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11. Deciphering human macrophage development at single-cell resolution

Author

Bian, Zhilei, Gong, Yandong, Huang, Tao, Lee, Christopher Z. W., Bian, Lihong, Bai, Zhijie, Shi, Hui, Zeng, Yang, Liu, Chen, He, Jian, Zhou, Jie, Li, Xianlong, Li, Zongcheng, Ni, Yanli, Ma, Chunyu, Cui, Lei, Zhang, Rui, Chan, Jerry K. Y., Ng, Lai Guan, Lan, Yu, Ginhoux, Florent, and Liu, Bing

Published
2020
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15. Single-cell dissection of cellular and molecular features underlying human cervical squamous cell carcinoma initiation and progression

Author

Liu, Chao, primary, Zhang, Min, additional, Yan, Xinlong, additional, Ni, Yanli, additional, Gong, Yandong, additional, Wang, Cong, additional, Zhang, Xiaoling, additional, Wan, Lingfei, additional, Yang, Hui, additional, Ge, Chen, additional, Li, Yunqiao, additional, Zou, Wenxue, additional, Huang, Rui, additional, Li, Xiaohui, additional, Sun, Bing, additional, Liu, Bing, additional, Yue, Jinbo, additional, and Yu, Jinming, additional

Published
2023
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19. Tracing haematopoietic stem cell formation at single-cell resolution

Author

Zhou, Fan, Li, Xianlong, Wang, Weili, Zhu, Ping, Zhou, Jie, He, Wenyan, Ding, Meng, Xiong, Fuyin, Zheng, Xiaona, Li, Zhuan, Ni, Yanli, Mu, Xiaohuan, Wen, Lu, Cheng, Tao, Lan, Yu, Yuan, Weiping, and Tang, Fuchou

Subjects
Embryo -- Physiological aspects, Stem cells -- Physiological aspects, Endothelium -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Haematopoietic stem cells (HSCs) are derived early from embryonic precursors, such as haemogenic endothelial cells and pre-haematopoietic stem cells (pre-HSCs), the molecular identity of which still remains elusive. Here we use potent surface markers to capture the nascent pre-HSCs at high purity, as rigorously validated by single-cell-initiated serial transplantation. Then we apply single-cell RNA sequencing to analyse endothelial cells, CD45.sup.- and CD45.sup.+ pre-HSCs in the aorta-gonad-mesonephros region, and HSCs in fetal liver. Pre-HSCs show unique features in transcriptional machinery, arterial signature, metabolism state, signalling pathway, and transcription factor network. Functionally, activation of mechanistic targets of rapamycin (mTOR) is shown to be indispensable for the emergence of HSCs but not haematopoietic progenitors. Transcriptome data-based functional analysis reveals remarkable heterogeneity in cell-cycle status of pre-HSCs. Finally, the core molecular signature of pre-HSCs is identified. Collectively, our work paves the way for dissection of complex molecular mechanisms regulating stepwise generation of HSCs in vivo, informing future efforts to engineer HSCs for clinical applications. Successful identification of mouse embryonic pre-haematopoietic stem cells at single-cell resolution. Haematopoietic stem cell formation dissected Fuchou Tang and colleagues have isolated the earliest haematopoietic stem cell (HSC) precursors -- rare CD45-negative pre-HSCs -- from developing mouse embryos using a combination of surface marker expression and single-cell-based transplantation assays, assessing blood-forming capacity. Single-cell RNA-seq was used to analyse the transcriptomes for five types of cells related to HSC formation, revealing a role for mTOR activation in the emergence of HSCs but not haematopoietic progenitors., Author(s): Fan Zhou [sup.1] , Xianlong Li [sup.2] , Weili Wang [sup.3] , Ping Zhu [sup.2] [sup.4] , Jie Zhou [sup.1] , Wenyan He [sup.1] , Meng Ding [sup.1] , [...]

Published
2016
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21. Transcriptomic landscape of circulating mononuclear phagocytes in Langerhans cell histiocytosis at the single-cell level

Author

Shi, Hui, primary, He, Han, additional, Cui, Lei, additional, Kvedaraite, Egle, additional, Bian, Zhilei, additional, Huang, Tao, additional, Lee, Christopher Z. W., additional, Li, Zhigang, additional, He, Jian, additional, Gong, Yandong, additional, Li, Zongcheng, additional, Zhou, Jie, additional, Zeng, Yang, additional, Li, Xianlong, additional, Ni, Yanli, additional, Bai, Zhijie, additional, Liu, Chen, additional, Li, Na, additional, Ma, Honghao, additional, Wang, Dong, additional, Lan, Yu, additional, Ginhoux, Florent, additional, Zhang, Rui, additional, and Liu, Bing, additional

