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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

Single-cell and spatial omics:exploring hypothalamic heterogeneity

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Neural Regeneration Research 2025年第6期20卷 1525-1540页

作者： Muhammad Junaid Eun Jeong Lee Su Bin Lim Department of Biochemistry&Molecular Biology Ajou University School of MedicineSuwonSouth Korea Department of biomedical sciences Graduate School of Ajou UniversitySuwonSouth Korea Department of Brain Science Ajou University School of MedicineSuwonSouth Korea

Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.

关键词： cellular diversity hypothalamus multi-omics single-cell transcriptomics spatial transcriptomics

Insights from an academic endeavor into central nervous system drug discovery

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Neural Regeneration Research 2025年第6期20卷 1717-1718页

作者： Lieve van Veggel An M.Voets Tim Vanmierlo Rudy Schreiber BIOMED biomedical Research Institute Faculty of Medicine and Life SciencesHasselt UniversityHasseltBelgium Department of Psychiatry and Neuropsychology Division of Translational NeuroscienceEuropean Graduate School of NeuroscienceSchool for Mental Health and NeuroscienceMaastricht UniversityMaastrichtThe Netherlands Section of Psychopharmacology Neuropsychology and PsychopharmacologyFaculty of Psychology and NeuroscienceMaastricht UniversityMaastrichtThe Netherlands University MS Center(UMSC) Hasselt-PeltBelgium

Historically,"big pharma"did most central nervous system drug discovery R&D ***,in modern times their"management reductionism"resulted in disappointing pipelines and pharma resided to(late)development,regulatory approval,and marketing(Thong,2015).This had significant consequences for financing and executing research,resulting in a larger role for funding by governments and patient-organizations and a shift of research to academia(Mazzucato,2013).

关键词： academic approval consequences

PGLYRP1 protein as a novel mediator of cellular dialogue in neuroinflammation

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Neural Regeneration Research 2025年第7期20卷 1993-1994页

作者： Anup Bhusal Won-Ha Lee Kyoungho Suk Department of Pharmacology School of MedicineKyungpook National UniversityDaeguRepublic of Korea BK21 Plus KNU biomedical Convergence Program Department of Biomedical ScienceSchool of MedicineKyungpook National UniversityDaeguRepublic of Korea school of Life sciences BK21 plus KNU Creative BioResearch GroupKyungpook National UniversityDaeguRepublic of Korea Brain Science and Engineering Institute Kyungpook National UniversityDaeguRepublic of Korea

Neuroinflammation has been identified as a crucial element in several neurological disorders. Glial cells play a critical role in directing neuroinflammation, both in deleterious and beneficial ways.

关键词： inflammation considerably

Anti-nitric oxide production, anti-proliferation and antioxidant effects of the aqueous extract from Tithonia diversifolia

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Asian Pacific Journal of Tropical Biomedicine 2016年第11期6卷 950-956页

作者： Poonsit Hiransai Jitbanjong Tangpong Chuthamat Kumbuar Namon Hoonheang Onrunee Rodpech Padchara Sangsuk Urairat Kajklangdon Waraphorn Inkaow Molecular Medicine and Cancer Biology Research Unit School of Allied Health Sciences and Public Health Walailak University Department of Medical Technology School of Allied Health Sciences and Public Health Walailak University biomedical sciences Research Unit School of Allied Health Sciences and Public Health Walailak University

Objective: To determine the cytotoxicity, reduction in nitric oxide production and antioxidative activity of the aqueous leaf extract from Tithonia diversifolia(T. diversifolia) in an in vitro ***: Leaves of T. diversifolia were collected from natural habitats and extracted with distilled water using the decoction method. The cytotoxic effect of the extract in terms of cell viability was determined using RAW264.7 cells and human peripheral blood mononuclear cells(PBMCs) via the mitochondrial respiration method using the MTT reagent. The effect of the extract on lipopolysaccharide(LPS)-induced nitric oxide production in RAW264.7 cells was measured using the Griess reagent. The chemical antioxidant was evaluated by ABTS- and DPPH-radical scavenging ***: The half-maximal cytotoxic concentration values were 145.87 mg/m L and73.67 mg/m L for human PBMCs and RAW264.7 cells, respectively. In the presence of phytohemagglutinin-M, the IC_(50) on PBMCs proliferation was 4.42 mg/m L. The noncytotoxic range of the extracts inhibited LPS-induced nitrite production in RAW264.7 cells with an IC_(50) value of 11.63 mg/m L. To determine the anti-oxidative properties, the N-acetyl cysteine equivalent antioxidant capacity of the extract was(32.62 ± 1.87) and(20.99 ± 2.79)mg N-acetyl cysteine/g extract, respectively determined by the ABTS-radical and DPPHradical assay. However, the extract did not confer death protection in a hydrogen peroxideinduced RAW264.7 co-culturing ***: Our study demonstrated the immunomodulation caused by the aqueous leaf extract of T. diversifolia, resulting from the inhibition of phytohemagglutinin-Minduced PBMCs proliferation and LPS-induced nitric oxide production in RAW264.7macrophages. Although the anti-oxidative activity was presented in the chemical-based anti-oxidant assay, the extract cannot protect cell death from stress conditions.

