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Advances and applications in single-cell and spatial genomics

Science China Life Sciences 2025年

作者： Jingjing Wang Fang Ye Haoxi Chai Yujia Jiang Teng Wang Xia Ran Qimin Xia Ziye Xu Yuting Fu Guodong Zhang Hanyu Wu Guoji Guo Hongshan Guo Yijun Ruan Yongcheng Wang Dong Xing Xun Xu Zemin Zhang Beijing Advanced Innovation Center for Genomics (ICG) Peking University Guangdong Provincial Key Laboratory of Genome Read and Write BGI Research Bone Marrow Transplantation Center of the First affiliated hospital & Liangzhu Laboratory Zhejiang University School of Medicine Life Sciences Institute and The second affiliated hospital Zhejiang University BGI Research Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences Peking University Academy for Advanced Interdisciplinary Studies Peking University Institute of Hematology Zhejiang University Department of Laboratory medicine of The First affiliated hospital & Liangzhu Laboratory Zhejiang University School of Medicine Center for Stem Cell and Regenerative medicine Zhejiang University School of Medicine zhejiang Provincial Key Lab for Tissue Engineering and Regenerative medicine Dr.Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine

The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems. These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues. In this review, we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics. We have reviewed the breakthroughs in single-cell multi-omics technologies, spatial genomics methods, and the computational strategies employed toward the analyses of singlecell atlas data. Furthermore, we have highlighted the advances made in constructing cellular atlases and their clinical applications,particularly in the context of disease. Finally, we have discussed the emerging trends, challenges, and opportunities in this rapidly evolving field.

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Neuroprotective potential for mitigating ischemia-reperfusion-induced damage

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Neural Regeneration Research 2025年第8期20卷 2199-2217页

作者： Zi Ye Runqing Liu Hangxing Wang Aizhen Zuo Cen Jin Nan Wang Huiqi Sun Luqian Feng Hua Yang The Clinical Medical college Guizhou Medical UniversityGuiyangGuizhou ProvinceChina Division of Infectious Diseases Department of Internal MedicinePeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina School of Medical Imaging Guizhou Medical UniversityGuiyangGuizhou ProvinceChina Division of Gastroenterology First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan ProvinceChina The second Clinical Medical college Lanzhou UniversityLanzhouGansu ProvinceChina Department of Neurosurgery Affiliated Hospital of Guizhou Medical UniversityGuiyangGuizhou ProvinceChina

Reperfusion following cerebral ischemia causes both structural and functional damage to brain tissue and could aggravate a patient's condition;this phenomenon is known as cerebral ischemia-reperfusion *** studies have elucidated the neuroprotective role of the sirtuin protein family(Sirtuins)in modulating cerebral ischemia-reperfusion ***,the potential of utilizing it as a novel intervention target to influence the prognosis of cerebral ischemia-reperfusion injury requires additional *** this review,the origin and research progress of Sirtuins are summarized,suggesting the involvement of Sirtuins in diverse mechanisms that affect cerebral ischemia-reperfusion injury,including inflammation,oxidative stress,blood-brain barrier damage,apoptosis,pyroptosis,and *** therapeutic avenues related to Sirtuins that may improve the prognosis of cerebral ischemia-reperfusion injury were also investigated by modulating Sirtuins expression and affecting representative pathways,such as nuclear factor-kappa B signaling,oxidative stress mediated by adenosine monophosphate-activated protein kinase,and the forkhead box *** review also summarizes the potential of endogenous substances,such as RNA and hormones,drugs,dietary supplements,and emerging therapies that regulate Sirtuins *** review also reveals that regulating Sirtuins mitigates cerebral ischemia-reperfusion injury when combined with other risk *** Sirtuins show promise as a potential target for the treatment of cerebral ischemiareperfusion injury,most recent studies are based on rodent models with circadian rhythms that are distinct from those of humans,potentially influencing the efficacy of Sirtuinstargeting drug ***,this review provides new insights into the role of Sirtuins in the pathology and treatment of cerebral ischemia-reperfusion injury.

