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| 1 | Identification of HSC/MPP expansion units in fetal liver by single-cell spatiotemporal transcriptomics显示文摘Limited knowledge of cellular and molecular mechanisms underlying hematopoietic stem cell and multipotent progenitor(HSC/MPP)expansion within their native niche has impeded the application of stem cell-based therapies for hematological malignancies.Here,we constructed a spatiotemporal transcriptome map of mouse fetal liver(FL)as a platform for hypothesis generation and subsequent experimental validation of novel regulatory mechanisms.Single-cell transcriptomics revealed three transcriptionally heterogeneous HSC/MPP subsets,among which a CD93-enriched subset exhibited enhanced stem cell properties.Moreover,by employing integrative analysis of single-cell and spatial transcriptomics,we identified novel HSC/MPP‘pocket-like’units(HSC PLUS),composed of niche cells(hepatoblasts,stromal cells,endothelial cells,and macrophages)and enriched with growth factors.Unexpectedly,macrophages showed an 11-fold enrichment in the HSC PLUS.Functionally,macrophage-HSC/MPP co-culture assay and candidate molecule testing,respectively,validated the supportive role of macrophages and growth factors(MDK,PTN,and IGFBP5)in HSC/MPP expansion.Finally,cross-species analysis and functional validation showed conserved cell-cell interactions and expansion mechanisms but divergent transcriptome signatures between mouse and human FL HSCs/MPPs.Taken together,these results provide an essential resource for understanding HSC/MPP development in FL,and novel insight into functional HSC/MPP expansion ex vivo. | Suwei Gao Qiang Shi Yifan Zhang Guixian Liang Zhixin Kang Baofeng Huang Dongyuan Ma Lu Wang Jianwei Jiao Xiangdong Fang Cheng-Ran Xu Longqi Liu Xun Xu Berthold Gottgens Cheng Li Feng Liu | 2022 | Cell Research2022，32，1： | 4 |
| 2 | Dynamic cell transition and immune response landscapes of axolotl limb regeneration revealed by single-cell analysis显示文摘Dear Editor,The axolotl,Ambystoma mexicanum,has extraordinary capability to fully recover multiple tissues after lost,whereas such capability has disappeared in mammals.Thus,deci-phering detailed mechanisms underlying axolotl regenera-tion could provide valuable lessons for regenerative medicine.However,many questions,such as the origin of essential progenitor cells and key responses of individual types of cells for regeneration remain elusive(Haas and Whited,2017).Newly developed single-cell RNA sequenc-ing(scRNA-seq)method enables researchers to observe cellular and molecular dynamics in axolotl regeneration at the single-cell resolution(Gerber et al.,2018;Leigh et al.,2018),but the reported transcriptome landscapes are only for certain cell types or in certain regenerative stages.A complete overview of the regeneration process for all cell types is still lacking. | Hanbo Li Xiaoyu Wei Li Zhou Weiqi Zhang Chen Wang Yang Guo Denghui Li Jjianyang Chen Tianbin Liu Yingying Zhang Shuai Ma Congyan Wang Fujian Tan Jiangshan Xu Yang Liu Yue Yuan Liang Chen Qiaoran Wang Jing Qu Yue Shen Shanshan Liu Guangyi Fan Longqi Liu Xin Liu Yong Hou Guang-Hui Liu Ying Gu Xun Xu | 2021 | Protein & Cell2021，12，1： | 3 |
| 3 | An invasive zone in human liver cancer identified by Stereo-seq promotes hepatocyte–tumor cell crosstalk,local immunosuppression and tumor progression显示文摘Dissecting and understanding the cancer ecosystem,especially that around the tumor margins,which have strong implications for tumor cell infiltration and invasion,are essential for exploring the mechanisms of tumor metastasis and developing effective new treatments.Using a novel tumor border scanning and digitization model enabled by nanoscale resolution-SpaTial Enhanced REsolution Omics-sequencing(Stereo-seq),we identified a 500µm-wide zone centered around the tumor border in patients with liver cancer,referred to as“the invasive zone”.We detected strong immunosuppression,metabolic reprogramming,and severely damaged hepatocytes in this zone.We also identified a subpopulation of damaged hepatocytes with increased expression of