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DVsc:An Automated Framework for Efficiently Detecting Viral Infection from single-cell Transcriptomics Data

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 189-200页

作者： Fei Leng song Mei Xiaolin Zhou Xuanshi Liu Yefeng Yuan Wenjian Xu Chongyi Hao Ruolan Guo Chanjuan Hao Wei Li Peng Zhang Beijing Key Laboratory for Genetics of Birth Defects Beijing Pediatric Research Institute/MOE Key Laboratory of Major Diseases in Children/Rare Disease CenterBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijing 100045China institute of Biomedical Engineering University of TorontoTorontoM5S 3G9Canada

single-cell RNA sequencing(scRNA-seq)has emerged as a valuable tool for studying cellular heterogeneity in various fields,particularly in virological *** studying the viral and cellular transcriptomes,the dynamics of viral infection can be investigated at a single-cell ***,limited studies have been conducted to investigate whether RNA transcripts from clinical samples contain substantial amounts of viral RNAs,and a specific computational framework for efficiently detecting viral reads based on scRNA-seq data has not been ***,we introduce DVsc,an open-source framework for precise quantitative analysis of viral infection from single-cell transcriptomics *** applied to approximately 200 diverse clinical samples that were infected by more than 10 different viruses,DVsc demonstrated high accuracy in systematically detecting viral infection across a wide array of cell *** innovative bioinformatics pipeline could be crucial for addressing the potential effects of surreptitiously invading viruses on certain illnesses,as well as for designing novel medicines to target viruses in specific host cell subsets and evaluating the efficacy of *** supports the FAsTQ format as an input and is compatible with multiple single-cell sequencing ***,it could also be applied to sequences from bulk RNA sequencing *** is available at http://62.***.32.33:5000/DVsc.

关键词： single-cell RNA sequencing Viral transcriptome Cellular transcriptome Viral infection Quantitative analysis Bulk RNA sequencing

Function and dysfunction of GEMIN5:understanding a novel neurodevelopmental disorder

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Neural Regeneration research 2024年第11期19卷 2377-2386页

作者： Charles H.Nelson Udai B.Pandey Department of Pediatrics Division of Child NeurologyChildren’s Hospital of PittsburghUniversity of Pittsburgh Medical CenterPittsburghPAUSA children’s Neuroscience institute Children’s Hospital of PittsburghUniversity of Pittsburgh Medical CenterPittsburghPAUSA

The recent identification of a neurodevelopmental disorder with cerebellar atrophy and motor dysfunction(NEDCAM)has resulted in an increased interest in GEMIN5,a multifunction RNA-binding *** the largest member of the survival motor neuron complex,GEMIN5 plays a key role in the biogenesis of small nuclear ribonucleoproteins while also exhibiting translational regulatory functions as an independent *** many questions remain regarding both the pathogenesis and pathophysiology of this new disorder,considerable progress has been made in the brief time since its *** this review,we examine GEMIN5 within the context of NEDCAM,focusing on the structure,function,and expression of the protein specifically in regard to the disorder ***,we explore the current animal models of NEDCAM,as well as potential molecular pathways for treatment and future directions of *** review provides a comprehensive overview of recent advances in our understanding of this unique member of the survival motor neuron complex.

关键词： cerebellar atrophy GEMIN5 neurodevelopmental disorder neurological disease sMN complex

X-box binding protein 1 caused an imbalance in pyroptosis and mitophagy in immature rats with di-(2-ethylhexyl)phthalate-induced testis toxicity

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Genes & Diseases 2024年第2期11卷 935-951页

作者： Yifan Hong Xiazhu Zhou Qi Li Jing Chen Yuexin Wei Chunlan Long Lianju shen Xiangqin Zheng Dinggang Li Xia Wang Chenjun Yu shengde Wu Guanghui Wei Department of Urology Children's Hospital of Chongqing Medical UniversityChongqing 400014China Pediatric research institute Children's Hospital of Chongqing Medical UniversityChongqing 400014China Chongqing Key Laboratory of children Urogenital Development and Tissue Engineering Children's Hospital of Chongqing Medical UniversityChongqing 400014China Chongqing Key Laboratory of Pediatrics Children's Hospital of Chongqing Medical UniversityChongqing 400014China Ministry of Education Key Laboratory of Child Development and Disorders Children's Hospital of Chongqing Medical UniversityChongqing 400014China National Clinical research Center for Child Health and Disorders Children's Hospital of Chongqing Medical UniversityChongqing 400014China China International science and Technology Cooperation Base of Child Development and Critical Disorders Children's Hospital of Chongqing Medical UniversityChongqing 400014China