关键词： apoptosis autophagy blood-brain barrier dietary supplements drug hormones inflammation neuroprotection oxidative stress prognosis pyroptosis reperfusion injury risk factors RNA therapeutics

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Single-cell omics: experimental workflow, data analyses and applications

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Science China Life Sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji university) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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Advances in genotypic antimicrobialresistance testing: a comprehensive review

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Science China Life Sciences 2025年第1期68卷 130-143页

作者： Boheng Duan Xianjun Zeng Junping Peng Huan Kui college of Nanchang university Department of Imaging The Second Affiliated Hospital of Nanchang University NHC Key Laboratory of Systems Biology of Pathogens National Institute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical College Key Laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical Sciences & Peking Union Medical College Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education) State Key Laboratory of Respiratory Health and MultimorbidityNational Institute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical College

Antimicrobial resistance(AMR) represents a substantial threat to global public health, complicating the treatment of common infections and leading to prolonged illness and escalated healthcare expenses. To effectively combat AMR, timely and accurate detection is crucial for AMR surveillance and individual-based therapy. Phenotypic antibiotic resistance testing(AST) has long been considered the gold standard in clinical applications, serving as the foundation for clinical AMR diagnosis and optimized therapy. It has significantly contributed to ensuring patients′ health and the development of novel antimicrobials. Despite advancements in automated culture-based AST technologies,inherent limitations impede the widespread use of phenotypic AST in AMR surveillance. Genotypic AST technologies offer a promising alternative option, exhibiting advantages of rapidity, high sensitivity, and specificity. With the continuous advancement and expanding applications of genotypic AST technologies, such as microfluidics, mass spectrometry, and high-resolution melting curve analysis, new vigor has been injected into the development and clinical implementation of genotypic AST technologies. In this narrative review, we discuss the principles, applications, and advancements of emerging genotypic AST methods in clinical settings. The comprehensive review aims to highlight the significant scientific potential of emerging genotypic AST technologies in clinical AMR diagnosis, providing insights to enhance existing methods and explore novel approaches.

关键词： antimicrobial resistance (AMR) genotypic antibiotic resistance testing (AST) AST technologies review

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Rational design of lipid-activatable NIR-II probes for precisely imaging atherosclerotic plaque

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Science China Chemistry 2025年

作者： Xinyu Xu Yuan Ma Hui Cao Li Xu Haoming Chen Sulai Liu Wei Sun Guosheng Song Xiaobing Zhang State Key Laboratory for Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical EngineeringHunan University Department of Hepatobiliary Surgery/Central Laboratory Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University) Department of Cardiology the First Affiliated Hospital of Nanjing Medical University Key Laboratory of Targeted Intervention of Cardiovascular Disease Collaborative Innovation Center for Cardiovascular Disease Translational MedicineNanjing Medical University Shenzhen Research Institute of Hunan university

Atherosclerosis(AS) is a prevalent condition associated with cardiovascular and cerebrovascular diseases, featuring lipid-laden plaque; however, the insufficient resolution and low sensitivity of traditional medical imaging techniques limit their application in lipid imaging. Currently, the second near-infrared(NIR-II) fluorescence imaging offers promising sensitivity and convenience. However, existing probes have limitations in terms of signal-to-background ratio, penetration depth, and tissue scattering. Herein, we use a molecular regulatory strategy to design a lipid-activatable probe Rh-965 with high specificity and NIR-II emission for improved imaging potential in deep tissues. The potential of Rh-965 for imaging plaque lipids in mice with AS is demonstrated by localizing carotid artery plaques using NIR-II imaging. The development of more stable lipid-activated NIR-II probes can significantly enhance atherosclerosis diagnosis and facilitate in vivo imaging in deeper tissues.

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A comparative investigation of an AB- and AA-stacked bilayer graphene sheet under an applied electric field:A density functional theory study

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Chinese Physics B 2012年第6期21卷 451-455页

作者：汪涛郭清刘艳盛况 college of Electrical Engineering Zhejiang University second affiliated hospital Zhejiang University College of Medicine zhejiang university

An AB-and AA-stacked bilayer graphene sheet （BLG） under an electric field is investigated by ab initio calculation. The interlayer distance between the two layers, band structures, and atomic charges of the system are investigated in the presence of different electric fields normal to the BLG. The AB-stacked BLG is able to tune the bandgap into 0.234 eV with the increase of the external electronic field to 1 V/nm, however, the AA-stacked BLG is not sensitive to the external electric field. In both the cases, the spacing between the BLG slightly change in terms of the electric field. The charges in the AB-stacked BLG are increased with the increase of the electric field, which is considered to be the reason that causes the bandgap opening in the AB-stacked BLG.

