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A novel missense mutation in obscurin gene in a Chinese consanguineous family with left ventricular noncompaction

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Journal of Geriatric Cardiology 2022年第7期19卷 531-538页

作者： Xue-Qi DONG Pei-Pei QIN Di ZHANG Qiong-Yu ZHANG Yi QU Lin ZHAO Yi-Ting LU Yu-Xiao HU Chun-Xue YANG Xin-Chang LIU Ya-Xin LIU Xian-Liang ZHOU department of Cardiology Fuwai HospitalNational Center for Cardiovascular DiseaseChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina department of Obstetrics and Gynecology Peking Union Medical College HospitalBeijingChina

BACKGROUND Left ventricular noncompaction(LVNC) is an increasingly recognised cardiomyopathy of which a significant percentage are genetic in origin. The purpose of the present study was to identify potential pathogenic mutation leading to disease in a Chinese LVNC *** A 3-generation family affected by LVNC was recruited. Clinical assessments were performed on available family members, with clinical examination, ECG, echocardiography and cardiac MRI. The proband(Ⅰ-2), the proband’s daughter(Ⅱ-1, affected) and mother(Ⅲ-1, unaffected) were selected for WGS. Sanger sequencing were performed in all of the 4 surviving family *** Combined whole genome sequencing with linkage analysis identified a novel missense mutation in the giant protein obscurin(OBSCN NM_001098623, c.C19063T), as the only plausible disease-causing variant that segregates with disease among the four surviving individuals, with interrogation of the entire genome excluding other potential causes. This c.C19063T missense mutation resulted in p.R6355W in the encoded OBSCN protein. It affected a highly conserved residue in the C terminus of the obscurin-B-like isoform between the PH and STKc domains, which was predicted to affect the function of the protein by different bioinformatics *** Here we present clinical and genetic evidence implicating the novel R6355W missense mutation in obscurin as the cause of familial LVNC. This expands the spectrum of obscurin’s roles in cardiomyopathies. It furthermore highlights that rare obscurin missense variants, currently often ignored or left uninterpreted, should be considered to be relevant for cardiomyopathies and can be identified by the approach presented here. This study also provided new insights into the molecular basis of OBSCN mutation positive LVNC.

关键词： ventricular mother linkage

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

Metabolic syndrome, intracranial arterial stenosis and cerebral small vessel disease in community- dwelling populations

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Stroke & Vascular Neurology 2021年第4期6卷 589-594,I0055-I0059页

作者： Mei-Jun Shu Fei-Fei Zhai Ding-Ding Zhang Fei Han Lixin Zhou Jun Ni Ming Yao Shu-Yang Zhang Li-Ying Cui Zheng-Yu Jin Hui-Juan Zhu Yi-Cheng Zhu department of Neurology State Key Laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science and Peking Union Medical CollegeBeijingChina medical Research center State Key Laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science and Peking Union Medical CollegeBeijingChina department of Cardiology State Key Laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science and Peking Union Medical CollegeBeijingChina department of Radiology State Key Laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science and Peking Union Medical CollegeBeijingChina department of Endocrinology State Key Laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science and Peking Union Medical CollegeBeijingChina

Background and purpose This study aimed to investigate the association of metabolic syndrome(MetS)with both intracranial atherosclerotic stenosis(ICAS)and imaging markers of cerebral small vessel disease(CSVD)in a community-based *** This study included 943 participants(aged 55.6±9.2 years,36.1%male)from the community-based Shunyi cohort *** was defined according to the joint interim criteria and quantified by the MetS severity *** was evaluated by brain magnetic resonance *** MRI markers of CSVD,including white matter hyperintensities(WMHs),lacunes,cerebral microbleeds(CMBs)and enlarged perivascular spaces(EPVS),were *** regression models were used to investigate the association of MetS severity Z-score with ICAS and these CSVD *** We found that risk of ICAS(OR=1.75,95%CI 1.39 to 2.21,p<0.001)increased consistently with MetS *** severity was significantly associated with higher risks of WMH volume(β=0.11,95%CI 0.01 to 0.20,p=0.02)and lacunes(OR=1.28,95%CI 1.03 to 1.59,p=0.03)but not the presence of CMBs(OR=0.93,95%CI 0.74 to 1.16,p=0.51)and PVS severity(EPVS in basal ganglia:OR=0.96,95%CI 0.84 to 1.09,p=0.51 and EPVS in white matter:OR=1.09,95%CI 0.96 to 1.23,p=0.21).Conclusions Our findings suggest that WMH and lacunes share risk factors with atherosclerosis of the cerebral artery,whereas the impact of glucose and lipid metabolic disorder to CMB or EPVS might be weak.

