1.From Gene Expression to Transcriptome-wide Association Study: Development and Comparison of Methodology
Kun FANG ; Guozhuang LI ; Linting WANG ; Qing LI ; Kexin XU ; Lina ZHAO ; Zhihong WU ; Jianguo ZHANG ; Nan WU
Medical Journal of Peking Union Medical College Hospital 2026;17(1):223-229
Over the past two decades, genome-wide association study(GWAS) has identified numerous genetic variants and loci associated with heritable diseases. With the gradual maturation and saturation of GWAS methodologies, transcriptome-wide association study(TWAS) offers a novel perspective by linkinggenetic phenotypes to gene expression levels. By integrating TWAS with other multi-omics analyses, researchers can gain a deeper understanding of heritable diseases. This article provides an overview of recent groundbreaking and representative TWAS methods and tools, analyzes their strengths and limitations, and discusses future trends in TWAS development.
2.Screening and validation of chemoresistance marker in lung adenocarcinoma based on gene expression profile
Handong Wei ; Shuxing Chen ; Linting Liu ; Zihan Jing ; Yiting Yang ; Qiong Song ; Wenchu Wang ; Chunlin Zou ; Lihui Wang
Acta Universitatis Medicinalis Anhui 2025;60(10):1818-1827
Objective:
To discover molecular markers associated with lung adenocarcinoma diagnosis/prognosis and drug resistance through screening of differentially expressed genes based on published chip data in gene expression databases using bioinformatics methods.
Methods:
Comprehensive analysis was performed in available mRNA microarray datasets including lung adenocarcinoma tissues dataset GSE32863 and lung adenocarcinoma taxane-platin resistance dataset GSE77209 from the gene expression omnibus(GEO) database. Gene ontology enrichment analysis, gene pathway enrichment analysis and protein interaction network analysis were performed based on significantly correlated genes. The expression level of genes was validated in the cancer genome atlas(TCGA) dataset. Survival differences were assessed by the log-rank test in TCGA lung adenocarcinoma dataset. Based on the publications genomics of drug sensitivity in cancer(GDSC) database in CellMiner cross database(CellMiner CDB), Pearson correlation analysis was used to analyze the correlation between differentially expressed genes and the half-maximal inhibitory concentration(IC50) of anticancer drugs.
Results :
There were a total of 77 genes which had a different expression in resistance lung adenocarcinoma cells and lung adenocarcinoma cancer tissues. The functional enrichment analysis showed that these co-different expression genes were mainly enriched in microtubule, extracellular exosome, cell cycle and signaling by nuclear receptors. Protein-protein interactions(PPI) network screened 6 most connected genes as molecular complex(MCODE). Among the MCODE, overexpressed ubiquitin conjugating enzyme E2 T(UBE2T), kinesin family member 20A(KIF20A), PCNA clamp associated factor(KIAA0101), pituitary tumor-transforming gene 1(PTTG1) and NIMA related kinase 2(NEK2) were associated with poor outcomes. Survival analysis results showed that these five genes were upregulated in lung adenocarcinoma tissues and drug-resistant cells and were significantly associated with poor prognosis in lung adenocarcinoma patients. Drug sensitivity analysis results suggested that high expression of PTTG1 and UBE2T was significantly associated with sensitivity to multiple anticancer drugs, including paclitaxel and docetaxel. RT-PCR validation showed that PTTG1 andUBE2T were highly expressed in docetaxel-resistant cells A549-TXR and H358-TXR.
Conclusion
PTTG1 andUBE2T holds the potential to be chemoresistance markers in lung adenocarcinoma.