Published
2021
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22. Hlf Expression Marks Early Emergence of Hematopoietic Stem Cell Precursors With Adult Repopulating Potential and Fate

Author

Tang, Wanbo, primary, He, Jian, additional, Huang, Tao, additional, Bai, Zhijie, additional, Wang, Chaojie, additional, Wang, Haizhen, additional, Yang, Ruichuang, additional, Ni, Yanli, additional, Hou, Jun, additional, Wang, Junliang, additional, Zhou, Jie, additional, Yao, Yingpeng, additional, Gong, Yandong, additional, Hou, Siyuan, additional, Liu, Bing, additional, and Lan, Yu, additional

Published
2021
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25. Spatiotemporal and Functional Heterogeneity of Hematopoietic Stem Cell-Competent Hemogenic Endothelial Cells in Mouse Embryos

Author

Li, Yun-Qiao, primary, Gong, Yandong, additional, Hou, Siyuan, additional, Huang, Tao, additional, Wang, Haizhen, additional, Liu, Di, additional, Ni, Yanli, additional, Wang, Chaojie, additional, Wang, Junliang, additional, Hou, Jun, additional, Yang, Ruichuang, additional, Yan, Jing, additional, Zhang, Guangyu, additional, Liu, Bing, additional, and Lan, Yu, additional

Published
2021
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27. Lycopene antagonizes lead toxicity by reducing mitochondrial oxidative damage and mitochondria-mediated apoptosis in cultured hippocampal neurons

Author

Baoshi Guo, Mingyue Qu, Jiang Zheng, Ni Yanli, and Feng Xin

Subjects
chemistry.chemical_classification, Mitochondrial ROS, Reactive oxygen species, lead, Chemistry, lcsh:R, Neurotoxicity, lcsh:Medicine, Original Articles, Mitochondrion, medicine.disease_cause, medicine.disease, lycopene, Lycopene, Cell biology, mitochondria, chemistry.chemical_compound, Mitochondrial permeability transition pore, hippocampal neuron, Apoptosis, medicine, oxidative stress, Original Article, Oxidative stress
Abstract

Lead (Pb) exhibits serious adverse effects on the central nervous system, and the major pathogenic mechanism of Pb toxicity is oxidative stress. As one of the carotenoid family members with potent antioxidant properties, lycopene has shown its protections by inhibiting oxidative stress damage in numerous models of neurotoxicity. The current study was designed to explore the possible protective property in primary cultured rat hippocampal neurons challenged with Pb. We observed that 5 μM lycopene pretreatment for 4 h efficiently ameliorated Pb‐caused damage in cell viability, accumulation of reactive oxygen species (ROS), and apoptosis in a dose‐dependent manner. Moreover, lycopene (5 μM) attenuated the 50 μM Pb‐induced mitochondrial ROS production, improved the activities of mitochondrial respiratory chain enzymes and ATP production, and ameliorated the 50 μM Pb‐induced depolarization of mitochondrial membrane potential as well as opening of mitochondrial permeability transition pores. In addition, 5 μM lycopene restored the imbalance of Bax/Bcl‐2, inhibited translocation of cytochrome c, and reduced caspase‐3 activation. Taken together, these findings indicate that lycopene antagonizes against Pb‐induced neurotoxicity and the underlying mechanism probably involves reduction of mitochondrial oxidative damage and mitochondria‐mediated apoptosis., In this study, we demonstrated the neuroprotective effects of lycopene in primary cultured rat hippocampal neurons challenged with lead. The protective effects of lycopene may be attributable to its roles in reducing mitochondrial oxidative damage and mitochondria‐mediated apoptosis.

Published
2020

28. Dissecting human skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses

Author

He, Jian, primary, Yan, Jing, additional, Wang, Jianfang, additional, Zhao, Liangyu, additional, Xin, Qian, additional, Zeng, Yang, additional, Sun, Yuxi, additional, Zhang, Han, additional, Bai, Zhijie, additional, Li, Zongcheng, additional, Ni, Yanli, additional, Gong, Yandong, additional, Li, Yunqiao, additional, He, Han, additional, Bian, Zhilei, additional, Lan, Yu, additional, Ma, Chunyu, additional, Bian, Lihong, additional, Zhu, Heng, additional, Liu, Bing, additional, and Yue, Rui, additional

Published
2020
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29. Single-cell transcriptomic architecture and intercellular crosstalk of human intrahepatic cholangiocarcinoma