关键词： cerebral severity stenosis

Analysis of G-banding in tumor cell lines derived from human neural stem cells

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Neural Regeneration Research 2006年第2期1卷 115-117页

作者： Junhua Zou Yanhui Li department of medical genetics Peking University HealthScience Center Beijing100083 China

BACKGROUND： The application of neural stem cell （NSC） is restricted because of its tumorigenesis, and the possible pathogenesis needs investigation. OBJEETIVE： To compare the differences of chromosomal G-banding between human NSCs （hNSCs） derived tumor cell line and hNSCs derived normal cell lines. DESIGN： A randomized controlled observation SETTING ： Building of Anatomy, Peking University Health Science center MATERIALS ①The hNSC lines and hNSC-derived tumor cell lines were provided by the Research center of Stem Cells, Peking University; DMEM/F12 （1：1） medium, N2 additive, B27 additive epidermal growth factor （EGF） and basic fibroblast growth factor （bFGF） were produced by GIBCO BRL Company （USA）; fetal bovine serum by HYCLONE Company （USA）. METHODS： The experiments were carried out in the department of genetics, Peking University Health Science center from February 2003 to July 2004. Human fetal striatal NSCs were inoculated hypodermically on the right scapular of nude mice; Normal human fetal striatal NSCs were cultured to 5-8 passages as controls. Karyotyping was performed on the 5^th passage of hNSC-derived tumor cells at 6 weeks after hNSC transplantation into nude mice （T1） and tumor cells at 15 weeks after transplantation （T2）. Metaphase chromosomes were examined with microscope, G-banding cytogenetic analysis and karyotyping were performed according to the Cytoscan Karyotyping FISH and CGH software system （United biotechnology USA Corporation）. MAIN OUTCOME MEASURES： G-banded analytical results of human fetal striatal nerve stem cells derived tumor cell lines （T1 and T2） of metaphase chromosomes were observed. RESULTS： ① Chromosome analysis of hNSC-derived tumor cell lines 1 （T1）： Twenty-five well-spread metaphases were randomly selected for analysis. The karyotypes were 64, XX （8, 32%）; 65, XX （1, 4%）; 67, XX （5, 20%）; 68, XX （11, 44%）. The modal number of chromosomes in this cell lines was 68, which were all hypotriploid. The analysis of 8 G-ba

关键词： stem cell

Predicting(side) effects for patients with inflammatory bowel disease: The promise of pharmacogenetics

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World Journal of Gastroenterology 2019年第21期25卷 2539-2548页

作者： Michiel Dirk Voskuil Amber Bangma Rinse Karel Weersma Eleonora Anna Margaretha Festen department of Gastroenterology and Hepatology University of Groningen and University Medical Center GroningenGroningen 9713 GZthe Netherlands department of genetics University of Groningen and University Medical Center GroningenGroningen 9713 GZthe Netherlands

Inflammatory bowel disease (IBD) is a chronic and heterogeneous intestinal inflammatory disorder. The medical management of IBD aims for long-lasting disease remission to prevent complications and disease progression. Early introduction of immunosuppression forms the mainstay of medical IBD management. Large inter-individual variability in drug responses, in terms of both efficacy and toxicity, leads to high rates of therapeutic failure in the management of IBD. Better patient stratification is needed to maximize patient benefit and minimize the harm caused by adverse events. Pre-treatment pharmacogenetic testing has the potential to optimize drug selection and dose, and to minimize harm caused by adverse drug reactions. In addition, optimizing the use of cheap conventional drugs, and avoiding expensive ineffective drugs, will lead to a significant reduction in costs. Genetic variation in both TPMT and NUDT15, genes involved in thiopurine metabolism, is associated to an increased risk of thiopurine-induced myelosuppression. Moreover, specific HLA haplotypes confer risk to thiopurine-induced pancreatitis and to immunogenicity to tumor necrosis factor-antagonists, respectively. Falling costs and increased availability of genetic tests allow for the incorporation of pre-treatment genetic tests into clinical IBD management guidelines. In this paper, we review clinically useful pharmacogenetic associations for individualized treatment of patients with IBD and discuss the path from identification of a predictive pharmacogenetic marker to implementation into IBD clinical care.