3.Triptolide ameliorates renal interstitial fibrosis in mice with unilateral ureteral obstruction by inhibiting NLRP3-mediated pyroptosis
Linting WEI ; Pengbo GE ; Yan LI ; Ke LI ; Yinhong WANG ; Weihao ZHAO ; Chenkai CUI ; Rongguo FU
Journal of Xi'an Jiaotong University(Medical Sciences) 2025;46(6):947-952
Objective To investigate the effect of triptolide(TPL)on renal interstitial fibrosis in mice with unilateral ureteral obstruction(UUO)and its mechanism.Methods Six male C57BL/6J mice were randomly selected as the sham group,and 12 mice with UUO modeling were randomly divided into the model group(UUO)and the triptolide group(TPL).Changes in serum creatinine(SCr),blood urea nitrogen(BUN),and body weight were compared among the groups.Renal tissue specimens were collected at 14 d after UUO for HE and Masson staining.Immunohistochemistry staining was performed to observe the expression of α-smooth muscle actin(α-SMA)and fibronectin(Fn)in kidney tissues.Western blotting analysis was used to detect the protein expression levels of nucleotide combined with structure of oligomerization domain receptor protein 3(NLRP3),GSDMD,cGSDMD,IL-1β and IL-18.Results At week 1,the body weight of mice in the UUO and TPL groups significantly decreased compared with that in the sham group(P<0.05).Body weight reduced in the TPL group compared with that in the Sham group at week 2(P<0.01).There was no significant difference in body weight between the TPL and UUO groups.BUN levels did not differ significantly between the three groups.Compared with the sham group,the SCr level in the UUO group significantly increased[(15.680±1.508)μmol/L](P<0.01).A reduction in SCr level was observed following TPL administration[(12.550±3.004)μmol/L](P<0.05).HE staining showed that the renal tubules of mice in the UUO group were significantly dilated and atrophic,with interstitial edema and increased inflammatory cell infiltration,while the pathological damage of renal tissues was significantly alleviated after TPL treatment.Masson staining revealed that interstitial collagen deposition significantly increased in the UUO group(36.350±5.183)%(P<0.01)and reduced after TPL administration(20.820±3.290)%(P<0.01).Immunohistochemistry results demonstrated that the IOD levels of α-SMA(1.233±0.045)and Fn(1.337±0.045)were higher in UUO group mice than in the sham group,while the IOD levels of α-SMA(1.047±0.025)and Fn(1.113±0.021)were lower in the TPL group than in the UUO group(P<0.05).Western blotting analysis indicated that the expression levels of NLRP3,cGSDMD,IL-1β and IL-18 in the UUO group mice were higher than those in the sham group,while the protein expression levels of the above-mentioned indicators significantly decreased after TPL treatment(P<0.05).Conclusion TPL ameliorates renal interstitial fibrosis in mice with UUO by inhibiting NLRP3-mediated pyroptosis.
4.Summary of best evidence on discharge preparation services for adult patients with bronchial asthma
Linting BAI ; Shuying LI ; Yajing CHEN ; Jie SHI ; Caili NIU ; Xuemin WANG ; Xinxin RAN
Chinese Journal of Modern Nursing 2025;31(2):176-183
Objective:To search, evaluate, and summarize the best evidence regarding discharge preparation services for adult patients with bronchial asthma, providing references for clinical practice and guideline development.Methods:A computer search was conducted in BMJ Best Practice, UpToDate, PubMed, Australia Joanna Briggs Institute Evidence-based Healthcare Center Database, Cochrane Library, Embase, CINAHL, Web of Science, China National Knowledge Infrastructure, Wanfang Database, and China Biology Medicine disc, as well as relevant guideline and professional websites. The search period covered from the establishment of the databases to June 30, 2024. Two researchers independently conducted quality assessments of the included literature, evidence extraction, and synthesis.Results:A total of 14 articles were included, comprising five guidelines, four expert consensus, and five systematic reviews. Twenty-three pieces of evidence were summarized across six aspects: discharge preparation objectives, discharge preparation principles, health guidance during hospitalization, pre-discharge preparation, discharge instructions, and post-discharge follow-up.Conclusions:The best evidence for discharge preparation services for adult patients with bronchial asthma summarized in this study can be applied by clinical healthcare providers in China, considering the specific clinical context, to help adult patients with bronchial asthma manage their condition.
