1.Construction and identification of a sizeable naive human Fab phage display antibody library
Yakun ZHAO ; Xiaoyue WEI ; Fanliang MENG ; Wentao LIU ; Jiaming FAN ; Lijin LONG ; Wanting WANG ; Jianling CHEN ; Jianzhong ZHANG ; Lihua HE ; Liyong LIU ; Rui ZHAO ; Di SUN ; Xuezhen YUAN ; Xiaomei YAN
Chinese Journal of Epidemiology 2025;46(2):288-295
Objective:To construct a sizeable naive human Fab phage display antibody library to screen high-affinity specific antibodies in vitro. Methods:Total RNA was extracted from peripheral blood mononuclear cells (PBMCs) of 126 healthy individuals, subsequently reverse-transcribed into cDNA, and used as a template. PCR amplification was performed to obtain the V H from IgG, IgM and light chain κ, λ, separately, with the initial PCR products serving as templates for a second round of PCR. Overlap extension PCR was employed to generate fragments of the κ and λ light chains. These fragments were ligated with the phage vector pNC3, which harbors the variable region 1 of the heavy chain, to construct a recombinant phage plasmid. This plasmid was then electroporated into competent Escherichia Coli TG1 cells to establish a naive human Fab phage display antibody library. One hundred clones were randomly selected for identification and sequencing, and antibody gene polymorphisms were analyzed using the IMGT database and MAFFT software. Recombinant α-hemolysin from Staphylococcus aureus was utilized to screen Fab antibody fragments through biopanning of the antibody library, followed by random selection of phage ELISA-identified clones. The positive clones (antigen A450∶blank control A450≥2.1) were sequenced. Results:Two large naive Fab phage display antibody libraries were successfully constructed, in which the capacity of κ and λ chain antibody libraries were 1.25×10 11 and 1.54×10 11, respectively. The titers for two antibody libraries were 6.04×10 13 CFU/ml and 3.50×10 13 CFU/ml. The positive transformation insertion rates for κ and λ chain antibody libraries were 96% (96/100) and 100% (100/100), respectively. Sequence analysis revealed that all antibody sequences were unique. The amino acid sequences in the skeletal region were relatively conserved. In contrast, significant variations in the length of the complementarity determining region (CDR) were found, and the diversity of amino acid sequence of the complementary determining region was high, especially the CDR3. Analysis using the IMGT database indicated that the sequences exhibited a broad distribution across variable-diversity-joining gene families. After six rounds of panning, specific phage antibodies enrichment targeting α-hemolysin were achieved. A total of 142 monoclonal antibodies were sequenced, yielding 8 distinct Fab antibody sequences. Conclusion:This study successfully constructed two naive human Fab phage display antibody libraries with large capacity and good diversity, which can be used for screening human antibodies for serum epidemiology.
2.Bioinformatics analysis and expression of the major genetic type of TcdB
Yitai Fang ; Nianzhi Ning ; Yakun Sun ; Deyu Li ; Hui Wang ; Deyan Luo
Acta Universitatis Medicinalis Anhui 2025;60(12):2273-2280
Objective:
To analyze the bioinformatics of domestic Clostridium difficile toxin B(TcdB) and prepare it to provide data support for the development of effective vaccines.
Methods:
Using bioinformatics software such as Snippy, Blast, Muscle, and the dist.alignment() and hclust() functions in R, 1 355 strains of Clostridium difficile from NCBI GenBank in China were compared and analyzed, and TcdB were grouped. The maximum likelihood tree and phylogenetic tree were beautified and displayed using iTOL. An online bioinformatics analysis website was used to predict and analyze the spatial structure and antigenic epitopes of the two largest subgroups, TcdB1 and TcdB2. The antigen protein TcdB was expressed and purified by prokaryotic system.
Results:
According to the genotype of toxin B, the 1 355 prevalent strains of Clostridium difficile in China could be roughly divided into 12 subtypes, among which TcdB1 and TcdB2 were the main subtypes, accounting for more than 93.94% of all isolated strains, and about 17.20% of the strains were nontoxigenic or lack TcdB. The antigen epitope prediction of TcdB1 and TcdB2 showed that their antigen epitope distributions were basically the same, and many of them were distributed outside the C-terminal combined repetitive oligopeptides domains.
Conclusion
A specialized typing system for C. difficile TcdB in China has been established, and its main subtypes have been predicted for antigenic epitopes. The screened TcdB has been expressed for recombinant preparation.
