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Future of non-invasive graft evaluation:A systematic review of proteomics in kidney transplantation

World Journal of Transplantation 2025年第1期15卷 135-149页

作者： Eleni Avramidou Konstantina Psatha Kallisti St John Georgios Tsoulfas Michalis Aivaliotis Department of Transplantation Surgery Center for Research and Innovation in Solid Organ TransplantationAristotle University of ThessalonikiSchool of MedicineThessaloniki 54642Greece Laboratory of Medical biology-Genetics School of MedicineAristotle University of ThessalonikiThessaloniki 54124Greece Functional Proteomics and systems biology(FunPATh) Center for Interdisciplinary Research and Innovation(CIRI-AUTH)Thessaloniki GR-57001Greece Laboratory of Biological Chemistry School of MedicineAristotle University of ThessalonikiThessaloniki 54124Greece

BACKGROUND Despite the developments in the field of kidney transplantation,the already existing diagnostic techniques for patient monitoring are considered *** biomarkers that can be derived from modern approaches of proteomic analysis of liquid biopsies(serum,urine)represent a promising innovation in the monitoring of kidney transplant *** To investigate the diagnostic utility of protein biomarkers derived from proteomics approaches in renal allograft *** A systematic review was conducted in accordance with PRISMA guidelines,based on research results from the PubMed and Scopus *** primary focus was on evaluating the role of biomarkers in the non-invasive diagnosis of transplant-related *** criteria included protein biomarkers and urine and blood samples,while exclusion criteria were language other than English and the use of low resolution and sensitivity *** selected research articles,were categorized based on the biological sample,condition and methodology and the significantly and reproducibly differentiated proteins were manually selected and *** and network analysis of the selected proteins was *** In 17 included studies,58 proteins were studied,with the cytokine CXCL10 being the most *** pathways related to immune response and fibrosis have shown to be *** of biomarkers for the assessment of renal damage as well as the prediction of short-term and long-term function of the graft were ***,all studies have shown satisfactory diagnostic accuracy of proteins alone or in combination with conventional methods,as far as renal graft assessment is *** Our review suggests that protein biomarkers,evaluated in specific biological fluids,can make a significant contribution to the timely,valid and non-invasive assessment of kidney graft.

关键词： Proteomics Kidney transplantation Graft evaluation Non-invasive diagnosis Kidney graft function

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Determination and evaluation of serum monosaccharides in patients with early-stage lung adenocarcinoma

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中华医学杂志(英文版) 2025年第03期

作者： Su Wenhao Hao Cui Yang Yifei Zeng Pengjiao Dou Huaiqian Zhang Meng He Yanli Zhang Yiran Shan Ming Du Wenxing Jiao Wenjie Zhang Lijuan Department of Thoracic Surgery Affiliated Hospital of Qingdao University Qingdao Shandong China systems biology & medicine center for complex diseases Center for Clinical Research Affiliated Hospital of Qingdao University Qingdao Shandong China

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Fibrotic liver extracellular matrix induces cancerous phenotype in biomimetic micro-tissues of hepatocellular carcinoma model

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Hepatobiliary & Pancreatic diseases International 2025年第1期24卷 92-103页

作者： Kosar Nouri Abbas Piryaei Homeyra Seydi Ibrahim Zarkesh Ibrahim Ghoytasi Bahare Shokouhian Mustapha Najimi Massoud Vosough Department of Developmental biology University of Science and CultureACECR 14155-4364 TehranIran Department of Regenerative medicine Cell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECR 14155-4364 TehranIran Department of Stem Cells and Developmental biology Cell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECR 14155-4364 TehranIran Department of biology and Anatomical Sciences School of MedicineShahid Beheshti University of Medical SciencesTehranIran Department of Tissue Engineering and Applied Cell Sciences School of Advanced Technologies in MedicineShahid Beheshti University of Medical SciencesTehranIran Department of Cell Engineering Cell Science Research CenterRoyan Institute for Stem Cell Biology and TechnologyACECR 14155-4364 TehranIran Department of Medical Biotechnology School of Advanced Technologies in MedicineTehran University of Medical SciencesTehranIran Laboratory of Pediatric Hepatology and Cell Therapy Institute of Experimental and Clinical Research(IREC)UCLouvainBrusselsBelgium Experimental Cancer medicine Institution for Laboratory MedicineKarolinska InstituteStockholmSweden