As a widely used plasticizer,di-(2-ethylhexyl)phthalate(DEHP)is known to induce significant testicular ***,the potential mechanism and effects of pubertal exposure to DEHP on testis development remain *** vivo,postnatal day(PND)21 male rats were gavaged with 0,250,and 500 mg/kg DEHP for ten *** to the seminiferous epithelium and disturbed spermatogenesis were observed after DEHP ***,oxidative stress-induced injury and pyroptosis were *** endoplasmic reticulum(ER)stress and mitophagy were involved in this *** phthalate(MEHP)was used as the biometabolite of DEHP in *** GC-1 and GC-2 cell lines were exposed to 0,100μM,200μM,and 400μM MEHP for 24 *** oxygen species(ROs)generation,oxidative stress damage,ER stress,mitophagy,and pyroptosis were significantly increased after MEHP *** ultrastructure of the ER and mitochondria was destroyed.X-box binding protein 1(XBP1)was observed to be activated and translocated into the *** generation was inhibited by *** levels of antioxidative stress,ER stress,mitophagy,and pyroptosis were decreased as *** the administration of the ER stress inhibitor 4-phenyl-butyric acid,both mitophagy and pyroptosis were ***-induced XBP1 down-regulation decreased the levels of mitophagy and *** equilibrium between pyroptosis and mitophagy was disturbed by XBP1 *** summary,our findings confirmed that DEHP induced a ROs-mediated imbalance in pyroptosis and mitophagy in immature rat testes via ***,XBP1 might be the key target in DEHP-related testis dysfunction.

关键词： DEHP Mitophagy Pyroptosis Testicular development XBP1

Epitranscriptomic Regulation of NMDA Receptors Rears its Ugly Head in Chemotherapy-Induced Neuropathic Pain

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Neuroscience Bulletin 2024年第8期40卷 1209-1211页

作者： Wing Lam Yu Gerald W.Zamponi Department of Clinical Neurosciences Hotchkiss Brain InstituteAlberta Children's Hospital Research InstituteUniversity of CalgaryCalgaryAB T2N 4N1Canada

number of different cancer chemotherapy agents such as cisplatin,oxaliplatin,and paclitaxel can lead to nerve damage,thereby giving rise to neuropathic pain states that present with mechanical and cold allodynia[1].Although these pain conditions often resolve after completion of the chemotherapy,a significant portion of patients exhibit longlasting pain that can persist longer than 12 months with a negative impact on the quality of life of affected individuals[1].

关键词： chemotherapy pain damage

Mitochondria replacement from transplanted amniotic fluid stem cells:a promising therapy for non-neuronal defects in spinal muscular atrophy

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Neural Regeneration research 2024年第5期19卷 971-972页

作者： Michela Pozzobon Camilla Bean Women’s and children’s Health Department University of Padova Foundation institute of Pediatric research Cittàdella speranza PadovaItaly Department of Medicine University of UdineUdineItaly

spinal muscular atrophy(sMA)is a genetic disorder that primarily affects infants and leads to muscle weakness,atrophy,and *** main cause is the homozygous mutation or deletion of the sMN1 gene,resulting in inadequate levels of the survival motor neuron(sMN)*** treatments focus on restoring sMN levels through various approaches,but there is a need for“sMN-independent”therapies that target other pathological *** muscle is closely involved in sMA pathology,with impaired muscle function observed before motor neuron *** have revealed that sMN loss leads to skeletal muscle mitochondrial structural abnormalities,impaired respiration,and accumulation of reactive oxygen species.

关键词： impaired atrophy muscular

The current situation of semen analysis in China,based on a survey of 296 laboratories

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Asian Journal of Andrology 2024年第2期26卷 220-221页

作者： Long-Long Fu Ying Liu Xiao-Wei Wang Fang Zhou Ying Guo Wen-Hong Lu Yi-Qun Gu National Health Commission Key Laboratory of Male Reproductive Health Reproductive Health Research CenterNational Research Institute for Family PlanningBeijing 100081China institute of Pediatric research Children's Hospitalof Soochow UniversitySuzhou 215025China

Dear Editor,semen analysis is a basic test to assess male fertility and is a fundamental test in assisted reproductive *** the first publication of World Health Organization(WHO)Laboratory Manual of Human semen and sperm-Cervical Mucus Interaction in 1980,to the publication of the WHO Manual,6th edition in 2021,these 40 years have been recognized as providing a global standard that is widely used in research and clinical laboratories *** WHO Manual,6th edition in Chinese,which we have been authorized by the WHO to translate,will be published soon.

