan Liu, Jie Xiong, Wei Zhang, and Feng Li
- Subjects
Science - Abstract
Abstract Aggresomes are the product of misfolded protein aggregation, and the presence of aggresomes has been correlated with poor prognosis in cancer patients. However, the exact role of aggresomes in tumorigenesis and cancer progression remains largely unknown. Herein, the multiomics screening reveal that OTUD1 protein plays an important role in retaining ovarian cancer stem cell (OCSC) properties. Mechanistically, the elevated OTUD1 protein levels lead to the formation of OTUD1-based cytoplasmic aggresomes, which is mediated by a short peptide located in the intrinsically disordered OTUD1 N-terminal region. Furthermore, OTUD1-based aggresomes recruit ASK1 via protein-protein interactions, which in turn stabilize ASK1 in a deubiquitinase-independent manner and activate the downstream JNK signaling pathway for OCSC maintenance. Notably, the disruption of OTUD1-based aggresomes or treatment with ASK1/JNK inhibitors, including ibrutinib, an FDA-approved drug that was recently identified as an MKK7 inhibitor, effectively reduced OCSC stemness (OSCS) of OTUD1high ovarian cancer cells. In summary, our work suggests that aggresome formation in tumor cells could function as a signaling hub and that aggresome-based therapy has translational potential for patients with OTUD1high ovarian cancer.
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- 2024
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19. Non-Faradaic optoelectrodes for safe electrical neuromodulation
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Jian Chen, Yanyan Liu, Feixiang Chen, Mengnan Guo, Jiajia Zhou, Pengfei Fu, Xin Zhang, Xueli Wang, He Wang, Wei Hua, Jinquan Chen, Jin Hu, Ying Mao, Dayong Jin, and Wenbo Bu
- Subjects
Science - Abstract
Abstract Nanoscale optoelectrodes hold the potential to stimulate optically individual neurons and intracellular organelles, a challenge that demands both a high-density of photoelectron storage and significant charge injection. Here, we report that zinc porphyrin, commonly used in dye-sensitized solar cells, can be self-assembled into nanorods and then coated by TiO2. The J-aggregated zinc porphyrin array enables long-range exciton diffusion and allows for fast electron transfer into TiO2. The formation of TiO2(e−) attracts positive charges around the neuron membrane, contributing to the induction of action potentials. Far-field cranial irradiation of the motor cortex using a 670 nm laser or an 850 nm femtosecond laser can modulate local neuronal firing and trigger motor responses in the hind limb of mice. The pulsed photoelectrical stimulation of neurons in the subthalamic nucleus alleviates parkinsonian symptoms in mice, improving abnormal stepping and enhancing the activity of dopaminergic neurons. Our results suggest injectable nanoscopic optoelectrodes for optical neuromodulation with high efficiency and negligible side effects.
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- 2024
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20. Author Correction: Cytoplasmic Endonuclease G promotes nonalcoholic fatty liver disease via mTORC2-AKT-ACLY and endoplasmic reticulum stress
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Wenjun Wang, Junyang Tan, Xiaomin Liu, Wenqi Guo, Mengmeng Li, Xinjie Liu, Yanyan Liu, Wenyu Dai, Liubing Hu, Yimin Wang, Qiuxia Lu, Wen Xing Lee, Hong-Wen Tang, and Qinghua Zhou
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Science - Published
- 2024
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21. A proteomic landscape of diffuse-type gastric cancer