Background: Despite considerable advancements in identifying factors contributing to the development of hepatocellular carcinoma(HCC), the pathogenesis of HCC remains unclear. In many cases, HCC is a consequence of prolonged liver fibrosis, resulting in the formation of an intricate premalignant microenvironment. The accumulation of extracellular matrix(ECM) is a hallmark of premalignant microenvironment. Given the critical role of different matrix components in regulating cell phenotype and function, this study aimed to elucidate the interplay between the fibrotic matrix and malignant features in HCC. Methods: Liver tissues from both control(normal) and carbon tetrachloride(CCl_(4))-induced fibrotic rats were decellularized using sodium dodecyl sulfate(SDS) and Triton X-100. The resulting hydrogel from decellularized ECM was processed into micro-particles via the water-in-oil emulsion method. Microparticles were subsequently incorporated into three-dimensional liver biomimetic micro-tissues(MTs) comprising Huh-7 cells, human umbilical vein endothelial cells(HUVECs), and LX-2 cells. The MTs were evaluated using the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium(MTS) assay at day 11, immunofluorescence staining, immunoblotting, and spheroid migration assay at day 14 after co-culture. Results: Fibrotic matrix from CCl4-treated rat livers significantly enhanced the growth rate of the MTs and their expression of CCND1 as compared to the normal one. Fibrotic matrix, also induced the expression of epithelial-to-mesenchymal transition(EMT)-associated genes such as TWIST1, ACTA2, MMP9, CDH2, and VIMENTIN in the MTs as compared to the normal matrix. Conversely, the expression of CDH1 and hepatic maturation genes HNF4A, ALB, CYP3A4 was decreased in the MTs when the fibrotic matrix was used. Furthermore, the fibrotic matrix increased the migration of the MTs and their secretion of alpha-fetoprotein. Conclusions: Our findings suggest a

关键词： Liver fibrosis Decellularized extracellular matrix Spheroid Epithelial-to-mesenchymal transition Cell differentiation Hepatocellular carcinoma

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Magnaporthe oryzae infection triggers rice resistance to brown planthopper through the influence of jasmonic acid on the flavonoid biosynthesis pathway

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Insect Science 2025年第1期32卷 243-259页

作者： Su Chen Zhihuan Tao Yanjie Shen Rui Yang Siyuan Yan Zixu Chen Bo Sun Xiaofang Yang Precision medicine Laboratory for Chronic Non-communicable diseases of Shandong Province Institute of Precision MedicineJining Medical UniversityJiningShandong ProvinceChina Key Laboratory of Insect Developmental and Evolutionary biology CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina College of Medical Engineering&The Key Laboratory for Medical Functional Nanomaterials Jining Medical UniversityJiningShandong ProvinceChina Institute of Bioengineering College of Chemical and Biological EngineeringZhejiang UniversityHangzhouChina