serum amyloid A1 and A2(referred to collectively as SAAs)located close to the border on the paratumor side.Overexpression of CXCL6 in adjacent malignant cells could induce activation of the JAK-STAT3 pathway in nearby hepatocytes,which subsequently caused SAAs’overexpression in these hepatocytes.Furthermore,overexpression and secretion of SAAs by hepatocytes in the invasive zone could lead to the recruitment of macrophages and M2 polarization,further promoting local immunosuppression,potentially resulting in tumor progression.Clinical association analysis in additional five independent cohorts of patients with primary and secondary liver cancer(n=423)showed that patients with overexpression of SAAs in the invasive zone had a worse prognosis.Further in vivo experiments using mouse liver tumor models in situ confirmed that the knockdown of genes encoding SAAs in hepatocytes decreased macrophage accumulation around the tumor border and delayed tumor growth.The identification and characterization of a novel invasive zone in human cancer patients not only add an important layer of understanding regarding the mechanisms of tumor invasion and metastasis,but may also pave the way for developing novel therapeutic strategies for advanced liver cancer and other solid tumors. | Liang Wu Jiayan Yan Yinqi Bai Feiyu Chen Xuanxuan Zou Jiangshan Xu Ao Huang Liangzhen Hou Yu Zhong Zehua Jing Qichao Yu Xiaorui Zhou Zhifeng Jiang Chunqing Wang Mengnan Cheng Yuan Ji Yingyong Hou Rongkui Luo Qinqin Li Liang Wu Jianwen Cheng Pengxiang Wang Dezhen Guo Waidong Huang Junjie Lei Shang Liu Yizhen Yan Yiling Chen Sha Liao Yuxiang Li Haixiang Sun Na Yao Xiangyu Zhang Shiyu Zhang Xi Chen Yang Yu Yao Li Fengming Liu Zheng Wang Shaolai Zhou Huanming Yang Shuang Yang Xun Xu Longqi Liu Qiang Gao Zhaoyou Tang Xiangdong Wang Jian Wang Jia Fan Shiping Liu Xinrong Yang Ao Chen Jian Zhou | 2023 | Cell Research2023，33，8： | 1 |
| 4 | Anomaly detection based on efficient Euclidean projection显示文摘 | YANG Longqi HU Guyu LI Dong | 2015 | Security and Communication Networks2015，8，17： | 1 |
| 5 | Elastic dflections of Simply Supported Steel 1 -Beams with a Web Opening 显示文摘 | Donghua Zhou Longqi Li Jtirgen Schnell etal | 2012 | Pro- cedia Engineering2012，31，： | 1 |
| 6 | Nitrogen‐Doped Porous Carbon Nanofiber Webs as Anodes for Lithium Ion Batteries with a Superhigh Capacity and Rate Capability显示文摘 | LongQie Wei‐MinChen Zhao‐HuiWang Qing‐GuoShao XiangLi Li‐XiaYuan Xian‐LuoHu Wu‐XingZhang Yun‐HuiHuang | 2012 | Adv Mater2012，，15： | 1 |
| 7 | Computational Approaches and Challenges in Spatial Transcriptomics显示文摘The development of spatial transcriptomics(ST)technologies has transformed genetic research from a single-cell data level to a two-dimensional spatial coordinate system and facilitated the study of the composition and function of various cell subsets in different environments and organs.The large-scale data generated by these ST technologies,which contain spatial gene expression information,have elicited the need for spatially resolved approaches to meet the requirements of computational and biological data interpretation.These requirements include dealing with the explosive growth of data to determine the cell-level and gene-level expression,correcting the inner batch effect and loss of expression to improve the data quality,conducting efficient interpretation and in-depth knowledge mining both at the single-cell and tissue-wide levels,and conducting multi-omics integration analysis to provide an extensible framework toward the in-depth understanding of biological processes.However,algorithms designed specifically for ST technologies to meet these requirements are still in their infancy.Here,we review computational approaches to these problems in light of corresponding issues and challenges,and present forward-looking insights into algorithm development. | Shuangsang Fang Bichao Chen Yong Zhang Haixi Sun Longqi Liu Shiping Liu Yuxiang Li Xun Xu | 2023 | Genomics, Proteomics & Bioinformatics2023，21，1： | 0 |