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Jianming Xu, Yumei Li, Weimin Zhu, Wanlin Liu, Lianhai Zhang, Jiayuan Wang, Lin Shen, Mingwei Liu, Yilin Li, Yumei Lai, Antrix Jain, Jong Min Choi, Rui Chen, Wenwen Huang, Yi Wang, Chunchao Zhang, Tieliu Shi, Jiafu Ji, Sung Yun Jung, Chen Ding, Jing Gao, Zhongqi Ge, Xia Xia, Jinwen Feng, Ying Hu, Sai Ge, Jun Qin, Yin Huang, Lei Song, Gaigai Guo, Jiajia Yuan, Quan Zhou, Zhongwu Li, Tongqing Gong, Yang Qiu, Lin Chen, Bei Zhen, Fuchu He, and Yanyan Li
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0301 basic medicine ,medicine.medical_treatment ,Science ,General Physics and Astronomy ,Biology ,medicine.disease_cause ,Proteomics ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Stomach surgery ,medicine ,lcsh:Science ,Exome ,Mutation ,Multidisciplinary ,Cancer ,General Chemistry ,Immunotherapy ,Cell cycle ,medicine.disease ,3. Good health ,030104 developmental biology ,Proteome ,Cancer research ,lcsh:Q - Abstract
The diffuse-type gastric cancer (DGC) is a subtype of gastric cancer with the worst prognosis and few treatment options. Here we present a dataset from 84 DGC patients, composed of a proteome of 11,340 gene products and mutation information of 274 cancer driver genes covering paired tumor and nearby tissue. DGC can be classified into three subtypes (PX1–3) based on the altered proteome alone. PX1 and PX2 exhibit dysregulation in the cell cycle and PX2 features an additional EMT process; PX3 is enriched in immune response proteins, has the worst survival, and is insensitive to chemotherapy. Data analysis revealed four major vulnerabilities in DGC that may be targeted for treatment, and allowed the nomination of potential immunotherapy targets for DGC patients, particularly for those in PX3. This dataset provides a rich resource for information and knowledge mining toward altered signaling pathways in DGC and demonstrates the benefit of proteomic analysis in cancer molecular subtyping., Diffuse-type gastric cancer (DGC) accounts for 30% of gastric cancers and has few treatment options. Here the authors present a mutation and proteome dataset for 84 patients, identifying three major classes of DGC and indicating potential targets for therapy.
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- 2018
22. Cytoplasmic Endonuclease G promotes nonalcoholic fatty liver disease via mTORC2-AKT-ACLY and endoplasmic reticulum stress
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Wenjun Wang, Junyang Tan, Xiaomin Liu, Wenqi Guo, Mengmeng Li, Xinjie Liu, Yanyan Liu, Wenyu Dai, Liubing Hu, Yimin Wang, Qiuxia Lu, Wen Xing Lee, Hong-Wen Tang, and Qinghua Zhou
- Subjects
Science - Abstract
Abstract Endonuclease G (ENDOG), a nuclear-encoded mitochondrial intermembrane space protein, is well known to be translocated into the nucleus during apoptosis. Recent studies have shown that ENDOG might enter the mitochondrial matrix to regulate mitochondrial genome cleavage and replication. However, little is known about the role of ENDOG in the cytosol. Our previous work showed that cytoplasmic ENDOG competitively binds with 14-3-3γ, which released TSC2 to repress mTORC1 signaling and induce autophagy. Here, we demonstrate that cytoplasmic ENDOG could also release Rictor from 14-3-3γ to activate the mTORC2-AKT-ACLY axis, resulting in acetyl-CoA production. Importantly, we observe that ENDOG could translocate to the ER, bind with Bip, and release IRE1a/PERK to activate the endoplasmic reticulum stress response, promoting lipid synthesis. Taken together, we demonstrate that loss of ENDOG suppresses acetyl-CoA production and lipid synthesis, along with reducing endoplasmic reticulum stress, which eventually alleviates high-fat diet-induced nonalcoholic fatty liver disease in female mice.
