1.N6-methyladenosine related regulatory factors in osteoarthritis:bioinformatics analysis and experimental validation
Changshen YUAN ; Shuning LIAO ; Zhe LI ; Yanbing GUAN ; Siping WU ; Qi HU ; Qijie MEI ; Kan DUAN
Chinese Journal of Tissue Engineering Research 2024;28(11):1724-1729
BACKGROUND:Increasing evidence suggests that N6-methyladenosine(m6A)regulators are closely associated with osteoarthritis and are considered to be a new direction in the prevention and treatment of osteoarthritis,but their specific mechanism of action is unknown. OBJECTIVE:To conduct a bioinformatics analysis of the osteoarthritis gene microarray dataset in order to explore the role of m6A in osteoarthritis and analyze the pathogenesis of osteoarthritis. METHODS:The m6A regulators associated with osteoarthritis and their expression were first extracted from the GSE1919 dataset in the GEO database using R software,and then the results were analyzed by gene difference analysis and GO and KEGG enrichment analyses.Subsequently,the results of protein-protein interaction network topology analysis and machine learning results were intersected to obtain the m6A Hub regulators,which were validated by in vitro cellular experiments. RESULTS AND CONCLUSION:A total of 16 osteoarthritis-related m6A regulators were extracted and 11 m6A differential regulators,including ZC3H13,YTHDC1,YTHDF3 and HNRNPC,were obtained by differential analysis.GO enrichment analysis showed that osteoarthritis-related m6A differential regulators played a role in the biological processes such as mRNA transport,RNA catabolism,and regulation of insulin-like growth factor receptor signaling pathway.(3)KEGG enrichment analysis showed that the differential regulators were mainly involved in the p53,interleukin-17 and AMPK signaling pathways.The combined protein-protein interaction network topology analysis and machine learning results obtained the m6A Hub regulator-YTHDC1.(5)The results of in vitro cellular experiments showed that there was a significant difference in the expression of m6A key regulator between the control and experimental groups(P<0.05).To conclude,YTHDC1 is closely related to the development of osteoarthritis,which is expected to be a molecular target of m6A for the treatment of osteoarthritis.
2.Machine learning combined with bioinformatics to identify and validate key genes for cellular senescence in osteoarthritis
Changshen YUAN ; Shuning LIAO ; Zhe LI ; Siping WU ; Lewei CHEN ; Jinyi LIU ; Yanhong LI ; Kan DUAN
Chinese Journal of Tissue Engineering Research 2024;28(20):3196-3201
BACKGROUND:Cellular senescence is closely related to the development and progression of osteoarthritis,but the specific targets and regulatory mechanisms are not yet clear. OBJECTIVE:To mine key genes in cellular senescence-mediated osteoarthritis by integrating bioinformatics and machine learning approaches and validate them via experiments to explore the role of cellular senescence in osteoarthritis. METHODS:The osteoarthritis gene expression profiles obtained from the GEO database were intersected with cellular senescence-related genes obtained from the CellAge database and the expression of the intersected genes was extracted for differential analysis,followed by GO and KEGG analysis of the differential genes.The key osteoarthritis cellular senescence genes were then screened by protein-protein interaction network analysis and machine learning,and in vitro cellular experiments were performed.Finally,the expression of the key genes was detected by qPCR. RESULTS AND CONCLUSION:A total of 31 osteoarthritis cell senescence differential genes were identified.GO analysis showed that these genes were mainly involved in the biological processes,such as regulation of leukocyte differentiation,monocyte differentiation,regulation of T cell differentiation and exerted roles in DNA transcription factor binding,histone deacetylase binding,chromatin DNA binding,and chemokine binding.KEGG analysis showed that osteoarthritis cell senescence differential genes were mainly activated in the JAK/STAT signaling pathway,PI3K/Akt signaling pathway and FoxO signaling pathway.MYC,a key gene for osteoarthritis cellular senescence,was identified by protein-protein interaction network topology analysis and machine learning methods.The results of the in vitro cellular assay showed that the mRNA expression of MYC was significantly lower in the experimental group(osteoarthritis group)than the control group(normal group)(P<0.05).To conclude,MYC can be a key gene in the senescence of osteoarthritic cells and may be a new target in the prevention and treatment of osteoarthritis by mediating immune response,inflammatory response and transcriptional regulation.