3.Construction and identification of a sizeable naive human Fab phage display antibody library
Yakun ZHAO ; Xiaoyue WEI ; Fanliang MENG ; Wentao LIU ; Jiaming FAN ; Lijin LONG ; Wanting WANG ; Jianling CHEN ; Jianzhong ZHANG ; Lihua HE ; Liyong LIU ; Rui ZHAO ; Di SUN ; Xuezhen YUAN ; Xiaomei YAN
Chinese Journal of Epidemiology 2025;46(2):288-295
Objective:To construct a sizeable naive human Fab phage display antibody library to screen high-affinity specific antibodies in vitro. Methods:Total RNA was extracted from peripheral blood mononuclear cells (PBMCs) of 126 healthy individuals, subsequently reverse-transcribed into cDNA, and used as a template. PCR amplification was performed to obtain the V H from IgG, IgM and light chain κ, λ, separately, with the initial PCR products serving as templates for a second round of PCR. Overlap extension PCR was employed to generate fragments of the κ and λ light chains. These fragments were ligated with the phage vector pNC3, which harbors the variable region 1 of the heavy chain, to construct a recombinant phage plasmid. This plasmid was then electroporated into competent Escherichia Coli TG1 cells to establish a naive human Fab phage display antibody library. One hundred clones were randomly selected for identification and sequencing, and antibody gene polymorphisms were analyzed using the IMGT database and MAFFT software. Recombinant α-hemolysin from Staphylococcus aureus was utilized to screen Fab antibody fragments through biopanning of the antibody library, followed by random selection of phage ELISA-identified clones. The positive clones (antigen A450∶blank control A450≥2.1) were sequenced. Results:Two large naive Fab phage display antibody libraries were successfully constructed, in which the capacity of κ and λ chain antibody libraries were 1.25×10 11 and 1.54×10 11, respectively. The titers for two antibody libraries were 6.04×10 13 CFU/ml and 3.50×10 13 CFU/ml. The positive transformation insertion rates for κ and λ chain antibody libraries were 96% (96/100) and 100% (100/100), respectively. Sequence analysis revealed that all antibody sequences were unique. The amino acid sequences in the skeletal region were relatively conserved. In contrast, significant variations in the length of the complementarity determining region (CDR) were found, and the diversity of amino acid sequence of the complementary determining region was high, especially the CDR3. Analysis using the IMGT database indicated that the sequences exhibited a broad distribution across variable-diversity-joining gene families. After six rounds of panning, specific phage antibodies enrichment targeting α-hemolysin were achieved. A total of 142 monoclonal antibodies were sequenced, yielding 8 distinct Fab antibody sequences. Conclusion:This study successfully constructed two naive human Fab phage display antibody libraries with large capacity and good diversity, which can be used for screening human antibodies for serum epidemiology.
4.Influencing factors of severe pneumonia in children with respiratory syncytial virus infection
Zhihui YAN ; Yakun WANG ; Weiran DONG ; Wei SUN ; Bojuan ZHENG ; Liyuan TIAN
Journal of Chinese Physician 2023;25(1):56-60
Objective:To explore the influencing factors of severe pneumonia in children with respiratory syncytial virus (RSV) infection.Methods:A retrospective case-control study was used to collect 210 children with RSV infected pneumonia admitted to Hebei Children′s Hospital from October 2017 to October 2020. Among them, 70 children with severe pneumonia were included in the severe pneumonia group, and 140 children with common pneumonia were included in the common pneumonia group; the baseline data and relevant laboratory indicators of the two groups were compared; Logistic regression was used to analyze the influencing factors of severe pneumonia in children infected with RSV.Results:The proportions of wheezing, congenital heart disease, respiratory failure, heart failure and pleural effusion of children in severe pneumonia group were higher than those in common pneumonia group, and the forced vital capacity (FVC) and forced expiratory volume in the first second (FEV 1) were lower than those in common pneumonia group (all P<0.05); the levels of C-reactive protein (CRP), CD8 + cells, RSV load and Beclin-1 in severe pneumonia group were higher than those in common pneumonia group, and the levels of CD4 + cells and 1, 25-dihydroxyvitamin D [1, 25-(OH) 2D] were lower than those in common pneumonia group (all P<0.05). After treatment, the levels of CRP, CD8 + cells and Beclin-1 in children with severe pneumonia were lower than those before treatment, and the levels of CD4 + cells and 1, 25-(OH) 2D were higher than those before treatment (all P<0.05). Multiple regression model analysis was established. The results showed that congenital heart disease, high CRP level, high CD8 + cells, high RSV load and high Beclin-1 level were risk factors for severe pneumonia in children with RSV infected pneumonia (all OR>1, P<0.05), and high CD4 + cells and 1, 25-(OH) 2D level were protective factors (all OR<1, P<0.05). Conclusions:Severe pneumonia in children with RSV infected pneumonia may be affected by congenital heart disease, CRP, CD4 + cells, CD8 + cells, 1, 25-(OH) 2D, RSV load and Beclin-1.