关键词： Inflammatory bowel disease Crohn’s disease Ulcerative colitis Pharmacogenetics Personalized medicine

A hydrogel spinal dural patch with potential anti-inflammatory,pain relieving and antibacterial effects

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Bioactive Materials 2022年第8期7卷 389-401页

作者： Jiahao Li Jingjing Tian Chunxu Li Longyun Chen Yu Zhao department of Orthopaedic Surgery Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina medical Science Research center Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina department of Pathology State Key Laboratory of Complex Severe and Rare DiseaseMolecular Pathology Research CenterPeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina

CSFL caused by spinal dural defect is a common complication of spinal surgery,which need repair such as suture or ***,low intracranial pressure symptoms,wound infection and prolonged hospital associated with pin-hole leakage or loose seal effect were often occurred after surgical suture or sealants ***,pressure resistance and high viscosity spinal dural repair patch in wet environment without suture or sealants was highly ***,a bioactive patch composed of alginate and polyacrylamide hydrogel matrix cross-linked by calcium ions,and chitosan adhesive was *** fabricated patch exhibits the capabilities of promoting defect closure and good tight seal ability with the bursting pressure is more than 790 mm H2O in wet *** addition,the chitosan adhesive layer of the patch could inhibit the growth of bacterial in vitro,which is meaningful for the postoperative ***,the patch also significantly reduced the expression of GFAP,IBA-1,MBP,TNF-α,and COX-2 in early postoperative period in vivo study,exerting the effects of anti-inflammatory,analgesic and adhesion ***,the bioactive patch expected to be applied in spinal dural repair with the good properties of withstanding high pressure,promoting defect closure and inhibiting postoperative infection.

关键词： Alginate hydrogel Chitosan adhesive Dural defect repair Anti-inflammatory Bacteriostasis

Simplified microsatellite instability detection protocol provides equivalent sensitivity to robust detection strategies in Lynch syndrome patients

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Cancer Biology & Medicine 2017年第2期14卷 142-150页

作者： Hadi Babaei Mehrdad Zeinalian Mohammad Hassan Emami Mortaza Hashemzadeh Najmeh Farahani Rasoul Salehi department of genetics and Molecular Biology School of MedicineIsfahan University of Medical Sciences Clinic of Gastrointestinal diseases Poursina Hakim Research CenterIsfahan University of Medical Sciences Cellular and Molecular Research center Shahrekord University of Medical Sciences

Objective:Germline mutations in mismatch repair(MMR)genes cause Lynch syndrome(LS).LS is an inherited disease,and an important consequence of MMR deficiency is microsatellite instability(MSI)*** phenotype influences the efficacy of5 fluorouracil(5-FU)***,cost effective,and easy to perform laboratory tests are required to include MSI detection in routine laboratory *** of CAT25 as monomorphic short tandem repeat sequence enables CAT25 to be an efficient screening tool among hereditary nonpolyposis colorectal cancer(HNPCC)patients compared with other methods used ***:Based on Amsterdam II criteria,31 patients in 31 families were shortlisted from a total number of 1,659 colorectal cancer *** status was examined in these patients using CAT25 and a commercially available Promega MSI five-markerbased detection system as well as immunohistochemical(IHC)staining of four important MMR *** were scored as high microsatellite instable(MSI-H),low(MSI-L),or stable(MSS).MSI status determined by CAT25 single mononucleotide marker was compared with that of five mononucleotide markers,Promega commercial kit,and IHC ***:MMR protein deficiency was observed on 7/31 probands using IHC methodology and 6/31 categorized as MSI-H using commercial kit or CAT25 single *** sensitivity and specificity of the CAT25 single marker were the same as those detected by five-marker Promega commercial kit in our ***:Based on our results,the performance of the CAT25 single mononucleotide marker for MSI status determination in our HNPCC patients is the same as that of the five-marker-based commercial kit.

