Transcriptome profiling reveals an integrated mRNA–lncRNA signature with predictive value for long-term survival in diffuse large B-cell lymphoma

Gao, Qian; Li, Zhiyao; Meng, Lingxian; Ma, Jinsha; Xi, Yanfeng; Wang, Tong

doi:10.18632/aging.104100

Cited by 6 publications

(7 citation statements)

References 29 publications

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“…For example, the lncNBAT1-APOBEC3A network mediates HBX-induced chemoresistance and lncRNA TUG1 plays an oncogenic role by inhibiting MET ubiquitination (9). Some integrated lncRNA-mRNA signatures are also used for DLBCL prognosis (10). These findings support the use of the lncRNA-mRNA regulatory network as a potential predictive biomarker for DLBCL.…”

Section: Introductionmentioning

confidence: 60%

“…Instead, they help to regulate their target protein-coding genes at multiple levels, including epigenetic regulation, transcriptional regulation, and post-transcriptional regulation, and are involved in the progression of different tumors (4,5). Although some lncRNAs involved in DLBCL progression were identified using new sequencing technologies (9,10,22), the role of LINC00654 in DLBCL progression remains unknown. For the first time, LINC00654 was selected using a computational algorithm as the most important hub lncRNA associated with the PFI among patients with DLBCL, which is of significant diagnostic value.…”

Section: Discussionmentioning

confidence: 99%

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Identification of LINC00654-NINL Regulatory Axis in Diffuse Large B-Cell Lymphoma In Silico Analysis

Chen

Wang

et al. 2022

Front. Oncol.

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BackgroundThe long non-coding RNA (lncRNA)-mRNA regulation network plays an important role in the development of diffuse large B-cell lymphoma (DLBCL). This study uses bioinformatics to find an innovative regulation axis in DLBCL that will provide a positive reference for defining the mechanism of disease progression.MethodsBatch Cox regression was used to screen prognosis-related lncRNAs, and a random forest model was used to identify hub lncRNA. The clinical value of the lncRNA was evaluated and Spearman correlation analysis was used to predict the candidate target genes. Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were used to define the biological function of the lncRNA. A batch Cox regression model, expression validation, and Spearman correlation analysis were used to select the best downstream target genes. The expression and prognostic value validation of this gene was conducted using public data. Gene Set Enrichment Analysis (GSEA) was performed to explore potential mechanisms for this gene in DLBCL.ResultsLINC00654 was identified as the hub lncRNA and 1443 mRNAs were selected as downstream target genes of the lncRNA. The target genes were enriched in the regulation of GTPase and Notch signaling pathways. After validation, the ninein-like (NINL) gene was selected as the potential target of LINC00654 and the LINC00654-NINL axis was constructed. Patients with better responses to therapy were shown to have high NINL gene expression (p-value = 0.036). NINL also had high expression in the DB cell line and low expression in the OCILY3 cell line. Survival analysis showed that high NINL expression was a risk factor for overall survival (OS) and disease-specific survival (DSS) within older patients and those with advanced-stage cancer. GSEA results showed that NINL may be involved in neutrophil-mediated immunity and NF-κB signaling.ConclusionThis study identified a novel LncRNA00654-NINL regulatory axis in DLBCL, which could provide a favorable reference for exploring the possible mechanisms of disease progression.

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Section: Introductionmentioning

confidence: 60%

Section: Discussionmentioning

confidence: 99%

Identification of LINC00654-NINL Regulatory Axis in Diffuse Large B-Cell Lymphoma In Silico Analysis

Chen

Wang

et al. 2022

Front. Oncol.

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“…Like any other type of cancers, the un-controlled growth and metathetic ability of DLBC lead to the high recurrent and mortality rate of the disease [18][19][20]. Therefore, an effective molecular therapeutic target of DLBC should be a key regulator that affect the proliferation and migration of the DLBC cells.…”

Section: Discussionmentioning

confidence: 99%

LncRNA SNHG5 can Regulate the Proliferation and Migration of Diffuse Large B Cell Lymphoma Progression via Targeting miR-181-5p/XIAP