关键词： technology. analysis translate

Interleukins in Epilepsy:Friend or Foe

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Neuroscience Bulletin 2024年第5期40卷 635-657页

作者： Yuan Dong Xia Zhang Ying Wang Neuropsychiatry research institute The Affiliated Hospital of Qingdao UniversityQingdao UniversityQingdao266000China Program in Cellular and Molecular Medicine Boston Children’s HospitalBostonMA02115USA

Epilepsy is a chronic neurological disorder with recurrent unprovoked seizures,affecting~65 million *** in patients with epilepsy and animal models suggests a contribution of neuroinflammation to epileptogenesis and the development of ***(ILs),as one of the major contributors to neuroinflammation,are intensively studied for their association and modulatory effects on ictogenesis and *** are commonly divided into pro-and anti-inflammatory cytokines and therefore are expected to be pathogenic or neuroprotective in ***,both protective and destructive effects have been reported for many *** may be due to the complex nature of ILs,and also possibly due to the different disease courses that those ILs are involved *** this review,we summarize the contributions of different ILs in those processes and provide a current overview of recent research advances,as well as preclinical and clinical studies targeting ILs in the treatment of epilepsy.

关键词： Epilepsy Interleukins Neuroinflammation

Therapeutic potential of urine-derived stem cells in renal regeneration following acute kidney injury:A comparative analysis with mesenchymal stem cells

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World Journal of stem Cells 2024年第5期16卷 525-537页

作者： Fang Li Bin Zhao Lei Zhang Guo-Qing Chen Li Zhu Xiao-Ling Feng Meng-Jia Gong Cheng-Chen Hu Yuan-Yuan Zhang Ming Li Yong-Qiang Liu Department of General surgery Chongqing General HospitalChongqing 401147China Department of Pediatric research institute Children’s Hospital of Chongqing Medical UniversityChongqing 401147China

BACKGROUND Acute kidney injury(AKI)is a common clinical syndrome with high morbidity and mortality *** use of pluripotent stem cells holds great promise for the treatment of ***-derived stem cells(UsCs)are a novel and versatile cell source in cell-based therapy and regenerative medicine that provide advantages of a noninvasive,simple,and low-cost approach and are induced with high multidifferentiation *** these cells could serve as a potential stem cell source for the treatment of AKI has not been *** stem cell markers with multidifferentiation potential were isolated from human amniotic *** severe combined immune deficiency(sCID)mice models were induced by means of an intramuscular injection with *** isolated from human-voided urine were administered via tail *** functional changes in the kidney were assessed by the levels of blood urea nitrogen and serum *** histologic changes were evaluated by hematoxylin and eosin staining and transferase dUTP nick-end labeling ***,we compared the regenerative potential of UsCs with bone marrow-derived mesenchymal stem cells(MsCs).REsULTs Treatment with UsCs significantly alleviated histological destruction and functional *** renal function was rapidly restored after intravenous injection of 5×105 human UsCs into sCID mice with glycerol-induced AKI compared with injection of *** from secretion assays conducted in vitro demonstrated that both stem cell varieties released a wide array of cytokines and growth *** suggests that a mixture of various mediators closely interacts with their biochemical *** types of stem cells showed enhanced tubular cell prolif-eration and decreased tubular cell apoptosis,although UsC treatment was not more effective than MsC *** found that UsC therapy significantly improved renal function and histological damage,inhibited inflammation and apoptosis processes in the kid

关键词： Urine-derived stem cells Regenerative medicine Acute kidney injury Renal function recovery Cell therapy

Novel de novo TRPV4 mutation identified in a Chinese family with metatropic dysplasia inhibits chondrogenic differentiation

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Genes & Diseases 2024年第3期11卷 83-86页

作者： Ping Wei Weizhe shi Tianying Nong Caixia Xian Xia Li Zhaohui Li Xin Li Jianping Wu Liyuan shang Fulong Xu Yibo Xu Hongwen Xu Mingwei Zhu Guangzhou institute of Pediatrics Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangdong Provincial Clinical Research Center for Child HealthGuangzhouGuangdong 510623China Department of Pediatric Orthopedics Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangdong Provincial Clinical Research Center for Child HealthGuangzhouGuangdong 510623China

Metatropicdysplasia(MD,MIM156530)is a rare congenital bone dysplasia primarily characterized by severe platyspondyly with long and wide vertebral bodies and dumbbell deformity of the tubular *** can be caused by heterozygous mutations in the gene encoding transient receptor potential vanilloid family member 4(TRPV4).We identifieda novel de novo mutation,c.2353T>C,in the TRPV4 gene,in a Chinese family with mild MD.

关键词： TRPV4 dysplasia congenital