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| 1 | Single-cell RNA sequencing in breast cancer: Understanding tumor heterogeneity and paving roads to individualized therapy显示文摘Single-cell RNA sequencing(scRNA-seq)is a novel technology that allows transcriptomic analyses of individual cells.During the past decade,scRNA-seq sensitivity,accuracy,and efficiency have improved due to innovations including more sensitive,automated,and cost-effective single-cell isolation methods with higher throughput as well as ongoing technological development of scRNA-seq protocols.Among the variety of current approaches with distinct features,researchers can choose the most suitable method to carry out their research.By profiling single cells in a complex population mix,scRNA-seq presents great advantages over traditional sequencing methods in dissecting heterogeneity in cell populations hidden in bulk analysis and exploring rare cell types associated with tumorigenesis and metastasis.scRNA-seq studies in recent years in the field of breast cancer research have clustered breast cancer cell populations with different molecular subtypes to identify distinct populations that may correlate with poor prognosis and drug resistance.The technology has also been used to explain tumor microenvironment heterogeneity by identifying distinct immune cell subsets that may be associated with immunosurveillance and are potential immunotherapy targets.Moreover,scRNA-seq has diverse applications in breast cancer research besides exploring heterogeneity,including the analysis of cell-cell communications,regulatory single-cell states,immune cell distributions,and more.scRNA-seq is also a promising tool that can facilitate individualized therapy due to its ability to define cell subsets with potential treatment targets.Although scRNA-seq studies of therapeutic selection in breast cancer are currently limited,the application of this technology in this field is prospective.Joint efforts and original ideas are needed to better implement scRNA-seq technologies in breast cancer research to pave the way for individualized treatment management.This review provides a brief introduction on the currently available scRNA-seq approaches along with their corresponding strengths and weaknesses and may act as a reference for the selection of suitable methods for research.We also discuss the current applications of scRNA-seq in breast cancer research for tumor heterogeneity analysis,individualized therapy,and the other research directions mentioned above by reviewing corresponding published studies.Finally,we discuss the limitations of current scRNA-seq technologies and technical problems that remain to be overcome. | Shuning Ding Xiaosong Chen Kunwei Shen | 2020 | Cancer Communications2020，40，8： | 12 |
| 2 | Single-cell atlas reveals a distinct immune profile fostered by T cell-B cell crosstalk in triple negative breast cancer显示文摘Background:Characterizing the unique immune microenvironment of each tumor is of great importance for better predicting prognosis and guiding cancer immunotherapy.However,the unique features of the immune microenvironment of triple negative breast cancer(TNBC)compared with other subtypes of breast cancer remain elusive.Therefore,we aimed to depict and compare the immune landscape among TNBC,human epidermal growth factor receptor 2-positive(HER2^(+))breast cancer,and luminal-like breast cancer.Methods:Single-cell RNA sequencing(scRNA-seq)was performed on CD45^(+)immune cells isolated from human normal breast tissues and primary breast tumors of various subtypes.By analyzing the scRNA-seq data,immune cell clusters were identified and their proportions as well as transcriptome features were compared among TNBC,human HER2^(+)breast cancer,and luminal-like breast cancer.Pseudotime and cell-cell communication analyses were also conducted to characterize the immune microenvironment.Results:ScRNA-seq data of 117,958 immune cells were obtained and 31 immune clusters were identified.A unique immunosuppressive microenvironment in TNBC was decoded as compared to that in HER2^(+)or luminal-like breast cancer,which was characterized by higher proportions of regulatory T cells(Tregs)and exhausted CD8+T cells and accompanied by more abundant plasma cells.Tregs and exhausted CD8+T cells in TNBC exhibited increased immunosuppression signature and dysfunctional scores.Pseudotime analyses showed that B cells tended to differentiate to plasma cells in TNBC.Cell-cell communication analyses indicated that these unique features are fostered by the diversified T cell-B cell crosstalk in TNBC.Based on the T cell-B cell crosstalk,a prognostic signaturewas established that could effectively predict the prognosis status for patients with TNBC.Additionally,it was found that TNBC had a higher proportion of cytotoxic natural killer(NK)cells,whereas HER2^(+)or luminal-like breast cancer lost this feature,suggesting thatHER2^(+)or luminal-like breast cancer,but not TNBC,may benefit from NK-based immunotherapy.Conclusions:This study identified a distinct immune feature fostered by T cell-B cell crosstalk in TNBC,which provides better prognostic information and effective therapeutic targets for breast cancer. | Shuning Ding Niu Qiao Qingchen Zhu Yiwei Tong Shengyue Wang Xiaosong Chen Qiang Tian Yichuan Xiao Kunwei Shen | 2023 | Cancer Communications2023，43，6： | 2 |
| 3 | MAGUS:machine learning and graph theory assisted universal structure searcher显示文摘Crystal structure predictions based on first-principles calculations have gained great success in materials science and solid state physics.However,the remaining challenges still limit their applications in systems with a large number of atoms,especially the complexity of conformational space and the cost of local optimizations for big systems.Here,we introduce a crystal structure prediction method,MAGUS,based on the evolutionary algorithm,which addresses the above challenges with machine learning and graph theory.Techniques used in the program are summarized in detail and benchmark tests are provided.With intensive tests,we demonstrate that on-the-fly machine-learning potentials can be used to significantly reduce the number of expensive first-principles calculations,and the crystal decomposition based on graph theory can efficiently decrease the required configurations in order to find the target structures.We also summarized the representative applications of this method on several research topics,including unexpected compounds in the interior of planets and their exotic states at high pressure and high temperature(superionic,plastic,partially diffusive state,etc.);new functional materials(superhard,high-energy-density,superconducting,photoelectric materials),etc.These successful applications demonstrated that MAGUS code can help to accelerate the discovery of interesting materials and phenomena,as well as the significant value of crystal structure predictions in general. | Junjie Wang Hao Gao Yu Han Chi Ding Shuning Pan Yong Wang Qiuhan Jia Hui-Tian Wang Dingyu Xing Jian Sun | 2023 | National Science Review2023，10，7： | 1 |
| 4 | Highly selective and efficient photocatalytic NO removal:Charge carrier kinetics and interface molecular process显示文摘The widespread nitrogen oxides(NOx,mainly in NO)in the atmosphere have threatened human health and ecological environment.The dilute NO(ppb)is difficult to efficiently remove via the traditional process due to its characteristics of low concentration,wide range,large total amount,etc.Photocatalysis can utilize solar energy to purify NO pollutants under mild conditions,but its application is limited due to the low selectivity of nitrate and poor activity of NO removal.The underlying reason is that the interface mechanism of NO oxidation is not clearly understood,which leads to the inability to accurately regulate the NO oxidation process.Herein,the recent advances in the photocatalytic oxidation of NO are summarized.Firstly,the common strategies to effectively regulate carrier dynamics such as morphology control,facet engineering,defect engineering,plasma coupling,heterojunction and single-atom catalysts are discussed.Secondly,the progress of enhancing the adsorption and activation of reactants such as NO and O_(2) during NO oxidation is described in detail,and the corresponding NO oxidation mechanisms are enumerated.Finally,the challenges and prospects of photocatalytic NO oxidation are presented in term of nanotechnology for air pollution control.This review can shed light on the interface mechanism of NO oxidation and provide illuminating information on designing novel catalysts for efficient NOx control. | Huan Shang Hongbao Jia Pengpeng Li Hao Li Wenbin Zhang Shuangjun Li Qing Wang Shuning Xiao Ding Wang Guisheng Li Dieqing Zhang | 2024 | Nano Research2024，17，3： | 0 |
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