Author

Zhang, Min, primary, Yang, Hui, additional, Wan, Lingfei, additional, Wang, Zhaohai, additional, Wang, Haiyang, additional, Ge, Chen, additional, Liu, Yunhui, additional, Hao, Yajing, additional, Zhang, Dongdong, additional, Shi, Gaona, additional, Gong, Yandong, additional, Ni, Yanli, additional, Wang, Chaojie, additional, Zhang, Yuan, additional, Xi, Jiafei, additional, Wang, Sen, additional, Shi, Lei, additional, Zhang, Lina, additional, Yue, Wen, additional, Pei, Xuetao, additional, Liu, Bing, additional, and Yan, Xinlong, additional

Published
2020
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33. Dissecting endothelial to haematopoietic stem cell transition by single-cell transcriptomic and functional analyses

Author

Hou, Siyuan, primary, Li, Zongcheng, additional, Zheng, Xiaona, additional, Gao, Yun, additional, Dong, Ji, additional, Ni, Yanli, additional, Wang, Xiaobo, additional, Li, Yunqiao, additional, Ding, Xiaochen, additional, Chang, Zhilin, additional, Li, Shuaili, additional, Hu, Yuqiong, additional, Fan, Xiaoying, additional, Hou, Yu, additional, Wen, Lu, additional, Liu, Bing, additional, Tang, Fuchou, additional, and Lan, Yu, additional

Published
2020
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34. Single-Cell RNA Sequencing Resolves Spatiotemporal Development of Pre-thymic Lymphoid Progenitors and Thymus Organogenesis in Human Embryos

Author

Zeng, Yang, primary, Liu, Chen, additional, Gong, Yandong, additional, Bai, Zhijie, additional, Hou, Siyuan, additional, He, Jian, additional, Bian, Zhilei, additional, Li, Zongcheng, additional, Ni, Yanli, additional, Yan, Jing, additional, Huang, Tao, additional, Shi, Hui, additional, Ma, Chunyu, additional, Chen, Xueying, additional, Wang, Jinyong, additional, Bian, Lihong, additional, Lan, Yu, additional, Liu, Bing, additional, and Hu, Hongbo, additional

Published
2019
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38. Combined Single-Cell Profiling of lncRNAs and Functional Screening Reveals that H19 Is Pivotal for Embryonic Hematopoietic Stem Cell Development

Author

Zhou, Jie, primary, Xu, Jiayue, additional, Zhang, Linlin, additional, Liu, Siqi, additional, Ma, Yanni, additional, Wen, Xin, additional, Hao, Junkai, additional, Li, Zongcheng, additional, Ni, Yanli, additional, Li, Xianlong, additional, Zhou, Fan, additional, Li, Qingqing, additional, Wang, Fang, additional, Wang, Xiaoshuang, additional, Si, Yanmin, additional, Zhang, Pengcheng, additional, Liu, Chen, additional, Bartolomei, Marisa, additional, Tang, Fuchou, additional, Liu, Bing, additional, Yu, Jia, additional, and Lan, Yu, additional

Published
2019
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39. Selective Enrichment and MALDI-TOF MS Analysis of Small Molecule Compounds with Vicinal Diols by Boric Acid-Functionalized Graphene Oxide

Author

Jing Zhang, Xiao-ling Zheng, and Ni Yanli

Subjects
Chemistry, Graphene, Radical polymerization, Oxide, Mass spectrometry, Combinatorial chemistry, law.invention, chemistry.chemical_compound, Matrix-assisted laser desorption/ionization, Boric Acids, Models, Chemical, Structural Biology, law, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Desorption, Organic chemistry, Molecule, Graphite, Spectroscopy, Vicinal
Abstract

In this study, a 4-vinylphenylboronic acid-functionalized graphene oxide (GO) material was prepared via atom-transfer radical polymerization (ATRP) method and applied for the first time as a novel matrix for the selective enrichment and analysis of small-molecule compounds with vicinal diols, which have been the focus of intense research in the field of life science, by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in positive-ion mode. There are two main factors playing a decisive role in assisting laser D/I process comparing to some traditional matrices: (1) GO provides π-conjugated system by itself for laser absorption and energy transfer; (2) the modified 4-vinylphenylboronic acid can selectively capture small-molecule compounds with vicinal diols. The results demonstrate that the novel material has distinct advantages over previously reported matrices in enriching and assisting the highly efficient ionization of target molecules for mass spectrometry analysis. This work indicates a new application branch for graphene-based matrices and provides an alternative solution for small-molecules analysis.

