1.Development of a High-throughput Sequencing Platform for Detection of Viral Encephalitis Pathogens Based on Amplicon Sequencing
Li Ya ZHANG ; Zhe Wen SU ; Chen Rui WANG ; Yan LI ; Feng Jun ZHANG ; Hui Sheng LIU ; He Dan HU ; Xiao Chong XU ; Yu Jia YIN ; Kai Qi YIN ; Ying HE ; Fan LI ; Hong Shi FU ; Kai NIE ; Dong Guo LIANG ; Yong TAO ; Tao Song XU ; Feng Chao MA ; Yu Huan WANG
Biomedical and Environmental Sciences 2024;37(3):294-302
Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laboratory diagnosis of viral encephalitis is a worldwide challenge.Recently,high-throughput sequencing technology has provided new tools for diagnosing central nervous system infections.Thus,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon sequencing. Methods We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant literature.The detection ability of the primers was verified by software simulation and the detection of known positive samples.Amplicon sequencing was used to validate the samples,and consistency was compared with Sanger sequencing. Results The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted amplicons.The sequences were verified using the National Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger sequencing. Conclusion Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral encephalitis.It is also a useful tool for the high-volume screening of clinical samples.
2.Risk factors for neonatal asphyxia and establishment of a nomogram model for predicting neonatal asphyxia in Hubei Enshi Tujia and Miao Autonomous Prefecture: a multicenter study.
Fang JIN ; Yu CHEN ; Yi-Xun LIU ; Su-Ying WU ; Chao-Ce FANG ; Yong-Fang ZHANG ; Lu ZHENG ; Li-Fang ZHANG ; Xiao-Dong SONG ; Hong XIA ; Er-Ming CHEN ; Xiao-Qin RAO ; Guang-Quan CHEN ; Qiong YI ; Yan HU ; Lang JIANG ; Jing LI ; Qing-Wei PANG ; Chong YOU ; Bi-Xia CHENG ; Zhang-Hua TAN ; Ya-Juan TAN ; Ding ZHANG ; Tie-Sheng YU ; Jian RAO ; Yi-Dan LIANG ; Shi-Wen XIA
Chinese Journal of Contemporary Pediatrics 2023;25(7):697-704
OBJECTIVES:
To investigate the risk factors for neonatal asphyxia in Hubei Enshi Tujia and Miao Autonomous Prefecture and establish a nomogram model for predicting the risk of neonatal asphyxia.
METHODS:
A retrospective study was conducted with 613 cases of neonatal asphyxia treated in 20 cooperative hospitals in Enshi Tujia and Miao Autonomous Prefecture from January to December 2019 as the asphyxia group, and 988 randomly selected non-asphyxia neonates born and admitted to the neonatology department of these hospitals during the same period as the control group. Univariate and multivariate analyses were used to identify risk factors for neonatal asphyxia. R software (4.2.2) was used to establish a nomogram model. Receiver operator characteristic curve, calibration curve, and decision curve analysis were used to assess the discrimination, calibration, and clinical usefulness of the model for predicting the risk of neonatal asphyxia, respectively.
RESULTS:
Multivariate logistic regression analysis showed that minority (Tujia), male sex, premature birth, congenital malformations, abnormal fetal position, intrauterine distress, maternal occupation as a farmer, education level below high school, fewer than 9 prenatal check-ups, threatened abortion, abnormal umbilical cord, abnormal amniotic fluid, placenta previa, abruptio placentae, emergency caesarean section, and assisted delivery were independent risk factors for neonatal asphyxia (P<0.05). The area under the curve of the model for predicting the risk of neonatal asphyxia based on these risk factors was 0.748 (95%CI: 0.723-0.772). The calibration curve indicated high accuracy of the model for predicting the risk of neonatal asphyxia. The decision curve analysis showed that the model could provide a higher net benefit for neonates at risk of asphyxia.