3.Clinicopathological and molecular genetic features of Crohn′s disease
Yuxi GONG ; Chunni CHEN ; Yefan YANG ; Shuning SUN ; Yang SHAO ; Liuqing ZHU ; Yuqian SHI ; Xiao LI ; Xue HAN ; Zhihong ZHANG
Chinese Journal of Pathology 2024;53(4):351-357
Objective:To investigate the clinicopathological and molecular genetic characteristics of Crohn′s disease (CD).Methods:A retrospective analysis was conducted on 52 CD patients who underwent surgical resection at the First Affiliated Hospital of Nanjing Medical University between January 2014 and June 2023. Clinical presentations and histopathological features were assessed. Whole-genome sequencing was performed on 17 of the samples, followed by sequencing and pathway enrichment analyses. Immunohistochemistry was used to assess the expression of frequently mutated genes.Results:Among the 52 patients, 34 were males and 18 were females, male-to-female ratio was 1.9∶1.0, with a median age of 45 years at surgery and 35 years at diagnosis. According to the Montreal classification, A3 (51.9%,27/52), B2 (61.5%, 32/52), and L3 (50.0%,26/52) subtypes were the most predominant. Abdominal pain and diarrhea were the common symptoms. Histopathological features seen in all 52 patients included transmural inflammation, disruption of cryptal architecture, lymphoplasmacytic infiltration, varying degrees of submucosal fibrosis and thickening, increased enteric nerve fibers and neuronal proliferation. Mucosal defects, fissure ulcers, abscesses, pseudopolyps, and adenomatous proliferation were also observed in 51 (98.1%), 38 (73.1%), 28 (53.8%), 45 (86.5%), and 28 (53.8%) cases, respectively. Thirty-one (59.6%) cases had non-caseating granulomas, and 3 (5.8%) cases had intestinal mucosal glandular epithelial dysplasia. Molecular analysis showed that 12/17 CD patients exhibited mutations in at least one mucin family gene (MUC2, MUC3A, MUC4, MUC6, MUC12, MUC17), and MUC4 was the most frequently mutated in 7/17 of cases. Immunohistochemical stains showed reduced MUC4 expression in epithelial cells, with increased MUC4 expression in the epithelial surface, particularly around areas of inflammatory cell aggregation; and minimal expression in the lower half of the epithelium.Conclusions:CD exhibits diverse clinical and pathological features, necessitating a comprehensive multidimensional analysis for diagnosis. Mutations and expression alterations in mucin family genes, particularly MUC4, may play crucial roles in the pathogenesis of CD.
4.Venetoclax combined with dose-reduced HAD as induction treatment for patients with de-novo acute myeloid leukemia
Zhangsong YAN ; Yang LI ; Bin ZHANG ; Jinsong HE ; Jiesi LI ; Shuning WEI ; Qi WANG ; Qiuling LI ; Kaiqi LIU ; Yingchang MI
Chinese Journal of Hematology 2024;45(4):387-390
The efficacy and safety of venetoclax combined with reduced dose HAD regimen in the treatment of newly diagnosed acute myeloid leukemia (AML) was investigated. From May 2022 to January 2023, a total of 25 patients with newly diagnosed AML were treated with venetoclax combined with reduced-dose HAD regimen as induction therapy. Accoding to the 2017 ELN recommendations, 13 (52.0%) in favoable, 3 (12.0%) in intemediate, and 9 (36.0%) in adverse. The ORR (CR rate+PR rate) was 88.0%, and the CR rate was 84.0%. By May 30, 2023, with a median follow-up of 9 months, 1 year overall survival, event-free survival, and relapse-free survival were 100%, 94.7%, and 94.7%, respectively. All patients received 1-5 cycles of consolidation therapy and two median cycles. Treatment with venetoclax and reduced dose of HAD regimen in the treatment of patients with newly diagnosed AML was high effective and safe.