关键词： graphene bandgap density functional theory study

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Gastric foregut cystic developmental malformation: Case series and literature review

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World Journal of Gastroenterology 2015年第2期21卷 432-438页

作者： Yan-Hua Geng Chang-Xing Wang Jiang-Tao Li Qing-Yu Chen Xiu-Zhen Li Hao Pan Department of Pathology Second Affiliated Hospital of Zhejiang University College of Medicine Department of Osteology Second Affiliated Hospital of Zhejiang University of Traditional Chinese Medicine Department of Surgery Second Affiliated Hospital of Zhejiang University College of Medicine Department of Gastroenterology Second Affiliated Hospital of Zhejiang University College of Medicine

Foregut cystic developmental malformation(FCDM) is a very rare lesion of the alimentary tract, especially in the stomach. We discuss the concepts of gastric duplication cyst, bronchogenic cysts, and FCDM. Nomenclature has been inconsistent and confusing, but, by some definitions, gastric duplication cysts involve gastric mucosa and submucosal glands, bronchogenic cysts involve respiratory mucosa with underlying cartilage and glands, and FCDM lacks gastric mucosa or underlying glands or cartilage but has pseudostratified ciliated columnar epithelium(PCCE). We searched our departmental case files from the past 15 years and identified 12 cases of FCDM in the alimentary tract. We summarize the features of these 12 cases including a report in detail on a 52-year-old man with a submucosal cyst lined with simple PCCE and irregular and stratified circular muscle layers that merged with gastric smooth muscle bundles near the lesser curvature of the gastric cardia. A literature review of cases with this histology yielded 25 cases. We propose the term gastric-FCDM for such cases. Our own series of 12 cases confirms that preoperative recognition of the entity is infrequent and problematic. The rarity of this developmental disorder, as well as a lack of understanding of its embryologic origins, may contribute to missing the diagnosis. Not appreciating the diagnosis preoperatively can lead to an inappropriate surgical approach. In contrast, presurgical recognition of the entity will contribute to a good outcome and reduced risk of complications.

关键词： Endoscopic ultrasound-guided fine-needle aspiratio

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Contrast-enhanced ultrasonography assessment of gastric cancer response to neoadjuvant chemotherapy

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World Journal of Gastroenterology 2012年第47期18卷 7026-7032页

作者： Jian Ang Liang Hu Pin-Tong Huang Jin-Xiu Wu Ling-Na Huang Chun-Hui Cao Yi-Xiong Zheng Li Chen Department of Gastroenterology the Second Affiliated HospitalZhejiang University School of Medicine Department of Surgery the Second Affiliated HospitalZhejiang University School of Medicine Binjiang hospital the Second Affiliated Hospital(Binjiang Branch)Zhejiang University School of Medicine Department of Ultrasonography the Second Affiliated HospitalZhejiang University School of Medicine Department of Radiology the Second Affiliated HospitalZhejiang University School of Medicine

AIM:To quantitatively assess the ability of double contrast-enhanced ultrasound(DCUS) to detect tumor early response to pre-operative ***:Forty-three patients with gastric cancer treated with neoadjuvant chemotherapy followed by curative resection between September 2011 and February 2012 were ***-operative chemotherapy regimens of fluorouracil + oxaliplatin or S-1 + oxaliplatin were administered in 2-4 cycles over 6-12 wk *** patients underwent contrast-enhanced computed tomography(CT) scan and DCUS before and after two courses of pre-operative *** therapeutic response was assessed by CT using the response evaluation criteria in solid tumors(RECIST 1.1) *** area was assessed by DCUS as enhanced appearance of gastric carcinoma due to tumor vascularity during the contrast phase as compared to the normal gastric *** analysis was carried out according to the Mandard tumor regression grade criteria and used as the reference *** operating characteristic(ROC) analysis was used to evaluate the efficacy of DCUS parameters in differentiating histopathological responders from ***:The study population consisted of 32 men and 11 women,with mean age of 59.7 ± 11.4 *** age,sex,histologic type,tumor site,T stage,nor N stage was associated with pathological *** responders had significantly smaller mean tumor size than the non-responders(15.7 ± 7.4 cm vs 33.3 ± 14.1 cm,P < 0.01).According to Mandard's criteria,27 patients were classified as responders,with 11(40.7%) showing decreased tumor size by *** contrast,only three(18.8%) of the 16 non-responders showed decreased tumor size by DCUS(P < 0.01).The area under the ROC curve was 0.64,with a 95%CI of *** effects of several cut-off points on diagnostic parameters were calculated in the ROC curve *** maximizing Youden's index(sensitivity + specificity-1),the best cut-off point for distingu