5.Clinical characteristics of a case of developmental and epileptic encephalopathy caused by PPP3CA gene mutation and literature review
Xin LI ; Lingyu PANG ; Yakun DU ; Suzhen SUN
Chinese Journal of Neurology 2023;56(2):158-163
Objective:To improve clinicians′ understanding of developmental and epileptic encephalopathy (DEE) caused by PPP3CA gene mutation. Methods:Clinical data of a patient with DEE diagnosed in the First Department of Neurology, Hebei Children′s Hospital in September 2018 were collected. The whole-exome sequencing of the proband′s family was performed, and the characteristics of gene mutation were analyzed. Literature review was carried out based on the reported cases related to PPP3CA gene. Results:The proband, a 3 months and 20 days old girl, was admitted to the hospital with a history of paroxysmal confusion with extremities shaking for 2 days. The clinical manifestations included frequent epilepsy seizures and hypoevolutism. Brain magnetic resonance imaging showed that the bilateral frontotemporal extracerebral space was slightly wider. The video electroencephalography showed hyperarrhythmia and a cluster of spastic seizures. Whole exome sequencing of the family revealed that the proband had a heterozygous de novo frameshift truncating mutation in the PPP3CA gene: c.1255-1256delAG (p.Ser419Cysfs*31). From the establishment of the database to May 2022, 8 foreign literatures and 1 Chinese literature were retrieved, and a total of 21 children with PPP3CA gene mutation were reported, with clinical developmental delay, cognitive dysfunction and abnormal electroencephalography activity. Conclusions:The frameshift truncating mutation of the PPP3CA gene (c.1255-1256delAG) is the hereditary etiology of this patient. For cases of frequent seizures with poor efficacy of antiepileptic drugs, and developmental delay, genetic testing should be performed to confirm diagnosis and treatment.
6.Signal mining and analysis of adverse drug events for tolvaptan based on FAERS database
Yakun CHEN ; Pengxiang ZHOU ; Ruifang SUN ; Rongsheng ZHAO
China Pharmacy 2022;33(3):352-357
OBJECTIVE To mine the signals of adverse dr ug events (ADE)for tolvaptan based on FAERS database ,and to provide reference for safe use of drugs in clinic. METHODS The data of tolvaptan-induced ADE were collected from FAERS database during the first quarter of 2004 to the third quarter of 2020;the reporting odds ratio (ROR)method and the proportional reporting ratio (PRR)method of disproportional method were used for data mining. RESULTS A total of 4 744 ADE reports of the target drug tolvaptan were extracted ,involving 1 279 ADEs. The reporting countries were mainly the United States and Japan ,etc. A total of 199 ADE signals were obtained ,involving 21 system organ classes (SOCs),which mainly focused on various examinations(n=56),hepatobiliary disorders (n=17),renal and urinary disorders (n=14),etc. Among them ,80 signals were not mentioned in existing instructions for tolvaptan in China ,such as decreased glomerular filtration rate ,positional vertigo , rupture of renal cyst ,renal cyst infection ,pulmonary malignant tumor. CONCLUSIONS Before using tolvaptan ,drug evaluation should be performed well ,especially the patients with basic diseases such as heart failure ,liver insufficiency and renal insufficiency. During treatment ,the indexes of liver function and renal function should be closely monitored ;timely intervention measures should be taken to avoid related injury and disease deterioration caused by ADE when ADE or disease progression occurs.