In agroecosystems,plants are constantly exposed to attack from diverse herbivorous insects and microbes,and infestation with one species may change the plant defense response to other *** our investigation of the relationships among rice plants,the brown planthopper Nilaparvata lugens(Stål)and the rice blast fungus Magnaporthe oryzae,we observed a significant increase in the resistance of rice treated with rice blast to ***,as evidenced by improved plant survival rates in a small population resistance *** transcriptome data analysis revealed that the rice blast fungus can induce the expression of genes in the jasmonic acid(JA)and flavonoid *** to the flavonoid pathway,the JA pathway also contains 2 types of genes that exhibit similar and opposite trends in response to *** and rice *** these genes,the osjaz1 mutant and the osmyc2 mutant were phenotypically confirmed to positively and negatively regulate rice resistance to *** and rice blast,*** mass spectrometry and quantification experiments showed that the exogenous application of methyl jasmonate(MeJA)can induce the accumulation of eriodictyol,naringenin and quercetin,as well as the expression of OsF3H,Os4CL5 and OsCHI in the flavonoid *** suggests a close connection between the JA pathway and the flavonoid ***,OsF3'H,which negatively regulates rice resistance to *** and rice blast,did not show increased *** and molecular experiments confirmed that OsMYC2 can bind to and inhibit the expression of OsF3'H,thus revealing the mechanism of rice resistance to *** after treatment with rice *** findings will deepen our understanding of the interactions among rice,*** and rice blast.

关键词： flavonoid jasmonic acid Nilaparvata lugens rice rice blast

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Longitudinal landscape of immune reconstitution after acute SARS-CoV-2 infection at single-cell resolution

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Science Bulletin 2025年第3期70卷 323-327页

作者： Lili Ren Yiwei Liu Yeming Wang Chao Wu Li Guo Lan Chen Xinming Wang Yan Xiao Lixue Huang Jingchuan Zhong Jiacheng Yao Lu Liu Hui Li Ying Wang Yongchao Ma Yichunzi Zhang Lin Di Tao Dong Julian Knight Jianbin Wang Yanyi Huang Bin Cao Xianwen Ren Jianwei Wang National Health Commission Key Laboratory of systems biology of Pathogens and Christophe Mérieux Laboratory National Institute of Pathogen BiologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 102629China Key Laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China State Key Laboratory of Respiratory Health and Multimorbidity Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100029China Department of Pulmonary and Critical Care medicine Institute of Respiratory Medicine of Chinese Academy of Medical ScienceNational Center for Respiratory MedicineCenter of Respiratory MedicineNational Clinical Research Center for Respiratory DiseasesChina-Japan Friendship HospitalBeijing 100029China College of Chemistry and Molecular Engineering Peking UniversityBeijing 100871China Biomedical Pioneering Innovation center(BIOPIC) Beijing Advanced Innovation Center for Genomics(ICG)College of Chemistryand Peking-Tsinghua Center for Life SciencesPeking UniversityBeijing 100871China MRC Human Immunology Unit MRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineThe University of OxfordOxford OX39DSUK Chinese Academy of Medical Science(CAMS)Oxford Institute(COI) University of OxfordOxford OX39DSUK Wellcome Centre for Human Genetics University of OxfordOxford OX39DSUK School of Life Sciences Tsinghua-Peking Center for Life SciencesTsinghua UniversityBeijing 100084China Beijing Advanced Innovation center for Structural biology(ICSB) Tsinghua UniversityBeijing 100084China Chinese Institute for Brain Research(CIBR) Beijing 102206China Institute for Cell Analysis Shenzhen Bay LaboratoryShenzhen 518107China Tsinghua University-Peking University Joint center for Life Sciences Beijing 100084China Biomedical Pioneering Innovation center(BIOPIC) Peking UniversityBeijing 100871China Changping Laboratory Beijing 102206China

The long-term consequences of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection,known as the post-acute sequelae of COVID-19(PASC),have been a growing concern.A significant proportion of COVID-19 patients experience persistent health issues even six to twelve months after recovering from acute infection[1],[2],[3],[4].Therefore,understanding the immune reconstitution process and identifying the molecular and cellular mechanisms underlying PASC is crucial.