5.Triptolide ameliorates renal interstitial fibrosis in mice with unilateral ureteral obstruction by inhibiting NLRP3-mediated pyroptosis
Linting WEI ; Pengbo GE ; Yan LI ; Ke LI ; Yinhong WANG ; Weihao ZHAO ; Chenkai CUI ; Rongguo FU
Journal of Xi'an Jiaotong University(Medical Sciences) 2025;46(6):947-952
Objective To investigate the effect of triptolide(TPL)on renal interstitial fibrosis in mice with unilateral ureteral obstruction(UUO)and its mechanism.Methods Six male C57BL/6J mice were randomly selected as the sham group,and 12 mice with UUO modeling were randomly divided into the model group(UUO)and the triptolide group(TPL).Changes in serum creatinine(SCr),blood urea nitrogen(BUN),and body weight were compared among the groups.Renal tissue specimens were collected at 14 d after UUO for HE and Masson staining.Immunohistochemistry staining was performed to observe the expression of α-smooth muscle actin(α-SMA)and fibronectin(Fn)in kidney tissues.Western blotting analysis was used to detect the protein expression levels of nucleotide combined with structure of oligomerization domain receptor protein 3(NLRP3),GSDMD,cGSDMD,IL-1β and IL-18.Results At week 1,the body weight of mice in the UUO and TPL groups significantly decreased compared with that in the sham group(P<0.05).Body weight reduced in the TPL group compared with that in the Sham group at week 2(P<0.01).There was no significant difference in body weight between the TPL and UUO groups.BUN levels did not differ significantly between the three groups.Compared with the sham group,the SCr level in the UUO group significantly increased[(15.680±1.508)μmol/L](P<0.01).A reduction in SCr level was observed following TPL administration[(12.550±3.004)μmol/L](P<0.05).HE staining showed that the renal tubules of mice in the UUO group were significantly dilated and atrophic,with interstitial edema and increased inflammatory cell infiltration,while the pathological damage of renal tissues was significantly alleviated after TPL treatment.Masson staining revealed that interstitial collagen deposition significantly increased in the UUO group(36.350±5.183)%(P<0.01)and reduced after TPL administration(20.820±3.290)%(P<0.01).Immunohistochemistry results demonstrated that the IOD levels of α-SMA(1.233±0.045)and Fn(1.337±0.045)were higher in UUO group mice than in the sham group,while the IOD levels of α-SMA(1.047±0.025)and Fn(1.113±0.021)were lower in the TPL group than in the UUO group(P<0.05).Western blotting analysis indicated that the expression levels of NLRP3,cGSDMD,IL-1β and IL-18 in the UUO group mice were higher than those in the sham group,while the protein expression levels of the above-mentioned indicators significantly decreased after TPL treatment(P<0.05).Conclusion TPL ameliorates renal interstitial fibrosis in mice with UUO by inhibiting NLRP3-mediated pyroptosis.
6.Summary of best evidence on discharge preparation services for adult patients with bronchial asthma
Linting BAI ; Shuying LI ; Yajing CHEN ; Jie SHI ; Caili NIU ; Xuemin WANG ; Xinxin RAN
Chinese Journal of Modern Nursing 2025;31(2):176-183
Objective:To search, evaluate, and summarize the best evidence regarding discharge preparation services for adult patients with bronchial asthma, providing references for clinical practice and guideline development.Methods:A computer search was conducted in BMJ Best Practice, UpToDate, PubMed, Australia Joanna Briggs Institute Evidence-based Healthcare Center Database, Cochrane Library, Embase, CINAHL, Web of Science, China National Knowledge Infrastructure, Wanfang Database, and China Biology Medicine disc, as well as relevant guideline and professional websites. The search period covered from the establishment of the databases to June 30, 2024. Two researchers independently conducted quality assessments of the included literature, evidence extraction, and synthesis.Results:A total of 14 articles were included, comprising five guidelines, four expert consensus, and five systematic reviews. Twenty-three pieces of evidence were summarized across six aspects: discharge preparation objectives, discharge preparation principles, health guidance during hospitalization, pre-discharge preparation, discharge instructions, and post-discharge follow-up.Conclusions:The best evidence for discharge preparation services for adult patients with bronchial asthma summarized in this study can be applied by clinical healthcare providers in China, considering the specific clinical context, to help adult patients with bronchial asthma manage their condition.
7.TRPC6 involves in endoplasmic reticulum stress induced apoptosis of glomerular mesangial cells
Linting WEI ; Pengbo GE ; Xiaoqin MA ; Jie GAO ; Dan LIU ; Peng ZHAO ; Shizhuo WEI ; Jing DONG ; Li WANG ; Rongguo FU
Journal of Xi'an Jiaotong University(Medical Sciences) 2023;44(6):898-903
【Objective】 To explore the role and mechanism of TRPC6 in apoptosis of glomerular mesangial cells (HBZY-1) induced by endoplasmic reticulum stress (ERS). 【Methods】 The experiment groups were classified as follows: normal control (NC), thapsigargin (TG), TG+SKF96365, and TG+TRPC6 siRNA groups. Transcription and protein expressions of TRPC6 and ERS related proteins (GRP78 and Caspase12) were detected by qRT-PCR and Western blotting. Additionally, cell apoptosis was measured by flow cytometry and Hoechst33258. Finally, Fluo-4 AM Ca2+ imaging technique was used to determine changes of intracellular calcium ( [Ca2+] i) by laser scanning confocal microscope. 【Results】 Morphological changes of apoptotic cells were characterized by nuclear enrichment or nuclear fragmentation, and the apoptosis rate was increased after TG stimulation. The expressions of TRPC6 and ERS related proteins (GRP78 and Caspase12) were elevated in TG group compared with NC group (P<0.05). Pre-incubation of HBZY-1 cells with SKF96365 and TRPC6 siRNA decreased cell apoptosis (P<0.05). The entry of [Ca2+] i also increased after TG stimulation (P<0.05). The expressions of TRPC6, GRP78 and Caspase12 were downregulated compared with TG group after treatment with SKF96365 and TRPC6 siRNA accompanied by decreased [Ca2+] i (P<0.05). 【Conclusion】 Taken together, this study suggests that inhibition of TRPC6 can alleviate TG-induced HBZY-1 cell apoptosis.