7.Voltage-gated sodium channel α2-subunit gene related epilepsy with autism spectrum disorder: a case report
Xin LI ; Jingjie LI ; Yakun DU ; Suzhen SUN
Chinese Journal of Neurology 2021;54(10):1041-1046
Objective:To summarize the clinical features and treatment of voltage-gated sodium channel α2-subunit (SCN2A) gene-related epilepsy.Methods:The clinical manifestion, video electroencephalography, head magnetic resonance imaging of a child diagnosed with epilepsy in Hebei Children′s Hospital were analyzed. Additionally, blood samples of the family were tested for the whole exome sequencing.Results:The boy aged 20 months,had been developed backward since childhood and accompanied by autism spectrum disorder manifestations. Seizures occurred at 19 months, manifested as isolated and clusters of spasms or generalized tonic seizures. The whole exome sequencing of the family revealed that the proband had c.4543C>T heterozygous mutation in the SCN2A gene, and both parents showed wild type. The effect of multiple anti-epileptic drugs on the children was not good, but the epilepsy was controlled after the final addition of perampane.Conclusions:The c.4543C>T heterozygous variant of SCN2A gene is the cause of disease in this child. This variant can cause epilepsy with autism spectrum disorder. The location and type of SCN2A mutations are strongly related with phenotypes, and a clear genetic etiology contributes to accurate treatment of children.
8.The expression and significance of peripheral lymphocyte immunity and humoral immunity in children with autoimmune encephalitis and children with mycoplasma encephalitis
Fang CHEN ; Suzhen SUN ; Yakun DU ; Xuefang LIU ; Jingjie LI
Chinese Journal of Postgraduates of Medicine 2020;43(10):922-926
Objective:To investigate the expression level and significance of peripheral lymphocyte immunity and humoral immunity in children with autoimmune encephalitis and children with mycoplasma encephalitis.Methods:From July 2018 to July 2019, 52 children with autoimmune encephalitis (autoimmune encephalitis group) and 68 children with mycoplasma encephalitis (mycoplasma encephalitis group) in Hebei Children′s Hospital were enrolled, and 43 children with mycoplasma infection who were treated at the same time were selected as control group. Serum immunoglobulin (IgA, IgG, IgM) levels were detected using a fully automated biochemical analyzer, and peripheral T-lymphocyte subsets (CD 3+, CD 4+, CD 8+, CD 4+/CD 8+) levels were measured using flow cytometry. The receiver operating characteristic (ROC) curve was used to analyze the clinical differential diagnostic value of serum immunoglobulin and T lymphocyte subsets indicators for autoimmune encephalitis and mycoplasma encephalitis. Results:The levels of serum IgA, IgM in three groups had significant differences ( P<0.05); the levels of serum IgA, IgM in mycoplasma encephalitis group were significantly higher than those in autoimmune encephalitis group and control group [(1.64 ± 0.56) g/L vs. (1.23 ± 0.48),(0.82 ± 0.25) g/L; (1.81 ± 0.45) g/L vs. (1.56 ± 0.48), (1.12 ± 0.34) g/L]( P<0.05); the level of IgG in three groups has no significant difference ( P>0.05). The levels of CD 4+,CD 8+ in mycoplasma encephalitis group were significantly higher than those in autoimmune encephalitis group and control group [(31.21 ± 3.86)% vs. (28.76 ± 3.57)%, (26.58 ± 3.49)%; (26.86 ± 1.89)% vs. (25.90 ± 2.16)%, (24.71 ± 2.46)%]( P<0.05); the level of CD 4+/CD 8+ in three groups has no significant difference ( P>0.05). The areas under the curve of serum IgA, IgM, CD 3+, CD 8+, CD 4+ and five combined diagnosis were 0.971, 0.835, 0.833, 0.631, 0.706 and 1.000. The optimal critical values were 1.255 g/L, 1.465 g/L, 57.435%, 26.456%, 29.750% and 1.858. The sensitivity was 100.0%, 64.7%, 95.6%, 92.6%, 69.1% and 100.0%, and the specificity was 95.6%, 57.0%, 57.1%, 23.4%, 36.4% and 100.0%. Conclusions:The expression levels of serum IgA, IgM and peripheral serum CD 3+, CD 4+ and CD 8+ in children with autoimmune encephalitis are significantly lower than those in children with mycoplasma encephalitis, and IgA, IgM, CD 3+, CD 8+ and CD 4+ has high differential diagnosis value.