Published
2015

40. Preparation of poly(vinylphenylboronic acid) chain grafted poly(glycidylmethacrylate-co-ethylenedimethacrylate) beads for the selective enrichment of glycoprotein

Author

Xiao-ling Zheng, Jing Zhang, and Ni Yanli

Subjects
Chromatography, Atom-transfer radical-polymerization, Chemistry, Filtration and Separation, Sorption, Bead, Mass spectrometry, Analytical Chemistry, chemistry.chemical_compound, Adsorption, visual_art, visual_art.visual_art_medium, Fourier transform infrared spectroscopy, Boronic acid, Egg white
Abstract

Surface-initiated atom transfer radical polymerization was successfully used to prepare 4-vinylphenylboronic acid functionalized poly(glycidylmethacrylate-co-ethylenedimethacrylate) beads for the selective enrichment of glycoprotein from complex biological samples in this study. The modified bead surfaces were characterized using Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. The sorption behaviors, including adsorption isotherms, incubation time, and pH effect, were investigated. The results demonstrated that the boronated beads have a high affinity for glycoprotein, which is due to the well-defined boronic acid brushes on the beads surfaces. Furthermore, the polyvinylphenylboronic acid grafted poly(glycidylmethacrylate-co-ethylenedimethacrylate) beads were used to efficiently enrich and purify glycoprotein from real egg white samples and α-fetoprotein from human serum samples. The mass spectrometry results demonstrated that the polyvinylphenylboronic acid grafted poly(glycidylmethacrylate-co-ethylenedimethacrylate) beads are a suitable material for the enrichment of glycosylated protein from complex biological samples.

Published
2014

42. Dissecting transcriptional heterogeneity in primary gastric adenocarcinoma by single cell RNA sequencing

Author

Zhang, Min, Hu, Shuofeng, Min, Min, Ni, Yanli, Lu, Zheng, Sun, Xiaotian, Wu, Jiaqi, Liu, Bing, Ying, Xiaomin, and Liu, Yan

Abstract

ObjectiveTumour heterogeneity represents a major obstacle to accurate diagnosis and treatment in gastric adenocarcinoma (GA). Here, we report a systematic transcriptional atlas to delineate molecular and cellular heterogeneity in GA using single-cell RNA sequencing (scRNA-seq).DesignWe performed unbiased transcriptome-wide scRNA-seq analysis on 27 677 cells from 9 tumour and 3 non-tumour samples. Analysis results were validated using large-scale histological assays and bulk transcriptomic datasets.ResultsOur integrative analysis of tumour cells identified five cell subgroups with distinct expression profiles. A panel of differentiation-related genes reveals a high diversity of differentiation degrees within and between tumours. Low differentiation degrees can predict poor prognosis in GA. Among them, three subgroups exhibited different differentiation grade which corresponded well to histopathological features of Lauren’s subtypes. Interestingly, the other two subgroups displayed unique transcriptome features. One subgroup expressing chief-cell markers (eg, LIPFand PGC) and RNF43with Wnt/β-catenin signalling pathway activated is consistent with the previously described entity fundic gland-type GA (chief cell-predominant, GA-FG-CCP). We further confirmed the presence of GA-FG-CCP in two public bulk datasets using transcriptomic profiles and histological images. The other subgroup specifically expressed immune-related signature genes (eg, LY6Kand major histocompatibility complex class II) with the infection of Epstein-Barr virus. In addition, we also analysed non-malignant epithelium and provided molecular evidences for potential transition from gastric chief cells into MUC6+TFF2+spasmolytic polypeptide expressing metaplasia.ConclusionAltogether, our study offers valuable resource for deciphering gastric tumour heterogeneity, which will provide assistance for precision diagnosis and prognosis.

Published
2021
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44. PD-1 mRNA expression in peripheral blood cells and its modulation characteristics in cancer patients

Author

Wang, Wei, primary, Shen, Ge, additional, Wu, Shikai, additional, Song, Shiping, additional, Ni, Yanli, additional, Suo, Zhuoyao, additional, Meng, Xiangying, additional, Li, Dan, additional, Zhou, Lin, additional, Hao, Rimin, additional, Zhao, Yaowei, additional, Bai, Li, additional, Hou, Lili, additional, Liu, Bing, additional, and Liu, Guangxian, additional

Published
2017
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45. A Meta-analysis on diagnostic value of serum cystatin C and creatinine for the evaluation of glomerular filtration function in renal transplant patients