8.Mechanism of TRPC in promoting extracellular matrix deposition of glomerular mesangial cells
Linting WEI ; Pengbo GE ; Ke LI ; Yan LI ; Yinhong WANG ; Weihao ZHAO ; Chenkai CUI ; Jing DONG ; Jie GAO ; Li WANG ; Rongguo FU
Journal of Xi'an Jiaotong University(Medical Sciences) 2023;44(4):518-524
【Objective】 To explore the role and mechanism of TRPC in promoting extracellular matrix (ECM) deposition in rat glomerular mesangial cells (HBZY-1). Methods Immunofluorescence staining was performed to observe the distribution and expression of TRPC1 and TRPC6 in HBZY-1 cells. After AngⅡ stimulation, qRT-PCR and Western blotting were used to detect the mRNA and protein expressions of Gαq/PLCβ4/TRPC signaling pathway main proteins and ECM deposition indicators (α-SMA, collagenⅢ and fibronectin). By silencing the expressions of TRPC1 and TRPC6 by RNA interference, the expressions of ECM deposition indicators were detected. Changes in [Ca2+]i influx were determined through Fluo-4AM Ca2+ imaging. 【Results】 Both TRPC1 and TRPC6 were expressed in HBZY-1, and were mainly located in cell membrane and cytoplasm. After AngⅡ stimulation, Gαq/PLCβ4/TRPC signaling pathway was activated, and the mRNA and protein expressions of Gαq, PLCβ4, TRPC1 and TRPC6 were all increased (P<0.05). [Ca2+]i influx also increased (P<0.01), and the mRNA and protein expressions of ECM deposition indicators (α-SMA, ColⅢ and Fn) were upregulated (P<0.05). Silencing the expressions of TRPC1 and TRPC6 by RNA interference led to decreased [Ca2+]i influx (P<0.05), and downregulated mRNA and protein expressions of ECM deposition indicators in HBZY-1 cells (P<0.05). The results suggested that inhibition of TRPC expressions could inhibit AngⅡ induced ECM deposition in HBZY-1 cells, which might be associated with decreased [Ca2+]i influx. 【Conclusion】 TRPC may be a novel therapeutic target of renal fibrosis.
9.Diagnosis and treatment recommendations of dialysis patients with SARS-CoV-2 infection for primary care clinicians
Rongguo FU ; Zhao CHEN ; Lining JIA ; Li WANG ; Jin HAN ; Lifang TIAN ; Xianghui CHEN ; Linting WEI ; Fuqian LEI ; Jiamei LU ; Xiaoqin MA ; Li ZHAO ; Shizhuo WEI ; Jing LIU ; Zhaoyang DUAN ; Jie GAO
Journal of Xi'an Jiaotong University(Medical Sciences) 2023;44(3):353-360
End-stage renal disease (ESRD) patients undergoing outpatient hemodialysis (HD) and home peritoneal dialysis (PD) are high risk population of severe and critical types caused by SARS-CoV-2 infection. In order to improve the quality of diagnosis and treatment in dialysis patients with SARS-CoV-2 infection, we wrote this recommendation for primary care clinicians. During the epidemic period of SARS-CoV-2 infection, all patients should be instructed to strengthen self-management. Once the SARS-CoV-2 infection was found in dialysis patients, early stratified management should be carried out within 72 hours after the first positive nucleic acid or antigen test results, which includes early antiviral therapy, early recognition, and transferring severe patients from community or primary hospital to a referral hospital promptly. Guidance for dietary and sports rehabilitation after SARS-CoV-2 infection should also be started as soon as possible.
10.A case of mitochondrial neurogastrointestinal encephalomyopathy
Guihua DUAN ; Hongrun YANG ; Min QI ; Zan ZUO ; Linting XUN ; Ying AN ; Jinshi WANG ; Qizhu LU ; Zhengji SONG
Chinese Journal of Inflammatory Bowel Diseases 2022;06(1):91-92
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is a rare autosomal recessive hereditary mitochondrial disease, which is mainly characterized by gastrointestinal and neurological system involvement. This article reports a rare case of MNGIE which presented as chronic diarrhea. The purpose is to improve the understanding of MNGIE.


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