关键词： Lynch syndrome HNPCC DNA mismatch repair IHC microsatellite instability

Wilson's disease in Lebanon and regional countries: Homozygosity and hepatic phenotype predominance

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World Journal of Gastroenterology 2017年第36期23卷 6715-6725页

作者： Kassem Barada Aline El Haddad Meghri Katerji Mustapha Jomaa Julnar Usta department of Internal Medicine American University of Beirut Medical Center department of Biochemistry and Molecular genetics Faculty of Medicine American University of Beirut

AIM To determine the phenotypes and predominant diseasecausing mutations in Lebanese patients with Wilson's disease,as compared to regional non-European *** The clinical profile of 36 patients diagnosed in Lebanon was studied and their mutations were determined by molecular *** patients underwent full physical exam,including ophthalmologic slit-lamp examination ultrasound imaging of the liver,as well as measurement of serum ceruloplasmin and 24-h urinaryCu *** addition,genetic screening using PCR followed by sequencing to determine disease-causing mutations and polymorphisms in the ATP7B gene was carried on extracted DNA from patients and immediate family *** phenotypic-genotypic findings were then compared to reported mutations in Wilson's disease patients from regional Arab and non-European countries. RESULTS Patients belonged to extended consanguineous *** majority were homozygous for the disease-causing mutation,with no predominant mutation identified. The most common mutation,detected in 4 out of 13families,involved the ATP hinge region and was present in patients from Lebanon,Egypt,Iran and ***,mutations in Lebanese patients and those of the region were scattered over 17 exons of *** the homozygous exon 12 mutation Trp939Cys was only detected in patients from Lebanon but none from the regional countries,the worldwide common mutation H1069Q was not present in the Lebanese and was rare in the *** hepatic phenotype was predominant in patients from both Lebanon and the region(25%-65%).Furthermore,the majority of patients,including those who were asymptomatic,had evidence of some hepatic *** neurologic phenotype was rare. CONCLUSION Findings do not support presence of a founder *** and genetic screening is recommended for family members with index patients and unexplained hepatic dysfunction.

关键词： Wilson disease Cu-metabolism Phenotype Genotype ATP7B Hepatic manifestations

Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli

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Science China(Life Sciences) 2015年第9期58卷 902-911页

作者： TALUKDER AliAzam ISHIHAMA Akira department of Microbiology Jahangirnagar University Micro-Nano Technology Research center Hosei University department of Molecular genetics National Institute of Genetics

The genomic DNA of bacteria is highly compacted in a single or a few bodies known as nucleoids. Here, we have isolated Escherichia coli nucleoid by sucrose density gradient centrifugation. The sedimentation rates, structures as well as pro- tein/DNA composition of isolated nucleoids were then compared under various growth phases. The nucleoid structures were found to undergo changes during the cell growth; i. e., the nucleoid structure in the stationary phase was more tightly com- pacted than that in the exponential phase. In addition to factor for inversion stimulation （Fis）, histone-like nucleoid structuring protein （H-NS）, heat-unstable nucleoid protein （HU） and integration host factor （IHF） here we have identified, three new can- didates of E. coli nucleoid, namely DNA-binding protein from starved cells （Dps）, host factor for phage QJ3 （Hfq） and sup- pressor of taC phenotype A （StpA）. Our results reveal that the major components of exponential phase nucleoid are Fis, HU, H-NS, StpA and Hfq, while Dps occupies more than half of the stationary phase nucleoid. It has been known for a while that Dps is the main nucleoid-associated protein at stationary phase. From these results and the prevailing information, we propose a model for growth phase dependent changes in the structure and protein composition of nucleoid in E. coli.

关键词： growth phase sucrose gradient bacterial nucleoid DNA binding protein DNA compaction