A cell-cycle signature classifier for pan-cancer analysis

Tabassum, Neha; Constantin, Theodora A.; Cereser, Biancastella; Stebbing, Justin

doi:10.1038/s41388-020-01426-5

Cited by 7 publications

(7 citation statements)

References 8 publications

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“…Cyclin D1 binds and activates its catalytic partners CDK4 or CDK6 to promote cell proliferation. CDK2 promotes cell transition from S phase to G2/M phase (27,28). The results of the present study showed that knockdown of lncRNA AL significantly inhibited the expression of CDK2 and cyclin D1 and promoted the expression of p21 in U266 cells.…”

Section: Discussionsupporting

confidence: 52%

Knockdown of lncRNA AL928768.3 inhibits multiple myeloma cell proliferation by inducing cell cycle arrest in G0/G1 phase

Shen¹,

Jiang²,

Cong³

et al. 2022

Ann Transl Med

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Background: Multiple myeloma (MM) is a B-lymphocyte-derived malignancy. It ranks as the second most common hematological malignancy, with relatively high morbidity and mortality. However, the molecular mechanisms of MM occurrence and development remain elusive. This study found that long noncoding RNA AL928768.3 (lncRNA AL) was abnormally expressed in MM samples. However, the effect and molecular mechanism of lncRNA AL on the occurrence and development of MM remains unclear. Methods: Bone marrow fluids of MM patients (n=54) and volunteers (n=13) were collected and CD138 + cells were isolated. The expression level of lncRNA AL in MM cells was detected by quantitative real-time polymerase chain reaction (qRT-PCR), and the correlation between the expression level of lncRNA AL and the clinicopathological features of patients was analyzed. Lentiviral vectors targeting lncRNA AL knockdown were constructed and transfected into cells. After transfection, the effects of lncRNA AL knockdown on MM cell proliferation and the cell cycle were detected by the CCK-8 assay, clone formation assay, and flow cytometry. The effect of lncRNA AL knockdown on MM cell cycle-related proteins was detected by Western blot. In addition, tumorigenicity experiments were performed in nude mice to detect the effect of lncRNA AL knockdown on MM cell proliferation in vivo. Results: LncRNA AL was highly expressed in MM patient samples and cell lines, and was significantly correlated with the disease stage of patients. Knockdown of lncRNA AL significantly inhibited the proliferation and colony formation of MM cells and induced cell cycle arrest in G0/G1 phase. Western blot analysis showed that knockdown of lncRNA AL significantly inhibited the expression of CDK2 and cyclin D1 and promoted the expression of cyclin suppressor p21. Knockdown of lncRNA AL significantly inhibited the proliferation of MM cells in nude mice. Conclusions: LncRNA AL was highly expressed in MM patients. Knockdown of this gene significantly inhibited the proliferative ability of MM cells and induced cell cycle arrest in G0/G1 phase. Therefore, lncRNA AL may be a novel biological target molecule for the early diagnosis, treatment, and prognostic evaluation of MM patients.

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Section: Discussionsupporting

confidence: 52%

Knockdown of lncRNA AL928768.3 inhibits multiple myeloma cell proliferation by inducing cell cycle arrest in G0/G1 phase

Shen¹,

Jiang²,

Cong³

et al. 2022

Ann Transl Med

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“…Therefore, a reliable BC risk model was constructed, which is an aggressive need to figure out the clinical outcomes of BC patients. For the extension of multi-omics data and database, optimized data mining algorithms have an important influence on tumor research ( Angus et al, 2019 ; Nacev et al, 2019 ; Liu et al, 2020 ; Tabassum et al, 2020 ). Multiple risk signatures and transcriptome profiling provided a novel insight into the prognosis of individual patients via combining the gene expression and clinical features ( Xie et al, 2021 ; Yan et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

A novel cuproptosis-related lncRNA signature predicts prognosis and therapeutic response in bladder cancer

et al. 2023

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Bladder cancer (BC) ranks the tenth in the incidence of global tumor epidemiology. LncRNAs and cuproptosis were discovered to regulate the cell death. Herein, we downloaded transcriptome profiling, mutational data, and clinical data on patients from The Cancer Genome Atlas (TCGA). High- and low-risk BC patients were categorized. Three CRLs (AL590428.1, AL138756.1 and GUSBP11) were taken into prognostic signature through least absolute shrinkage and selection operator (LASSO) Cox regression. Worse OS and PFS were shown in high-risk group (p < 0.05). ROC, independent prognostic analyses, nomogram and C-index were predicted via CRLs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated IncRNAs play a biological role in BC progression. Immune-related functions showed the high-risk group received more benefit from immunotherapy and had stronger immune responses, and the overall survival was better (p < 0.05). Finally, a more effective outcome (p < 0.05) was found from clinical immunotherapy via the TIDE algorithm and many potential anti-tumor drugs were identified. In our study, the cuproptosis-related signature provided a novel tool to predict the prognosis in BC patients accurately and provided a novel strategy for clinical immunotherapy and clinical applications.

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“…Therefore, there is an urgent need to identify key biomarkers that affect the outcome of BC. With future expansion of the database and multi-omics data, improved data mining algorithms can have an essential impact on tumor biology ( Angus et al, 2019 ; Nacev et al, 2019 ; Liu et al, 2020 ; Tabassum et al, 2020 ). Transcriptome profiling provided us with novel insights into assessing prognostic of the individual patient when combining the corresponding clinical information.…”

Section: Discussionmentioning

confidence: 99%

A Novel Ferroptosis-Related Prognostic Signature Reveals Macrophage Infiltration and EMT Status in Bladder Cancer

Yan

Cai

Huang

et al. 2021

Front. Cell Dev. Biol.

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Bladder cancer (BC) belongs to one of the most common and highly heterogeneous malignancies. Ferroptosis is a newly discovered regulated cell death (RCD), characterized by accumulation of toxic lipid peroxides, and plays a crucial role in tumor progression. Here, we conducted a comprehensive analysis on the transcriptomics data of ferroptosis-related genes in BC based on The Cancer Genome Atlas (TCGA) and three Gene Expression Omnibus (GEO) datasets. In our study, a 6-gene signature was identified based on the potential prognostic ferroptotic regulatory genes. Furthermore, our signature revealed a good independent prognostic ability in BC. Patients with low-risk score exhibited higher FGFR3 mutation rates while high risk score had a positive association with higher RB1 mutation rates. Meanwhile, higher proportions of macrophages were observed in high BC risk group simultaneously with four methods. Unexpectedly, the risk score showed a significant positive correlation with epithelial-mesenchymal transition (EMT) status. Functional assays indicated that CRYAB and SQLE knockdown was associated with attenuated invasion capacity. Our study revealed a ferroptosis-related risk model for predicting prognostic and BC progression. Our results indicate that targeting ferroptosis may be a therapeutic strategy for BC.

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A cell-cycle signature classifier for pan-cancer analysis

Cited by 7 publications

References 8 publications

Knockdown of lncRNA AL928768.3 inhibits multiple myeloma cell proliferation by inducing cell cycle arrest in G0/G1 phase

Knockdown of lncRNA AL928768.3 inhibits multiple myeloma cell proliferation by inducing cell cycle arrest in G0/G1 phase

A novel cuproptosis-related lncRNA signature predicts prognosis and therapeutic response in bladder cancer

A Novel Ferroptosis-Related Prognostic Signature Reveals Macrophage Infiltration and EMT Status in Bladder Cancer

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