CENPL, ISG20L2, LSM4, MRPL3 are four novel hub genes and may serve as diagnostic and prognostic markers in breast cancer

Yin, Jun; Lin, Chen; Jiang, Meng; Tang, Xuhai; Xie, Danlin; Chen, Jingwen; Ke, Rongqin

doi:10.1038/s41598-021-95068-6

Cited by 25 publications

(19 citation statements)

References 52 publications

(46 reference statements)

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“…A study of Ho et al showed the correlation between expression of LSM4 and ovarian cancer [ 90 ]. Interestingly, Yin et al reported that LSM4 significantly overexpressed in triple-negative breast cancer (TNBC) patients compared to other breast cancer subtypes, which strongly support our conclusion in this study [ 91 ]. In contrast, Wang et al found a consistent trend of LSM6 expression, which was down-regulated in Basal-like breast cancer subtype [ 92 ].…”

Section: Discussionsupporting

confidence: 91%

Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer

Wang

Phan

et al. 2021

Cancers

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In recent decades, breast cancer (BRCA) has become one of the most common diseases worldwide. Understanding crucial genes and their signaling pathways remain an enormous challenge in evaluating the prognosis and possible therapeutics. The “Like-Smith” (LSM) family is known as protein-coding genes, and its member play pivotal roles in the progression of several malignancies, although their roles in BRCA are less clear. To discover biological processes associated with LSM family genes in BRCA development, high-throughput techniques were applied to clarify expression levels of LSMs in The Cancer Genome Atlas (TCGA)-BRCA dataset, which was integrated with the cBioPortal database. Furthermore, we investigated prognostic values of LSM family genes in BCRA patients using the Kaplan–Meier database. Among genes of this family, LSM4 expression levels were highly associated with poor prognostic outcomes with a hazard ratio of 1.35 (95% confidence interval 1.21–1.51, p for trend = 3.4 × 10−7). MetaCore and GlueGo analyses were also conducted to examine transcript expression signatures of LSM family members and their coexpressed genes, together with their associated signaling pathways, such as “Cell cycle role of APC in cell cycle regulation” and “Immune response IL-15 signaling via MAPK and PI3K cascade” in BRCA. Results showed that LSM family members, specifically LSM4, were significantly correlated with oncogenesis in BRCA patients. In summary, our results suggested that LSM4 could be a prospective prognosticator of BRCA.

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Section: Discussionsupporting

confidence: 91%

Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer

Wang

Phan

et al. 2021

Cancers

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“…Breast cancer accounts for the largest number of datasets in TCGA. Yin et al integrated several bioinformatics tools and RNA in situ detection to identify and validate breast cancerrelated hub genes and found that the expression of four genes, including MRPL3, were upregulated in tumor tissues and correlated with cancer progression; these genes could serve as diagnostic and prognostic biomarkers (77). As a poor prognostic factor in breast cancer, MRPL13 expression is significantly higher in cancer tissues than in normal tissues (78)(79)(80).…”

Section: Prognosismentioning

confidence: 99%

Potential of Mitochondrial Ribosomal Genes as Cancer Biomarkers Demonstrated by Bioinformatics Results

Bao

Wang

et al. 2022

Front. Oncol.

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Next-generation sequencing and bioinformatics analyses have clearly revealed the roles of mitochondrial ribosomal genes in cancer development. Mitochondrial ribosomes are composed of three RNA components encoded by mitochondrial DNA and 82 specific protein components encoded by nuclear DNA. They synthesize mitochondrial inner membrane oxidative phosphorylation (OXPHOS)-related proteins and participate in various biological activities via the regulation of energy metabolism and apoptosis. Mitochondrial ribosomal genes are strongly associated with clinical features such as prognosis and foci metastasis in patients with cancer. Accordingly, mitochondrial ribosomes have become an important focus of cancer research. We review recent advances in bioinformatics research that have explored the link between mitochondrial ribosomes and cancer, with a focus on the potential of mitochondrial ribosomal genes as biomarkers in cancer.

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“…The small nuclear ribonucleoprotein Sm-like4 ( LSM4 ) has been shown to be involved in the occurrence and malignant procession of BRCA, pancreatic cancer (PC), and ovarian cancer (OC) ( Xue et al, 2018 ; Ta et al, 2021 ). For example, the expression of LSM4 in BRCA was significantly increased and was closely related to lymph node metastasis and tumor cell proliferation ( Yin et al, 2021 ). In OC, LSM4 knockdown blocked cell migration and invasion of OC cells, and LSM4 overexpression reversed the inhibitory effect of circ_0,025,033 knockdown on the above process ( Hou and Zhang, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Clinical Significance and Potential Role of LSM4 Overexpression in Hepatocellular Carcinoma: An Integrated Analysis Based on Multiple Databases

et al. 2022

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Background: Hepatocellular carcinoma (HCC) is a solid tumor with high recurrence rate and high mortality. It is crucial to discover available biomarkers to achieve early diagnosis and improve the prognosis. The effect of LSM4 in HCC still remains unrevealed. Our study is dedicated to exploring the expression of LSM4 in HCC, demonstrating its clinical significance and potential molecular mechanisms.Methods: Clinical information and LSM4 expression values of HCC were obtained from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Survival analysis and receiver operating characteristic (ROC) curve analysis were applied to evaluate the prognostic and diagnostic significance of LSM4. Calculating pooled standardized mean difference (SMD) and performing summary receiver operating characteristic (sROC) curve analysis to further determine its expression status and diagnostic significance. LSM4-related co-expressed genes (CEGs) were obtained and explored their clinical significance in HCC. LSM4-associated pathways were identified through Gene set enrichment analysis (GSEA).Results: Up-regulated LSM4 was detected in HCC tissues (SMD = 1.56, 95% CI: 1.29–1.84) and overexpressed LSM4 had excellent distinguishing ability (AUC = 0.91, 95% CI: 0.88–0.93). LSM4 was associated with clinical stage, tumor grade, and lymph node metastasis status (p < 0.05). Survival analysis showed that high LSM4 expression was related to poor overall survival (OS) of HCC patients. Cox regression analysis suggested that high LSM4 expression may be an independent risk factor for HCC. We obtained nine up-regulated CEGs of LSM4 in HCC tissues, and six CEGs had good prognostic and diagnostic significance. GSEA analysis showed that up-regulated LSM4 was closely related to the cell cycle, cell replication, focal adhesion, and several metabolism-associated pathways, including fatty acid metabolism.Conclusion: Overexpressed LSM4 may serve as a promising diagnostic and prognostic biomarker of HCC. Besides, LSM4 may play a synergistic effect with CEGs in promoting the growth and metastasis of HCC cells via regulating crucial pathways such as cell cycle, focal adhesion, and metabolism-associated pathways.

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CENPL, ISG20L2, LSM4, MRPL3 are four novel hub genes and may serve as diagnostic and prognostic markers in breast cancer

Cited by 25 publications

References 52 publications

Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer

Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer

Potential of Mitochondrial Ribosomal Genes as Cancer Biomarkers Demonstrated by Bioinformatics Results

Clinical Significance and Potential Role of LSM4 Overexpression in Hepatocellular Carcinoma: An Integrated Analysis Based on Multiple Databases

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