关键词： Tithonia diversifolia Anti-nitric oxide production Anti-proliferation Antioxidant

High mobility group box 1 in the central nervous system:regeneration hidden beneath inflammation

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Neural Regeneration Research 2025年第1期20卷 107-115页

作者： Hanki Kim Bum Jun Kim Seungyon Koh Hyo Jin Cho Xuelian Jin Byung Gon Kim Jun Young Choi Department of Brain Science Ajou University School of MedicineSuwonSouth Korea Department of biomedical sciences Ajou University Graduate School of MedicineSuwonSouth Korea Department of Neurology Ajou University School of MedicineSuwonSouth Korea Department of Geriatrics The Affiliated Suqian First People’s Hospital of Nanjing Medical UniversitySuqianJiangsu ProvinceChina

High-mobility group box 1 was first discovered in the calf thymus as a DNA-binding nuclear protein and has been widely studied in diverse fields,including neurology and ***-mobility group box 1 in the extracellular space functions as a pro-inflammatory damage-associated molecular pattern,which has been proven to play an important role in a wide variety of central nervous system disorders such as ischemic stroke,Alzheimer’s disease,frontotemporal dementia,Parkinson’s disease,multiple sclerosis,epilepsy,and traumatic brain *** drugs that inhibit high-mobility group box 1 as a damage-associated molecular pattern,such as glycyrrhizin,ethyl pyruvate,and neutralizing anti-high-mobility group box 1 antibodies,are commonly used to target high-mobility group box 1 activity in central nervous system *** it is commonly known for its detrimental inflammatory effect,high-mobility group box 1 has also been shown to have beneficial pro-regenerative roles in central nervous system *** this narrative review,we provide a brief summary of the history of high-mobility group box 1 research and its characterization as a damage-associated molecular pattern,its downstream receptors,and intracellular signaling pathways,how high-mobility group box 1 exerts the repair-favoring roles in general and in the central nervous system,and clues on how to differentiate the pro-regenerative from the pro-inflammatory *** targeting high-mobility group box 1 in the central nervous system may benefit from differentiating between the two functions rather than overall suppression of high-mobility group box 1.

关键词： central nervous system damage-associated molecular pattern ethyl pyruvate glycyrhizzin high mobility group box 1 inflammation neural stem cells neurodevelopment oligodendrocyte progenitor cells redox status regeneration

A functional tacrolimus-releasing nerve wrap for enhancing nerve regeneration following surgical nerve repair

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Neural Regeneration Research 2025年第1期20卷 291-304页

作者： Simeon C.Daeschler Katelyn J.W.So Konstantin Feinberg Marina Manoraj Jenny Cheung Jennifer Zhang Kaveh Mirmoeini JPaul Santerre Tessa Gordon Gregory HBorschel SickKids Research Institute Neuroscience and Mental Health ProgramTorontoONCanada Institute of Biomaterials and biomedical Engineering University of TorontoTorontoONCanada Indiana University school of Medicine IndianapolisINUSA Division of Plastic and Reconstructive Surgery the Hospital for Sick ChildrenTorontoONCanada Translational Biology and Engineering Program Ted Rogers Centre for Heart ResearchInstitute of Biomedical EngineeringFaculty of DentistryUniversity of TorontoTorontoONCanada

Axonal regeneration following surgical nerve repair is slow and often incomplete,resulting in poor functional recovery which sometimes contributes to lifelong ***,there are no FDA-approved therapies available to promote nerve *** accelerates axonal regeneration,but systemic side effects presently outweigh its potential benefits for peripheral nerve *** authors describe herein a biodegradable polyurethane-based drug delivery system for the sustained local release of tacrolimus at the nerve repair site,with suitable properties for scalable production and clinical application,aiming to promote nerve regeneration and functional recovery with minimal systemic drug *** is encapsulated into co-axially electrospun polycarbonate-urethane nanofibers to generate an implantable nerve wrap that releases therapeutic doses of bioactive tacrolimus over 31 *** and drug loading are adjustable for applications in small and large caliber nerves,and the wrap degrades within 120 days into biocompatible *** released from the nerve wrap promotes axon elongation in vitro and accelerates nerve regeneration and functional recovery in preclinical nerve repair models while off-target systemic drug exposure is reduced by 80%compared with systemic *** its surgical suitability and preclinical efficacy and safety,this system may provide a readily translatable approach to support axonal regeneration and recovery in patients undergoing nerve surgery.