CONCLUSIONS
The risk factors for neonatal asphyxia in Hubei Enshi Tujia and Miao Autonomous Prefecture are multifactorial, and the nomogram model based on these factors has good value in predicting the risk of neonatal asphyxia, which can help clinicians identify neonates at high risk of asphyxia early, and reduce the incidence of neonatal asphyxia.
Infant, Newborn
;
Humans
;
Male
;
Pregnancy
;
Female
;
Nomograms
;
Retrospective Studies
;
Cesarean Section
;
Risk Factors
;
Asphyxia Neonatorum/etiology*
3.Mechanism of Proliferation and Apoptosis of Acute Promyelocytic Leukemia Cell Line NB4 Induced by TPA.
Pan ZHAO ; Chong ZHANG ; Xue-Mei DONG ; Lu-Wei YAN ; Le-Yuan MI ; Ya-Jiao LI ; Jia-Chao KANG ; Jing WANG
Journal of Experimental Hematology 2023;31(5):1296-1302
OBJECTIVE:
To investigate the effect of phorbol-12-myristate-13-ace-tate (TPA) on the proliferation and apoptosis of acute promyelocytic leukemia cell line NB4 and its molecular mechanism.
METHODS:
The effect of different concentrations of TPA on the proliferation of NB4 cells at different time points was detected by CCK-8 assay. The morphological changes of NB4 cells were observed by Wright-Giemsa staining. The cell cycle and apoptosis of NB4 cells after TPA treatment were detected by flow cytometry. The mRNA expressions of NB4 cells after TPA treatment were analyzed by high-throughput microarray analysis and real-time quantitative PCR. Western blot was used to detect the protein expression of CDKN1A, CDKN1B, CCND1, MYC, Bax, Bcl-2, c-Caspase 3, c-Caspase 9, PIK3R6, AKT and p-AKT.
RESULTS:
Compared with the control group, TPA could inhibit the proliferation of NB4 cells, induce the cells to become mature granulocyte-monocyte differentiation, and also induce cell G1 phase arrest and apoptosis. Differentially expressed mRNAs were significantly enriched in PI3K/AKT pathway. TPA treatment could increase the mRNA levels of CCND1, CCNA1, and CDKN1A, while decrease the mRNA level of MYC. It could also up-regulate the protein levels of CDKN1A, CDKN1B, CCND1, Bax, c-Caspase 3, c-Caspase 9, and PIK3R6, while down-regulate MYC, Bcl-2, and p-AKT in NB4 cells.
CONCLUSION
TPA induces NB4 cell cycle arrest in G1 phase and promotes its apoptosis by regulating PIK3/AKT signaling pathway.
Humans
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Leukemia, Promyelocytic, Acute
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Caspase 3/metabolism*
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Caspase 9/pharmacology*
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Phosphatidylinositol 3-Kinases/metabolism*
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Proto-Oncogene Proteins c-akt/metabolism*
;
bcl-2-Associated X Protein/metabolism*
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Cell Line, Tumor
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Cell Division
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Apoptosis
;
RNA, Messenger
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Cell Proliferation
4.Publishing clinical prActice GuidelinEs (PAGE): Recommendations from editors and reviewers.
Nan YANG ; Wei ZHAO ; Wen-An QI ; Chen YAO ; Chong-Ya DONG ; Zhen-Guo ZHAI ; Tong CHEN ; En-Mei LIU ; Guo-Bao LI ; You-Lin LONG ; Xin-Yi WANG ; Zi-Jun WANG ; Ruo-Bing LEI ; Qi ZHOU ; Yao-Long CHEN ; Liang DU
Chinese Journal of Traumatology 2022;25(6):312-316
Transparency Ecosystem for Research and Journals in Medicine (TERM) working group summarized the essential recommendations that should be considered to review and publish a high-quality guideline. These recommendations from editors and reviewers included 10 components of essential requirements: systematic review of existing relevant guidelines, guideline registration, guideline protocol, stakeholders, conflicts of interest, clinical questions, systematic reviews, recommendation consensus, guideline reporting and external review. TERM working group abbreviates them as PAGE (essential requirements for Publishing clinical prActice GuidelinEs), and recommends guideline authors, editors, and peer reviewers to use them for high-quality guidelines.