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- 2023
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23. Author Correction: A proteomic landscape of diffuse-type gastric cancer
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Bei Zhen, Lei Song, Yumei Li, Wanlin Liu, Jing Gao, Jinwen Feng, Tongqing Gong, Xia Xia, Chunchao Zhang, Mingwei Liu, Jiayuan Wang, Rui Chen, Yi Wang, Jong Min Choi, Sung Yun Jung, Wenwen Huang, Gaigai Guo, Yin Huang, Jianming Xu, Jiajia Yuan, Lin Chen, Tieliu Shi, Quan Zhou, Zhongqi Ge, Jun Qin, Antrix Jain, Ying Hu, Yilin Li, Zhongwu Li, Yumei Lai, Lin Shen, Weimin Zhu, Lianhai Zhang, Fuchu He, Yanyan Li, Sai Ge, Yang Qiu, Jiafu Ji, and Chen Ding
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Proteomics ,0301 basic medicine ,Computer science ,Science ,DNA Mutational Analysis ,MEDLINE ,Datasets as Topic ,Down-Regulation ,General Physics and Astronomy ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Email address ,Gastrectomy ,Stomach Neoplasms ,Tandem Mass Spectrometry ,medicine ,Humans ,Diffuse type ,Exome ,Author Correction ,lcsh:Science ,Neoplasm Staging ,Oligonucleotide Array Sequence Analysis ,Multidisciplinary ,Information retrieval ,Published Erratum ,Stomach ,Cancer ,Chemoradiotherapy, Adjuvant ,Sequence Analysis, DNA ,General Chemistry ,Prognosis ,medicine.disease ,Immunohistochemistry ,Survival Analysis ,Neoadjuvant Therapy ,Neoplasm Proteins ,Up-Regulation ,030104 developmental biology ,030220 oncology & carcinogenesis ,Mutation ,ComputingMethodologies_DOCUMENTANDTEXTPROCESSING ,lcsh:Q ,Follow-Up Studies ,Genes, Neoplasm ,Signal Transduction - Abstract
The diffuse-type gastric cancer (DGC) is a subtype of gastric cancer with the worst prognosis and few treatment options. Here we present a dataset from 84 DGC patients, composed of a proteome of 11,340 gene products and mutation information of 274 cancer driver genes covering paired tumor and nearby tissue. DGC can be classified into three subtypes (PX1-3) based on the altered proteome alone. PX1 and PX2 exhibit dysregulation in the cell cycle and PX2 features an additional EMT process; PX3 is enriched in immune response proteins, has the worst survival, and is insensitive to chemotherapy. Data analysis revealed four major vulnerabilities in DGC that may be targeted for treatment, and allowed the nomination of potential immunotherapy targets for DGC patients, particularly for those in PX3. This dataset provides a rich resource for information and knowledge mining toward altered signaling pathways in DGC and demonstrates the benefit of proteomic analysis in cancer molecular subtyping.
- Published
- 2018
24. Highly selective and active CO2 reduction electrocatalysts based on cobalt phthalocyanine/carbon nanotube hybrid structures
- Author
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Zisheng Zhang, Xiao Zhang, Hailiang Wang, Zishan Wu, Yanyan Li, Xing Zhang, Liewu Li, Xiaoxiao Li, Xiaolu Yu, Haomin Xu, and Yongye Liang
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Materials science ,Science ,General Physics and Astronomy ,Nanotechnology ,02 engineering and technology ,Carbon nanotube ,Overpotential ,010402 general chemistry ,Electrocatalyst ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Article ,Catalysis ,law.invention ,chemistry.chemical_compound ,law ,Electrochemical reduction of carbon dioxide ,Multidisciplinary ,General Chemistry ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,chemistry ,0210 nano-technology ,Selectivity ,Faraday efficiency ,Carbon monoxide - Abstract
Electrochemical reduction of carbon dioxide with renewable energy is a sustainable way of producing carbon-neutral fuels. However, developing active, selective and stable electrocatalysts is challenging and entails material structure design and tailoring across a range of length scales. Here we report a cobalt-phthalocyanine-based high-performance carbon dioxide reduction electrocatalyst material developed with a combined nanoscale and molecular approach. On the nanoscale, cobalt phthalocyanine (CoPc) molecules are uniformly anchored on carbon nanotubes to afford substantially increased current density, improved selectivity for carbon monoxide, and enhanced durability. On the molecular level, the catalytic performance is further enhanced by introducing cyano groups to the CoPc molecule. The resulting hybrid catalyst exhibits >95% Faradaic efficiency for carbon monoxide production in a wide potential range and extraordinary catalytic activity with a current density of 15.0 mA cm−2 and a turnover frequency of 4.1 s−1 at the overpotential of 0.52 V in a near-neutral aqueous solution., Electrochemical reduction of carbon dioxide is a sustainable way of producing carbon-neutral fuels. Here, the authors take a combined nanoscale and molecular approach to develop a highly active and selective cobalt phthalocyanine/carbon nanotube hybrid electrocatalyst for carbon dioxide reduction to carbon monoxide.
- Published
- 2017
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