Author

Pan Pan, Hu Binjie, Ni Yanli, Zhou Junwen, Fan Lipei, Shi Xianghua, and Li Min

Subjects
medicine.medical_specialty, Urology, Renal function, urologic and male genital diseases, Sensitivity and Specificity, Cystatin C, creatinine, renal transplantation, glomerular filtration rate, meta-analysis, chemistry.chemical_compound, Serum cystatin, Internal medicine, Medicine, Humans, reproductive and urinary physiology, Kidney transplantation, Creatinine, biology, business.industry, General Medicine, Articles, medicine.disease, Kidney Transplantation, female genital diseases and pregnancy complications, Transplantation, Endocrinology, chemistry, ROC Curve, Renal transplant, Meta-analysis, biology.protein, business, Glomerular Filtration Rate
Abstract

Objectives : This meta-analysis aimed to perform a systematic review on comparing the diagnostic value of serum cystatin C and creatinine for glomerular filtration rate in renal transplant patients. Methods : The data was extracted into 2×2 table after the articles were assessed by the tool of QUADAS and heterogeneity analysis. The SROC curve and meta-analysis were performed by MetaDisc1.4. Results : Meta-analysis showed that the serum cystatin C had no heterogeneity (P=0.418, I2=2.2%, DOR=25.03), while creatinine heterogeneity was high (P=0.109, I2=37.5%, DOR=9.11). The values of SEN, SPE and SAUC were calculated as 0.86, 0.70 and 0.9015 for cystatin C , and 0.78, 0.73 and 0.8285 for creatinine individually. This study utilized GFR detection and subgroups analysis by cutoff. The PLR was 6.13 and the NLR was 0.12 for cystatin C , compared to SCr (3.72, 0.32). There was homogeneity among these studies using PENIA testing for cystatin C (χ 2 =2.61, P=0.4560, I2=0.0%. Conclusions : There were significant correlations among cystatin C , creatinine and glomerular filtration rate (GFR). Cystatin C had more sensitivity but less specificity than creatinine for evaluation of GFR. Cystatin C had strong ability in diagnosing renal function after renal transplant and ruling out diagnostic efficacy. Key words : Cystatin C; creatinine; renal transplantation; glomerular filtration rate; meta-analysis.

Published
2014

46. Embryonic lineage tracing with Procr-CreERmarks balanced hematopoietic stem cell fate during entire mouse lifespan

Author

Zheng, Xiaona, Zhang, Guangyu, Gong, Yandong, Ning, Xiaowei, Bai, Zhijie, He, Jian, Zhou, Fan, Ni, Yanli, Lan, Yu, and Liu, Bing

Abstract

The functional heterogeneity of hematopoietic stem cells (HSCs) has been comprehensively investigated by single-cell transplantation assay. However, the heterogeneity regarding their physiological contribution remains an open question, especially for those with life-long hematopoietic fate of rigorous self-renewing and balanced differentiation capacities. In this study, we revealed that Procrexpression was detected principally in phenotypical vascular endothelium co-expressing Dll4 and CD44 in the mid-gestation mouse embryos, and could enrich all the HSCs of the embryonic day 11.5 (E11.5) aorta-gonad-mesonephros (AGM) region. We then used a temporally restricted genetic tracing strategy to irreversibly label the Procr-expressing cells at E9.5. Interestingly, most labeled mature HSCs in multiple sites (such as AGM) around E11.5 were functionally categorized as lymphomyeloid-balanced HSCs assessed by direct transplantation. Furthermore, the labeled cells contributed to an average of 7.8% of immunophenotypically defined HSCs in E14.5 fetal liver (FL) and 6.9% of leukocytes in peripheral blood (PB) during one-year follow-up. Surprisingly, in aged mice of 24 months, the embryonically tagged cells displayed constant contribution to leukocytes with no bias to myeloid or lymphoid lineages. Altogether, we demonstrated, for the first time, the existence of a subtype of physiologically long-lived balanced HSCs as hypothesized, whose precise embryonic origin and molecular identity await further characterization.

Published
2019
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48. ATF4 is a positive regulator for hematopoietic stem cells partially via Angptl3 in mouse fetal liver microenvironment

Author

Zhao, Yunze, primary, Zhou, Jie, additional, Dong, Fang, additional, Cheng, Hui, additional, Wang, Weili, additional, Pang, Yakun, additional, Mu, Xiaohuan, additional, Ni, Yanli, additional, Li, Zhuan, additional, Xu, Huiyu, additional, Hao, Sha, additional, Wang, Xiaochen, additional, Yuan, Weiping, additional, Liu, Bing, additional, and Cheng, Tao, additional

Published
2015
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