Humans
;
Practice Guidelines as Topic
5.Mendelian randomization analysis: the causal relationship between the DNA methylation levels of JAK2 and obesity.
Xiao Tian LIU ; Run Qi TU ; Ya Ling HE ; Xiao Kang DONG ; Rui Ying LI ; Jian HOU ; Yu Qian LI ; Chong Jian WANG
Chinese Journal of Epidemiology 2022;43(8):1315-1320
Objective: Based on the Mendelian randomization analysis, to assess the causal relationship between DNA methylation levels of Janus kinase 2 (JAK2) and obesity. Methods: A case-control study was carried out, including 1 021 individuals [obesity (visceral fat index ≥10) vs. no obesity (visceral fat index <10) was 440 vs. 581] from the Henan Rural Cohort Study. MethylTargetTM target region methylation sequencing technology was used for testing the DNA methylation level of JAK2. logistic regression models were used to assess the association between the DNA methylation level of JAK2 and obesity. With SNP as the instrumental variable, the association between the DNA methylation level of JAK2 and obesity was explored by using the Mendelian randomization analysis method. Results: There was a positive association between Chr9:4984943 (one DNA methylation site in the promoter of JAK2) and obesity, and the OR (95%CI) was 1.22(1.04-1.42). Methylation level of five sites in the exon of JAK2 (Chr9:4985378, Chr9:4985404, Chr9:4985407, Chr9:4985409 and Chr9:4985435) were negatively associated with obesity, the corresponding OR (95%CI) were 0.53 (0.29-0.95), 0.58(0.36-0.93), 0.69 (0.49-0.97), 0.72 (0.53-0.99) and 0.58 (0.35-0.98) , respectively. Mendelian randomization analysis showed that there was a causal relationship between the DNA methylation levels of JAK2 and obesity, and the corresponding β (95%CI) were -1.985 (-3.520 - -0.450),-3.547 (-6.301 - -0.792) and -3.900 (-6.328 - -1.472) for Mendelian randomization method of inverse variance weighted, Mendelian randomization method of median based and Maximum-likelihood method, respectively. Conclusion: This study supported there was a causal relationship between the DNA methylation level of JAK2 and obesity.
Case-Control Studies
;
Cohort Studies
;
DNA Methylation
;
Genome-Wide Association Study
;
Humans
;
Janus Kinase 2/genetics*
;
Mendelian Randomization Analysis/methods*
;
Obesity/genetics*
;
Polymorphism, Single Nucleotide
6.Investigation on therapeutic potential and molecular mechanisms of Kunxian capsule against diabetic kidney disease via reversing the imbalance of "immune-inflammation" network
Yu-dong LIU ; Zhao-chen MA ; Cong-chong LI ; Ya LIN ; Yan-qiong ZHANG ; Na LIN
Acta Pharmaceutica Sinica 2022;57(2):375-384
Drug repositioning provides new clinical indications for existing drugs. The imbalance between body's "immune-inflammation" regulation is one of the important factors in the occurrence and development of diabetic nephropathy (DN). Chinese patent medicine Kunxian capsule is clinically used for treating rheumatoid arthritis with satisfying immune-modulatory and anti-inflammatory actions. Notably, accumulating clinical evidence based on small cohorts had shown that Kunxian capsule may be used to treat DN. But the underlying pharmacological mechanisms remain unclear. Therefore, this study integrated "drug target-disease gene-biological pathway-function module" multi-level associated network analysis, and
7.Poroid hidradenoma of the scalp
Byung Duk MIN ; Chong Kun LEE ; Chang Eun CHUNG ; Dong Chul KIM ; So Ya PAIK
Archives of Craniofacial Surgery 2021;22(3):154-156
Poroid hidradenoma has both features of hidradenoma and poroma. The histological hidradenoma framework consisting of solid and cystic components, and the presence of poroid and cuticular cells resembling a poroid neoplasm. Despite transforming into malignant neoplasm only in < 1% of cases, its histological characteristics may resemble those of malignant neoplasms. Although the risk of malignant transformation is very low, surgical excision is recommended to prevent growth and/or recurrence. To date, very few cases of poroid hidradenoma have been reported in the literature. Herein, we present a case of poroid hidradenoma on the scalp of a 74-year-old woman.
