Analysis of mRNA‑lncRNA and mRNA‑lncRNA-pathway co‑expression networks based on WGCNA in developing pediatric sepsis

Zhang, Xiaojuan; Cui, Yuqing; Ding, Xianfei; Liu, Shaohua; Han, Bing; Duan, Xiaoguang; Zhang, Haibo; Sun, Tongwen

doi:10.1080/21655979.2021.1908029

Cited by 53 publications

(37 citation statements)

References 42 publications

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“…In addition, Gong et al showed nine genes in three datasets (GSE95233, GSE57065, and GSE28750) that had diagnostic value for sepsis, some of which were validated by real-time PCR [ 24 ]. Zhang et al reported 4 lncRNAs and 15 mRNAs as the critical genes for diagnosing paediatric sepsis based on WGCNA [ 25 ]. Although several studies have found potential genetic markers for diagnosing sepsis, their sample size was small, and there was not enough verification of their results on other datasets.…”

Section: Discussionmentioning

confidence: 99%

[Retracted] Identification of a Four‐Gene Signature for Diagnosing Paediatric Sepsis

Yao

Zhao

et al. 2022

BioMed Research International

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Aim. Early diagnosis of paediatric sepsis is crucial for the proper treatment of children and reduction of hospitalization and mortality. Biomarkers are a convenient and effective method for diagnosing any disease. However, huge differences among the studies reporting biomarkers for diagnosing sepsis have limited their clinical application. Therefore, in this study, we aimed to evaluate the diagnostic value of key genes involved in paediatric sepsis based on the data of the Gene Expression Omnibus database. Methods. We used the GSE119217 dataset to identify differentially expressed genes (DEGs) between patients with and without paediatric sepsis. The most relevant gene modules of paediatric sepsis were screened through the weighted gene coexpression network analysis (WGCNA). Common genes (CGs) were found between DEGs and WGCNA. Genes with a potential diagnostic value in paediatric sepsis were selected from the CGs using least absolute shrinkage and selection operator regression and support vector machine recursive feature elimination. The principal component analysis, receiver operating characteristic curves, and C-index were used to verify the diagnostic value of the identified genes in six other independent sepsis datasets. Subsequently, a meta-analysis of the selected genes was performed to evaluate the value of these genes as biomarkers in paediatric sepsis. Results. A total of 41 CGs were selected from the GSE119217 dataset. A four-gene signature composed of ANXA3, CD177, GRAMD1C, and TIGD3 effectively distinguished patients with paediatric sepsis from those in the control group. The signature was verified using six other independent datasets. In addition, the meta-analysis results showed that the pooled sensitivity, specificity, and area under the curve values were 1.00, 0.98, and 1.00, respectively. Conclusion. The four-gene signature can be used as new biomarkers to distinguish patients with paediatric sepsis from healthy individuals.

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Section: Discussionmentioning

confidence: 99%

[Retracted] Identification of a Four‐Gene Signature for Diagnosing Paediatric Sepsis

Yao

Zhao

et al. 2022

BioMed Research International

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“…Due to their lack of protein-coding potential, they were initially defined as transcriptional noises without biological functions. Nevertheless, their abundance in the mammalian genome and various coding-independent functions enable them to be actively implicated in different cellular processes [ 4 , 5 ]. Apart from the aberrant expression of protein-coding genes, dysregulation of lncRNAs, like other non-coding RNAs, is critical in tumorigenesis and cancer progression [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

RETRACTED ARTICLE: The long non-coding RNA ASMTL-AS1 promotes hepatocellular carcinoma progression by sponging miR-1343-3p that suppresses LAMC1 (laminin subunit gamma 1)