Xing¹,

Xu²,

Liu³

et al. 2022

J. Cancer

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Background: It has been verified that long noncoding RNAs (lncRNAs) may participate in the pathogenesis of various human diseases. This study aims to investigate the roles of lncRNA SNHG5 in diffuse large B cell lymphoma (DLBC), especially the impacts of lncRNA SNHG5 on proliferation and migration of human diffuse large B cell lymphoma cells and the related mechanism. Methods: qRT-PCR analysis was carried out to examine the expression pattern of SNHG5 in DLBC tissue and adjacent normal tissue. The effect of SNHG5 on the proliferation, apoptosis, migration, and invasion of DLBC cells was detected by MTT, flow cytometry analysis, wound healing assay and transwell assay. The correlation between SNHG5, miR-181-5p and XIAP were certified by bioinformatics analysis, and dual-luciferase reporter assay. Furthermore, rescue assays were performed to analyze the effects of SNHG5-miR-181-5p-XIAP axis on the biological behaviors of diffuse large B cell lymphoma cells. Finally, the effects of SNHG5 axis on the growth of DLBC tumor was examined by in vivo analysis. Results: SNHG5 was significantly upregulated in diffuse large B cell lymphoma tissues. Knockdown of SNHG5 inhibited the proliferation, migration, and invasion of diffuse large B cell lymphoma cells in vitro and in vivo. LncRNA SNHG5 acted as a ceRNA through binding with miR-181-5p in DLBC cells. Conclusion: LncRNA SNHG5 may promote proliferation and migration of diffuse large B cell lymphoma cells via targeting miR-181-5p/XIAP.

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“…To date, predictive risk models based on mRNAs, 26 , 41 miRNAs, 42 , 43 lncRNAs, 44 , 45 , 46 and circRNAs 47 have been studied in DLBCL. However, no report exists on survival‐related snoRNA signatures in DLBCL patients.…”

Section: Discussionmentioning

confidence: 99%

Identification of three small nucleolar RNAs (snoRNAs) as potential prognostic markers in diffuse large B‐cell lymphoma

Huang

Xie

et al. 2022

Cancer Medicine

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Background Diffuse large B‐cell lymphoma (DLBCL) is a non‐Hodgkin lymphoma with high mortality rates. Small nucleolar RNAs (snoRNAs) are tumor‐specific biological markers, but there are few studies on the role of snoRNAs in DLBCL. Materials and Methods Survival‐related snoRNAs were selected to construct a specific snoRNA‐based signature via computational analyses (Cox regression and independent prognostic analyses) to predict the prognosis of DLBCL patients. To assist in clinical applications, a nomogram was built by combining the risk model and other independent prognostic factors. Pathway analysis, gene ontology analysis, transcription factor enrichment, protein–protein interactions, and single nucleotide variant analysis were used to explore the potential biological mechanisms of co‐expressed genes. Results Twelve prognosis‐correlated snoRNAs were selected from the DLBCL patient cohort of microarray profiles, and a three‐snoRNA signature consisting of SNORD1A, SNORA60, and SNORA66 was constructed. DLBCL patients could be divided into high‐risk and low‐risk cohorts using the risk model, and the high‐risk group and activated B cell‐like (ABC) type DLBCL were linked with disappointing survival. In addition, SNORD1A co‐expressed genes were inseparably linked to the biological functions of the ribosome and mitochondria. Potential transcriptional regulatory networks have also been identified. MYC and RPL10A were the most mutated SNORD1A co‐expressed genes in DLBCL. Conclusion Put together, our findings explored the potential biological effects of snoRNAs in DLBCL, and provided a new predictor for DLBCL prediction.

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Transcriptome profiling reveals an integrated mRNA–lncRNA signature with predictive value for long-term survival in diffuse large B-cell lymphoma

Cited by 6 publications

References 29 publications

Identification of LINC00654-NINL Regulatory Axis in Diffuse Large B-Cell Lymphoma In Silico Analysis

Identification of LINC00654-NINL Regulatory Axis in Diffuse Large B-Cell Lymphoma In Silico Analysis

LncRNA SNHG5 can Regulate the Proliferation and Migration of Diffuse Large B Cell Lymphoma Progression via Targeting miR-181-5p/XIAP

Identification of three small nucleolar RNAs (snoRNAs) as potential prognostic markers in diffuse large B‐cell lymphoma

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