| 8 | Downregulated miR-451a as a feature of the plasma cfRNA landscape reveals regulatory networks of IL-6/IL-6R-associated cytokine storms in COVID-19 patients显示文摘Rapidly spreading coronavirus disease 2019(COVID-19)is currently affecting the world.Specifically,cytokine storms are a key feature in a substantial num ber of COVID-19 patients,1 and studies from our group and others suggest that the IL-6/IL-6R cascade plays a dom inant role in symptom-correlated cytokine storms. | Penghui Yang Yingze Zhao Jie Li Chuanyu Liu Linnan Zhu Jie Zhang Yeya Yu Wen-Jing Wang Guanglin Lei Jin Yan Fang Sun Chengrong Bian Fanping Meng Zhe Xu Changqing Bai Beiwei Ye Yuanyuan Guo Liumei Shu Xiaoju Yuan Ning Zhang Yuhai Bi Yi Shi Guizhen Wu Shaogeng Zhang George F.Gao Longqi Liu William J.Liu Hai-Xi Sun | 2021 | Cellular & Molecular Immunology2021，18，4： | 0 |
| 9 | CDCP:a visualization and analyzing platform for single-cell datasets显示文摘Recently,the rapid advances of single-cell sequencing technologies,including sequencing of single-cell genomics,transcriptomes,epigenetics,and spatial transcriptomes,have empowered researchers to scrutinize cellular heterogeneity,gene expression,epigenetic modifications. | Yuejiao Li Tao Yang Tingting Lai Lijin You Fan Yang Jiaying Qiu Lina Wang Wensi Du Cong Hua Zhicheng Xu Jia Cai Zhiyong Li Yiqun Liu Ling Li Minwen Zhang Jing Chen Lei Zhang Dongsheng Chen Weiwen Wang Shiping Liu Liang Wu Wenjun Zeng Bo Wang Xiaofeng Wei Longqi Liu Fengzhen Chen | 2022 | Journal of Genetics and Genomics2022，49，7： | 0 |
| 10 | Spatial transcriptome unveils a discontinuous inflammatory pattern in proficient mismatch repair colorectal adenocarcinoma显示文摘The preexistence of immune cells in the tumor microenvironment substantiates the efficacy of immunotherapy in cancer patients.Although the complex intratumoral immune heterogeneity has been extensively studied in single cell resolution,hi-res spatial investigations are limited.In this study,we performed a spatial transcriptome analysis of 4 colorectal adenocarcinoma specimens and 2 paired distant normal specimens to identify the molecular pattern involved in a discontinuous inflammatory response in pathologically annotated cancer regions.Based on the location of spatially varied gene expression,we unmasked the spatially-varied immune ecosystem and identified the locoregional“warmed-up”immune response in predefined“cold”tumor with substantial infiltration of immune components.This“warmed-up”immune profile was found to be associated with the in-situ copy number variance and the tissue remodeling process.Further,“warmed-up”signature genes indicated improved overall survival in CRC patients obtained from TCGA database. | Rongxin Zhang Yu Feng Wenjuan Ma Yanying Guo Mei Luo Young Li Yupeng Zang Xuan Dong Shixun Lu Qiang Guo Qumiao Xu Huanyi Chen Yijian Li Longqi Liu Ao Chen Gong Chen Xun Xu | 2023 | Fundamental Research2023，3，4： | 0 |
| 11 | A Highly Selective and Sensitive Ratiometric Fluorescent Probe for Hypochlorite and Its Application显示文摘 | XUE Longqi FENG Yusha SONG Yan WANG Rui LIU Dahai DU Jianshi YANG Qingbiao LI Yaoxian | 2018 | Chemical Research in Chinese Universities2018，34，4： | 0 |
| 12 | Comprehensive landscape of resistance mechanisms for neoadjuvant therapy in esophageal squamous cell carcinoma by single-cell transcriptomics显示文摘Dear Editor,Preoperative neoadjuvant therapy combined with surgical resection is the standard treatment for locally advanced esopha-geal squamous cell carcinoma(ESCC).However,more than half of patients having a partial response to neoadjuvant therapy,which is considered as a therapy-resistant phenotype and the mechan-ism is still unclear.The heterogeneity of the ESCC with surgery alone therapy were characterized by single-cell RNA sequencing(scRNA-seq)previously,but few report was about ESCC patients with neoadjuvant therapy.1 It is emergent to illustrate the comprehensive hallmarks of neoadjuvant therapy-resistance in ESCC at single cell level. | Yushang Yang Yanguo Li Haopeng Yu Zhenyu Ding Longqi Chen Xiaoxi Zeng Shunmin He Qi Liao Yi Zhao Yong Yuan | 2023 | Signal Transduction and Targeted Therapy2023，8，9： | 0 |
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