关键词： Gastric cancer Chemotherapy Ultrasonic imaging Predictive value of tests Disease management

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CD97 promotes gastric cancer cell proliferation and invasion through exosome-mediated MAPK signaling pathway

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World Journal of Gastroenterology 2015年第20期21卷 6215-6228页

作者： Chao Li Da-Ren Liu Guo-Gang Li Hou-Hong Wang Xiao-Wen Li Wei Zhang Yu-Lian Wu Li Chen Department of Surgery Second Affiliated HospitalCollege of MedicineZhejiang University Department of Orthopedics Second Affiliated HospitalCollege of MedicineZhejiang University

AIM: To investigate the mechanism underlying the promoting role of CD97 in gastric cancer cell proliferation and invasion. METHODS: Two types of exosomes released by gastric cancer cells with high(SGC/wt) or low(SGC/kd) CD97 expression were isolated by ultracentrifugation and identified by electron microscopy and western blot analysis. The influences of the two exosomes on gastric cancer cell proliferation and invasion were investigated by proliferation and Matrigel invasion assays. Exosomal mi RNAs were subsequently isolated from the two samples and their mi RNA profiles were compared via microarray assay analysis. Reverse transcriptionquantitative real-time polymerase chain reaction was used to validate the microarray assay. Target genes of the differently expressed micro RNAs were predicted based on five independent algorithms and were then subjected to gene oncology enrichment and Kyoto encyclopedia of genes and genomes(KEGG) pathway analysis. After identifying the pathway that was the most likely altered, tumor cells were treated with the two exosomes at different concentrations, and the pathway activation was identified through western blot ***: Exosomes isolated from SGC/wt cells significantly promoted tumor cell proliferation in a dose-dependent manner in vitro. SGC/wt exosomesalso significantly elevated the invasiveness of both SGC/wt(129.67 ± 8.327 vs 76.00 ± 5.292, P 500 and a false discovery rate < 0.05. The following KEGG analysis defined the MAPK signaling pathway as the most likely candidate pathway that regulated tumor cell proliferation and invasion. Through western blot analysis, significant up-regulations of phosphorylated MAPKs, including extracellular signal-regulated kinase, Jun NH2-terminal ki

关键词： CD97 Exosome Proliferation Invasion miRNA Gastric cancer

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Oral malignant acanthosis nigricans associated with endometrial adenocarcinoma

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International Journal of Oral Science 2014年第4期6卷 247-249页

作者： Han-Wen Chu Jing-Min Li Guan-Fu Chen Jing-Yuan Ma Department of Oral and Maxillofacial Surgery Second Affiliated Hospital College of Medicine Zhejiang University Hangzhou Stomatological hospital Department of Oral medicine Second Affiliated Hospital College of Medicine Zhejiang University

We report a 59-year-old patient with malignant acanthosis nigricans associated with metastasis of endometrial carcinoma. The patient presented papillomatosis lesions that appeared to be benign on multiple skins of body folds, particularly on lips. The lesions in lips and axilla had histological characteristic appearances of acanthosis nigricans, while the masses in abdomen and pelvis were metastasis endometrial adenocarcinoma. The article highlights the importance of biopsy and histopathological diagnosis in presumed benign lesions and the role of doctors in screening for body internal tumors.

关键词： endometrial adenocarcinoma oral malignant acanthosis nigricans

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