5.PenKid is a risk factor for sepsis-associated acute kidney injury and death
Xuehua PU ; Ning GAO ; Dezhang WU ; Guang ZHU ; Shuning LI ; Haitao HU ; Jilu YE
Chinese Journal of Emergency Medicine 2023;32(8):1077-1082
Objective:To investigate the predictive value of serum proenkephalin A 119-159 (penKid) on incidence and the 28-day mortality in patients with sepsis-associated acute kidney injury (SA-AKI).Methods:This study was a single center, observational cohort study. Sepsis/septic shock patients admitted to Department of Critical Care Medicine of Taizhou People's Hospital Affiliated to Nanjing Medical University from September 2021 to September 2022 were selected and divided into the SA-AKI group and the non-SA-AKI group according to whether acute kidney injury (AKI) occurred within 28 days. Patients in the SA-AKI group were subdivided into the death group and the survival group according to whether death occurred within 28 days. Baseline data and laboratory indicators such as penKid concentration were compared among different groups. COX regression analysis was used to explore the risk factors of death within 28 days in the SA-AKI patients, And Kaplan-Meier curve was used to analyze patient prognosis.Result:A total of 161 patients were included in this study, of whom 66 (41.0%) developed AKI. The baseline penKid concentration in the SA-AKI group was significantly higher than that in the non-SA-AKI group [(2.99 ± 0.68) μg/L vs. (1.86±0.75) μg/L, P<0.05]. Multivariate COX regression analysis showed that the baseline penKid ( HR=5.608, 95% CI: 3.507-8.967, P<0.001) and lactate (LA) ( HR=1.089, 95% CI: 1.003-1.183, P=0.043) were independent risk factors for AKI in sepsis/septic shock patients. Of the 66 SA-AKI patients, 27 (40.9%) died within 28 days, and the baseline penKid concentration in the death group was significantly higher than that in the survival group [ (3.55 ± 0.54) μg/L vs. (2.60±0.47) μg/L, P<0.05]. COX regression analysis showed that penKid ( HR=5.892, 95% CI: 2.457-14.132, P<0.001) was an independent risk factor for mortality in SA-AKI patients. Kaplan-Meier curve showed that the 28-day mortality of patients with baseline penKid ≥ 3.24 μg/L was significantly higher than that of patients with baseline penKid <3.24 μg/L ( P<0.001). Conclusions:In sepsis/septic shock patients, the penKid concentration measured on the first day in the SA-AKI group is significantly higher than that in the non-SA-AKI group. In SA-AKI patients, the penKid concentration measured in patients who survived within 28 days is significantly lower than that in the death group. PenKid is an independent risk factor for the occurrence and death of SA-AKI.
6.Phenytoin induced chorea: a case report and literature review
Shuning DU ; Yang LI ; Xinyao LI ; Yuling TIAN ; Qiuyan WANG
Chinese Journal of Neurology 2023;56(11):1290-1293
Chorea is a rare adverse effect of phenytoin and is common in children, with widely variable clinical presentations. This article reported a case of an elderly woman presented chorea without nystagmus, ataxia, dysarthria and other typical vestibular-cerebellar symptoms, who took compound theophylline and ephedrine contained phenytoin to treat asthma for 1 year. The serum phenytoin concentrations were at toxic levels and chorea disappeared within 3 days after discontinuation of the drug. The clinical features of previously reported cases of phenytoin-induced chorea were also summarized.
7.Progress in research and application of risk assessment methods for imported malaria in China
Shuo YANG ; Hanyin YANG ; Shuning YAN ; Jiarui LIANG ; Mengru LI ; Bin ZHENG ; Zhigui XIA ; Shang XIA
Chinese Journal of Epidemiology 2023;44(11):1820-1824
With the gradual resumption of international travel, cross-border population movement has become frequent again, risk assessment of imported malaria has important public health significance to maintain malaria elimination status in China. Currently, risk index system construction method, risk index method, mathematical model method, and infectivity-receptivity- vulnerability method are mainly used in imported malaria risk assessment in China. This paper summarizes the common evaluation methods in the risk assessment of imported malaria research in China to provide references for the further research.
8.Acute leukemia with NUP98-DDX10 fusion gene-positive: report of 2 cases and review of literature
Zhe WANG ; Shuning WEI ; Qishan HAO ; Chengwen LI ; Zheng TIAN ; Yingchang MI
Journal of Leukemia & Lymphoma 2022;31(7):412-418
Objective:To investigate the clinical characteristics, diagnosis, treatment and prognosis of acute leukemia (AL) with NUP98-DDX10 fusion gene-positive.Methods:The clinical data of 2 AL patients with NUP98-DDX10 fusion gene-positive who admitted to Blood Diseases Hospital, Chinese Academy of Medical Sciences in April 2020 and February 2021, respectively were retrospectively analyzed. Transcriptome gene sequencing was used to detect fusion gene, and the fusion gene fragment was amplified by using reverse transcription polymerase chain reaction (RT-PCR), and Sanger sequencing was used to clarify sequences. The clinical and experimental indicators characteristics were analyzed and the relevant literatures were reviewed.Results:According to the clinical diagnosis, 1 patient was diagnosed as acute myeloid leukemia M 5 (AML-M 5) and 1 patient was diagnosed as acute leukemia of ambiguous lineage, not otherwise specified (ALAL-NOS). The AML-M 5 patient presented with severe coagulation abnormalities, and fulfilled the diagnostic criteria for diffuse intravascular coagulation (DIC) at the initial visit. Transcriptome sequencing of 2 patients showed NUP98-DDX10 fusion gene- positive. RT-PCR confirmed that sequencing results identified 2 different splice fusion modes: one was NUP98 exon 14 fused with DDX10 exon 7(usually called "type Ⅱ"), the other was NUP98 exon 14 fused with DDX10 exon 13, which was never reported and named as "type Ⅳ". From 1997 to 2018, a total of 16 cases with NUP98-DDX10 related hematologic neoplasms were reported in the literature. A summary analysis of 16 cases added with 2 patients in our center included 13 males and 5 females with median age 31.5 years (0.08-61 years). The median overall survival was 12 months (1-46 months). Conclusions:A novel fusion gene NUP98-DDX10 transcriptome is identified in ALAL-NOS patient. Hematological malignancies with NUP98-DDX10 are very rare. They respond poorly to conventional treatment and require allogeneic hematopoietic stem cell transplantation (allo-HSCT) to improve the prognosis.