关键词： landscape consequences acute

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Small extrachromosomal circular DNA in amyotrophic lateral sclerosis matter

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Neural Regeneration Research 2025年第5期20卷 1411-1413页

作者： Marcos J.Arauzo-Bravo Daniela Gerovska Matthias Schwab Alexandra Kretz Computational biology and systems Biomedicine Biodonostia Health Research InstituteSan SebastianSpain Basque Foundation for Science IKERBASQUEBilbaoSpainMax Planck Institute for Molecular BiomedicineComputational Biology and Bioinformatics GroupMünsterNorth Rhine-WestphaliaGermany Department of Cell biology and Histology Faculty of Medicine and NursingUniversity of Basque Country(UPV/EHU)LeioaSpain Department of Neurology Jena University HospitalJenaThuringiaGermany

Comprehensive studies identify motor neuron spectrum disorders including amyotrophic lateral sclerosis(ALS)as globally rising fatal disorders with the highest prevalence in aging populations,influenced by ethnicity and ancestry(GBD 2016 Motor Neuron Disease Colla borators,2018).While~10% of diagnoses involve a family history(fALS),most cases are considered sporadic(sALS).However,population-based studies suggest that even cases without a common index mutation impart heritability(Ryan et al.,2019),indicating a crucial role of rare and as yet unknown genetic denominators.

关键词： amyotrophic sclerosis

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Compound heterozygous mutation of AFG3L2 causes autosomal recessive spinocerebellar ataxia through mitochondrial impairment and MICU1 mediated Ca2+overload

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Science China(Life Sciences) 2025年第2期68卷 484-501页

作者： Hongyu Li Qingwen Ma Yan Xue Linlin Cai Liwen Bao Lei Hong Yitao Zeng Shu-Zhen Huang Richard H.Finnell Fanyi Zeng Shanghai Institute of Medical Genetics Shanghai Children’s HospitalShanghai Jiao Tong University School of MedicineShanghai 200040China Department of Histo-Embryology Genetics and Developmental BiologyShanghai Jiao Tong University School of MedicineShanghai 200025China NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular biology Shanghai Key Laboratory of Embryo and Reproduction EngineeringShanghai 200040China center for Precision Environmental Health Baylor College of MedicineHouston 77030USA School of Pharmacy Macao University of Science and TechnologyMacao 999078China

Autosomal recessive spinocerebellar ataxias(SCARs)are one of the most common neurodegenerative diseases characterized by progressive *** SCARs are known to be caused by mutations in multiple genes,there are still many cases that go undiagnosed or are *** this study,we presented a SCAR patient,and identified a probable novel pathogenic mutation(c.1A>G,p.M1V)in the AFG3L2 start *** proband's genotype included heterozygous mutations of the compound AFG3L2(p.[M1V];[R632X](c.[1A>G];[1894.C>T])),which were inherited from the father(c.1A>G,p.M1V)and mother(c.1894C>T,p.R632X).Functional studies performed on hi PSCs(human induced pluripotent stem cells)generated from the patients and HEK293T cells showed that the mutations impair mitochondrial function and the unbalanced expression of AFG3L2 mRNA and protein ***,this novel mutation resulted in the degradation of the protein and the reduction of the stability of the AFG3L2 protein,and MCU(mitochondrial calcium uniporter)complex mediated Ca2+overload.

关键词： AFG3L2 gene autosomal recessive spinocerebellar ataxia mitochondrial impairment Ca2+overload

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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)Wuhu 241000China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration(Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Frontier Science center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical center for Stem Cell Therapy and Institute for Regenerative medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Shanghai Research Institute for Intelligent Autonomous systems Shanghai 201210China center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of MedicineShanghai 200025China National Key Laboratory of Chinese medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China center for Bioinformatics and Computational biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China Peking-Tsinghua center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological diseases Women’s HospitalZhejiang University School of MedicineHangzhou 310006China Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal U

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular *** 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 *** the inception of the first single-cell RNA technology,technologies related to single-cell sequencing have experienced rapid advancements in recent *** 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 scRNA-seq and CRISPR ***-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases,including ***,we comprehensively summarize recent advances in single-cell omics technologies,with a specific focus on the methodology *** 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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Human cardiac organoid model reveals antibacterial triclocarban promotes myocardial hypertrophy by interfering with endothelial cell metabolism