8.Poroid hidradenoma of the scalp
Byung Duk MIN ; Chong Kun LEE ; Chang Eun CHUNG ; Dong Chul KIM ; So Ya PAIK
Archives of Craniofacial Surgery 2021;22(3):154-156
Poroid hidradenoma has both features of hidradenoma and poroma. The histological hidradenoma framework consisting of solid and cystic components, and the presence of poroid and cuticular cells resembling a poroid neoplasm. Despite transforming into malignant neoplasm only in < 1% of cases, its histological characteristics may resemble those of malignant neoplasms. Although the risk of malignant transformation is very low, surgical excision is recommended to prevent growth and/or recurrence. To date, very few cases of poroid hidradenoma have been reported in the literature. Herein, we present a case of poroid hidradenoma on the scalp of a 74-year-old woman.
9.Histone deacetylase 3 promotes innate antiviral immunity through deacetylation of TBK1.
Jie-Lin TANG ; Qi YANG ; Chong-Hui XU ; He ZHAO ; Ya-Ling LIU ; Can-Yu LIU ; Yuan ZHOU ; Dong-Wei GAI ; Rong-Juan PEI ; Yun WANG ; Xue HU ; Bo ZHONG ; Yan-Yi WANG ; Xin-Wen CHEN ; Ji-Zheng CHEN
Protein & Cell 2021;12(4):261-278
TANK-binding kinase 1 (TBK1), a core kinase of antiviral pathways, activates the production of interferons (IFNs). It has been reported that deacetylation activates TBK1; however, the precise mechanism still remains to be uncovered. We show here that during the early stage of viral infection, the acetylation of TBK1 was increased, and the acetylation of TBK1 at Lys241 enhanced the recruitment of IRF3 to TBK1. HDAC3 directly deacetylated TBK1 at Lys241 and Lys692, which resulted in the activation of TBK1. Deacetylation at Lys241 and Lys692 was critical for the kinase activity and dimerization of TBK1 respectively. Using knockout cell lines and transgenic mice, we confirmed that a HDAC3 null mutant exhibited enhanced susceptibility to viral challenge via impaired production of type I IFNs. Furthermore, activated TBK1 phosphorylated HDAC3, which promoted the deacetylation activity of HDAC3 and formed a feedback loop. In this study, we illustrated the roles the acetylated and deacetylated forms of TBK1 play in antiviral innate responses and clarified the post-translational modulations involved in the interaction between TBK1 and HDAC3.
10.Solitary sclerotic fibroma on the thigh
Ji Hoon KIM ; Chi Ho SHIN ; Dong Chul KIM ; So Ya PAIK ; Chong Kun LEE
Archives of Craniofacial Surgery 2020;21(5):323-325
Sclerotic fibroma is a rare fibrous tumor of the skin associated with Cowden’s disease. In 1989, Rapini described sclerotic fibroma without Cowden’s disease as solitary sclerotic fibroma of the skin. It is a solid, well-circumscribed, slow-growing nodular tumor and it looks similar to a keloid scar. Consequently, it is extremely difficult to make a differential diagnosis of solitary sclerotic fibroma with keloid scar based on clinical findings only. The authors report a case of solitary sclerotic fibroma arising at the left lateral thigh of a 25-year-old man.

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