Mou

Sun

2021

Bioengineered

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Long non-coding RNAs (lncRNAs) are critical regulators of hepatocellular carcinoma (HCC) carcinogenesis and development. We aimed to identify the function of the lncRNA ASMTL-AS1 during HCC malignancy. The expression of ASMTL-AS1, miR-1343-3p, and LAMC1 (laminin subunit gamma 1) was assessed in HCC tissues and cells. Cell Counting Kit-8 (CCK8) and Transwell migration assays were performed to determine the effect of ASMTL-AS1 on HCC cell proliferation and migration. Cell apoptosis was identified by detecting Bax and Bcl-2 protein expression using Western blotting, and a xenograft assay was performed to investigate tumor growth in vivo . The interplay between miR-1343-3p and ASMTL-AS1 or LAMC1 was verified through luciferase reporter and RNA immunoprecipitation assays. ASMTL-AS1 and LAMC1 were highly expressed in HCC tissues and cells, whereas miR-1343-3p showed low expression. Clinically, miR-1343-3p expression in HCC tissues showed a negative correlation with ASMTL-AS1 or LAMC1 expression. Functional assays demonstrated that ASMTL-AS1 silencing suppressed HCC cell proliferation and migration and increased cell apoptosis. More interestingly, ASMTL-AS1 sponged miR-1343-3p and miR-1343-3p to target the 3ʹ-UTR of LAMC1, thereby interfering with the malignant behavior of HCC cells. In conclusion, ASMTL-AS1 acts as a carcinogen in HCC through competing endogenous RNA (ceRNA) activity in the miR-1343-3p/LAMC1 axis. Our findings demonstrate that regulating ASMTL-AS1/miR-1343-3p/LAMC1-mediated HCC cell malignancy might be an effective method to interfere with HCC progression.

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“…LncRNAs are a family of RNAs with more than 200 nucleotides in length which do not code for proteins [ 5 ]. A growing number of studies have recently demonstrated that aberrant expression of lncRNAs play vital roles in many different types of human cancer, including OSCC, osteosarcoma, hepatocellular carcinoma, nasopharyngeal carcinoma, and gastric cancer [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

Long non-coding RNA HOXA-AS3 promotes cell proliferation of oral squamous cell carcinoma through sponging microRNA miR-218-5p

Zhao

Yao

2021

Bioengineered

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Increasing evidence demonstrated long non-coding RNAs (lncRNAs) play important roles in the occurrence and development of oral squamous cell carcinoma (OSCC). This study aimed to explore the role and molecular mechanism of lncRNA HOXA-AS3 in the progression of OSCC. Here, we found that t he expression of lncRNA HOXA-AS3 was upregulated in OSCC tissues and cell lines compared with the para-cancerous tissues and normal human oral keratinocyte (NHOK), respectively. Inhibition of HOXA-AS3 significantly inhibited the proliferation and colony formation of OSCC cells. Further, the luciferase reporter assay showed that HOXA-AS3 was directly bound to miR-218-5p. Moreover, the expression of miR-218-5p was negatively regulated by HOXA-AS3, and miR-218-5p could inhibit the expression of collagen type I alpha1 (COL1A1) and lysophosphatidylcholine acyltransferase 1 (LPCAT1). In addition, silencing miR-218-5p reversed the inhibitory effect of HOXA-AS3 knockdown on the proliferative potential of OSCC cells. In summary, our study illustrated that HOXA-AS3 promoted cancer cell proliferation in OSCC, possibly by sponging miR-218-5p for the first time, which provides a new target or a potential diagnostic biomarker for OSCC.

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Analysis of mRNA‑lncRNA and mRNA‑lncRNA-pathway co‑expression networks based on WGCNA in developing pediatric sepsis

Cited by 53 publications

References 42 publications

[Retracted] Identification of a Four‐Gene Signature for Diagnosing Paediatric Sepsis

[Retracted] Identification of a Four‐Gene Signature for Diagnosing Paediatric Sepsis

RETRACTED ARTICLE: The long non-coding RNA ASMTL-AS1 promotes hepatocellular carcinoma progression by sponging miR-1343-3p that suppresses LAMC1 (laminin subunit gamma 1)

Long non-coding RNA HOXA-AS3 promotes cell proliferation of oral squamous cell carcinoma through sponging microRNA miR-218-5p

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