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Science Bulletin 2025年第3期70卷 342-346页

作者： Nana Yang Jiahong Chen Yujie Zhu Wenxin Shan Zheng Cao Yiwen Fu Huanhuan Cao Yanyan Li Yukun Xiang Shusi Ding Huiqing Wang Yaobo Zhao Liang Ji Rui Zhan Yufei Wu Zhaomeng Wang Manyuan Dong Lemin Zheng School of Bioscience and Technology Weifang Key Laboratory of Animal Model Research on Cardiovascular and Cerebrovascular DiseasesShandong Second Medical UniversityWeifang 261053China The Institute of Cardiovascular Sciences and Institute of systems Biomedicine School of Basic Medical SciencesState Key Laboratory of Vascular Homeostasis and RemodelingNHC Key Laboratory of Cardiovascular Molecular Biology and Regulatory PeptidesBeijing Key Laboratory of Cardiovascular Receptors ResearchHealth Science CenterPeking UniversityBeijing 100191China University of Chinese Academy of Sciences Beijing 100049China Beijing Tiantan Hospital China National Clinical Research Center for Neurological DiseasesAdvanced Innovation Center for Human Brain ProtectionBeijing Institute of Brain DisordersThe Capital Medical UniversityBeijing 100050China Research center for Cardiopulmonary Rehabilitation University of Health and Rehabilitation Sciences Qingdao Hospital(Qingdao Municipal Hospital)School of Health and Life SciencesUniversity of Health and Rehabilitation SciencesQingdao 266071China

Environmental pollution is an important but often overlooked risk factor for cardiovascular diseases such as heart ***(3,4,4′-trichlorocarbanilide,TCC)is a broad-spectrum antibacterial agent commonly used in personal care products such as antibacterial soaps,detergents,toothpaste,and cosmetics[1].Unfortunately,due to its widespread use,TCC has become one of the top ten most common water pollutants globally,and it is present in the atmosphere,soil,and aquatic sediments[2].

关键词： metabolism cardiovascular diseases

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Inhibitory gamma-aminobutyric acidergic neurons in the anterior cingulate cortex participate in the comorbidity of pain and emotion

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Neural Regeneration Research 2025年第10期20卷 2838-2854页

作者： Lu Guan Mengting Qiu Na Li Zhengxiang Zhou Ru Ye Liyan Zhong Yashuang Xu Junhui Ren Yi Liang Xiaomei Shao Jianqiao Fang Junfan Fang Junying Du Department of Neurobiology and Acupuncture Research Third School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhouZhejiang ProvinceChina Key Laboratory for Research of Acupuncture Treatment and Transformation of Emotional diseases Third School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhouZhejiang ProvinceChina Fuchun Community Health Service center of Fuyang District HangzhouZhejiang ProvinceChina

Pain is often comorbid with emotional disorders such as anxiety and *** of the anterior cingulate cortex has been implicated in pain and pain-related negative emotions that arise from impairments in inhibitory gamma-aminobutyric acid *** review primarily aims to outline the main circuitry(including the input and output connectivity)of the anterior cingulate cortex and classification and functions of different gamma-aminobutyric acidergic neurons;it also describes the neurotransmitters/neuromodulators affecting these neurons,their intercommunication with other neurons,and their importance in mental comorbidities associated with chronic pain *** understanding on their role in pain-related mental comorbidities may facilitate the development of more effective treatments for these ***,the mechanisms that regulate gamma-aminobutyric acidergic systems remain *** is also unclear as to whether the mechanisms are presynaptic or *** exploration of the complexities of this system may reveal new pathways for research and drug development.

关键词： anterior cingulate cortex anxiety chronic pain circuit communication comorbidity depression gamma-aminobutyric acidergic neurons parvalbumin neurons synaptic transmission

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