关键词： biodegradable local drug delivery nerve injury nerve regeneration nerve wrap tacrolimus

Olfactory receptors in neural regeneration in the central nervous system

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Neural Regeneration Research 2025年第9期20卷 2480-2494页

作者： Rafael Franco Claudia Garrigós Toni Capó Joan Serrano-Marín Rafael Rivas-Santisteban Jaume Lillo Molecular Neurobiology Laboratory Department of Biochemistry and Molecular BiomedicineFacultat de BiologiaUniversitat de BarcelonaBarcelonaSpain CiberNed Network Center for biomedical Research in Neurodegenerative Diseases Spanish National Health Institute Carlos ⅢMadridSpain school of Chemistry Universitat de BarcelonaBarcelonaSpain Department of Biochemistry and Physiology School of Pharmacy and Food SciencesUniversitat de BarcelonaBarcelonaSpain Laboratory of Computational Medicine Biostatistics UnitFaculty of MedicineAutonomous University of BarcelonaCampus BellaterraBarcelonaSpain

Olfactory receptors are crucial for detecting odors and play a vital role in our sense of smell,influencing behaviors from food choices to emotional *** receptors also contribute to our perception of flavor and have potential applications in medical diagnostics and environmental *** ability of the olfactory system to regenerate its sensory neurons provides a unique model to study neural regeneration,a phenomenon largely absent in the central nervous *** gained from how olfactory neurons continuously replace themselves and reestablish functional connections can provide strategies to promote similar regenerative processes in the central nervous system,where damage often results in permanent *** the molecular and cellular mechanisms underpinning olfactory neuron regeneration could pave the way for developing therapeutic approaches to treat spinal co rd injuries and neurodegenerative diseases like Alzheimer's *** ctory receptors are found in almost any cell of eve ry orga n/tissue of the mammalian *** ectopic expression provides insights into the chemical structures that can activate olfactory *** addition to odors,olfactory receptors in ectopic expression may respond to endogenous compounds and molecules produced by mucosal colonizing *** analysis of the function of olfactory receptors in ectopic expression provides valuable information on the signaling pathway engaged upon receptor activation and the receptor's role in proliferation and cell differentiation *** review explo res the ectopic expression of olfa ctory receptors and the role they may play in neural regeneration within the central nervous system,with particular attention to compounds that can activate these receptors to initiate regenerative *** suggests that olfactory receptors could serve as potential therapeutic targets for enhancing neural repair and recovery following central nervous syste

关键词： adenosine receptors adrenergic receptors ectopic expression G proteincoupled receptors glia neurons

Antioxidant activity and phenol and flavonoid contents of eight medicinal plants from Western Nepal

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Journal of Traditional Chinese Medicine 2014年第5期34卷 584-590页

作者： Lalita Subedi Sunita Timalsena Pabitra Duwadi Ritu Thapa Anita Paudel Kalpana Parajuli Department of Pharmaceutical sciences School of Health and Allied SciencesPokhara University

OBJECTIVE: The purpose of this study was to evaluate the antioxidant activity, phenolic and flavonoids contents of selected medicinal plants form the Western region of ***: The antioxidant activity of selected medicinal plants were determined by using 2, 2-diphenyl-1-picrylhydrazyl radical scavenging activity; total ferric ion reducing ability through spectroscopic analysis. The content of total phenols was determined using Folin-Ciocalteu reagent, whereas Aluminum chloride colorimetric method was used for flavonoid ***: Extracts of Syzygium Operculatus(87%),Astilbe Rivularis(83%) and Mallotus Philippnensis(88%) showed significant free radical scavenging activity with effective concentration(EC50) close to that of ascorbic acid. Syzygium Operculatus(96%),Astilbe Rivularis(97%) and Mallotus Philippnensis(97%) had potent reducing power in concentration dependent fashion. Those plant extract with higher free radical scavenging and ferric reducing effect also showed the greater content of both phenols and flavonoids, suggesting the correlation between polyphenolic content and antioxidant activity. Those plant extracts which showed better antioxidant activity assays, also demonstrated higher total phenol and flavonoid contents. These three plants showed the presence of higher amount of phenols and ***: This study may provide the scientific basis for the traditional use of those plants and may provide valuable idea for further research.

关键词： Plants, medicinal Antioxidants 2, 2-di-phenyl-l-picrylhydrazyl Phenol Flavonoids