9.IGF-Ⅱrestores rapamycin-induced suppression of β-cell differentiation and expansion of adult pancreas stem cells
Haimin WANG ; Gang WANG ; Ruoxuan PENG ; Qin XU ; Yufeng DENG ; Hong ZHANG ; Yakun FENG ; Xianchao XIAO ; Ying GAO ; Chenglin SUN
Chinese Journal of Endocrinology and Metabolism 2018;34(8):678-683
Objective To investigate the mechanism of rapamycin inhibiting the differentiation and proliferation of newborn porcine pancreatic adult stem cells, and to explore the therapeutic methods that may effectively reduce the side effects of rapamycin. Method Porcine NPCCs were treated with rapamycin alone or in combination with IGF-Ⅱ, and the caspase-3 and [ 3 H ]-thymidine uptake assays were performed to detect apoptosis and proliferation. The expression of insulin, PDX-1, NeuroD/Beta2, and Foxo1, a downstream transcription factor of IGF-Ⅱ, were analyzed by RT-PCR and Western blot to evaluate the differentiation ability of pancreatic adult stem cells. Results The NPCCs treated with rapamycin inhibited the proliferation ofβ-cells, increased apoptosis, reduced insulin secretion, inhibited the expression of PDX-1 and NeuroD/Beta2, and decreased the expression of IGF-Ⅱ. Foxo1 expression and induction of Foxo1 from the cytoplasm to the nucleus of the ectopic. The combined treatment of rapamycin and IGF-Ⅱcan reduce the side effects of rapamycin, inhibit the decrease ofβ-cell number and insulin content, repair the expression of insulin, PDX-1, NeuroD/Beta2, inhibit Foxo1 expression and intracellular ectopic. Conclusion Aberrant expression of IGF-Ⅱ and Foxol genes is the key inducing factor of rapamycin inhibiting the proliferation and differentiation of NPCCs, and IGF-Ⅱtreatment can effectively reduce the side effects of rapamycin on NPCCs differentiation.
10.Immune system dysfunction in Niemann-Pick type C1 mice
Yuliang SUN ; Jichao YANG ; Yanan HE ; Yakun REN ; Liang QIAO ; Congrui WANG ; Yanli LIU ; Juntang LIN
Chinese Journal of Microbiology and Immunology 2018;38(10):739-747
Objective To analyze the differences in immune system between Npc1 gene mutant (Npc1-/ -) and wild-type (Npc1+/ +) mice for better understanding the pathogenesis of Niemann-Pick disease type C1 (NPC1) from an immunological perspective and providing reference for NPC1 treatment in clinic.Methods Body, thymus and spleen weight of Npc1-/ -and Npc1+/ + mice aged (14±2) days, (42±2) days and (63±2) days (Day14±2 , Day42±2 and Day63±2 ) were recorded and the associated organ index were calcu-lated. White blood cell count in peripheral blood of mice aged Day42±2 was examined by routine blood test. Expression of cytokines at mRNA level in mouse peripheral blood was detected by qPCR. Percentages of CD4+, CD8+ and CD19+ lymphocytes in peripheral blood and spleen of mice aged Day42±2 were measured by flow cytometry. Apoptosis and senescence of spleen in mice aged Day63±2 were examined by immunofluores-cence and β-galactosidase staining. Results Compared with Npc1+/ + mice, there was no significant differ-ence in the weight of spleen and thymus in Npc1-/ - mice aged Day14±2; the weight of spleen in Npc1-/ - mice aged Day42±2 significantly increased, but the weight of thymus showed a significant decrease; furthermore, both the weight of spleen and thymus in Npc1-/ - mice aged Day63±2 significantly decreased; and the body weight of Npc1-/ - mice of each age group significantly decreased. Moreover, compared with Npc1+/ + mice, the absolute number of lymphocytes in the peripheral blood of Npc1-/ - mice aged Day42±2 showed no signifi-cant difference, but the percentage in whole white blood cells significantly decreased due to the significantly increased neutrophils. Expression of cytokines ( IL-1, IL-2, IFN-γ, TNF-α, IL-4, granzyme A and granzyme B) at mRNA level in the peripheral blood leukocytes of Npc1-/ - mice aged Day42±2 was abnormal as compared with that in Npc1+/ + mice. The number of T (CD4+ and CD8+) lymphocytes in Npc1-/ - mice aged Day42±2 significantly decreased, while the number of B (CD19+) lymphocytes increased significantly as com-pared with those in the Npc1+/ + mice. Compared with Npc1+/ + mice, apoptosis and senescence of the spleen in Npc1-/ - mice aged Day63±2 aggravated significantly. Conclusion The abnormal lipid metabolism triggered by Npc1 gene mutation causes severe immune dysfunction in Npc1-/ - mice. Therefore, immune dysfunction should be taken into full consideration when treating patients with NPC1, which might help improve the life quality and prolong the survival time.


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