9.Vestibular dysfunction in Wernicke encephalopathy
Hui LI ; Chunling LIU ; Yanlu JIA ; Mengya XU ; Yuanyuan SUN ; Xueqing CUI ; Jun WU ; Yimin ZHAO ; Shuning SUN
Chinese Journal of Neurology 2022;55(8):854-860
Objective:To analyze the abnormal vestibular function of Wernicke encephalopathy (WE) and to explore its diagnostic value.Methods:WE patients who visited the Vertigo Center of the Second Affiliated Hospital of Zhengzhou University from January 2018 to January 2021 were retrospectively collected. All patients were evaluated by clinical neurology. Before treatment, all patients completed video head impulse test (vHIT) and video nystagmusgraphy (VNG) in addition to cranial magnetic resonance and serum thiamine level examination.Results:All 12 patients had a history of eating defects, including 8 cases of alcoholism. All 12 patients had walking instability, 7 cases had dizziness and 8 cases had oscillopsia. Six cases had ophthalmoplegia. All 12 cases showed positive gaze nystagmus. The pathological saccades of bilateral horizontal semicircular canals were found in 12 patients by vHIT before treatment, but there was only 1 patient showing abnormality in vertical semicircular canals, the difference being statistically significant ( P<0.05). All patients could detect bilateral, horizontal, gaze-evoked nystagmus, including 3 cases with vertical nystagmus, 1 case with abnormal saccade test, 3 cases with abnormal smooth tracking test and 1 case with abnormal optokinetic test. There were abnormalities in the caloric test, including 6 cases of bilateral dysfunction and 2 cases of unilateral dysfunction. Conclusions:WE patients may have abnormal vHIT and bilateral, horizontal, gaze-evoked nystagmus, which is similar to the special abnormal signs of simultaneous damage of both peripheral and central vestibular dysfunction.Vestibular function test is valuable for diagnosis of WE, and it is suitable for patients with a history of nutritional disorders who have dizziness or walking instability and suspected WE.
10.Quantitative determination of D4-cystine in mice using LC-MS/MS and its application to the assessment of pharmacokinetics and bioavailability
Li SHUNING ; Lu ZHENYAO ; Jiao LI ; Zhang RAN ; Hong YU ; Aa JIYE ; Wang GUANGJI
Journal of Pharmaceutical Analysis 2021;11(5):580-587
Cystine is the primary source material for the synthesis of glutathione.However,the pharmacokinetics and tissue distribution of cystine are largely unknown.A surrogate analyte D4-cystine was employed to generate calibration curves for the determination of levels of D4-cystine and endogenous cystine in mice by liquid chromatography-tandem mass spectrometry(LC-MS/MS).Validation assessments proved the sensitivity,specificity and reproducibility of the method with a lower limit of quantification(LLOQ)of 5 ng/mL over 5-5000 ng/mL in plasma.The pharmacokinetics of D4-cystine were evaluated after administering injections and oral solutions,both of which minimally impacted endogenous cystine levels.The absolute bioavailability of cystine was 18.6%,15.1%and 25.6%at doses of 25,50 and 100 mg/kg,respectively.Intravenously injected D4-cystine resulted in dramatically high plasma levels with reduced levels in the brain and liver.Intragastrically administered D4-cystine resulted in high levels in the plasma and stomach with relatively low levels in the lung,kidney,heart and brain.

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