Prognostic value of small nucleolar RNAs (snoRNAs) for colon adenocarcinoma based on RNA sequencing data

Huang, Li; Liang, Xuzhi; Deng, Yun; Liang, Yong; Zhu, Xu; Liang, Xiu-Yun; Luo, Dan; Chen, Gang; Fang, Ye‐Ying; Lan, Huihua; Zeng, Jiang‐Hui

doi:10.1016/j.prp.2020.152937

Cited by 23 publications

(18 citation statements)

References 29 publications

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“… 35 Shang et al 36 found that SNORD63 was elevated in the plasma and tumour tissues of patients with clear cell renal cell carcinoma, such that SNORD63 can be used as a diagnostic marker. The expression of SNORD12C was significantly increased in colorectal cancer, 37 and it played an important role in tumourigenesis, through the ZFAS1-NOP58-SNORD12C/78-EIF4A3/LAMC2 signaling axis. 38 At this time, there are no detailed reports or related studies regarding the other 4 TIIsno.…”

Section: Discussionmentioning

confidence: 99%

Identification of tumour immune infiltration-associated snoRNAs (TIIsno) for predicting prognosis and immune landscape in patients with colon cancer via a TIIsno score model

et al. 2022

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Background Colon cancer (CC) is the leading cause of tumour-related death worldwide. SnoRNA plays a critical role in the tumour microenvironment. The tumour microenvironment can be shaped by tumour-infiltrating immune cells, which control the destiny of immunotherapy efficacy. This study uniquely focused on snoRNAs derived from immune cells to identify new biomarkers for immune landscape.Methods A novel computational framework was initiated for identifying tumour immune infiltration-associated snoRNAs (TIIsno) signatures and developed a TIIsno score model from integrative snoRNA profiling analysis of 21 purified immune cell lines, 43 colon cancer cell lines, and three datasets (training, test, real-world validation set).Findings Our study found that a high TIIsno score was associated with poor CC prognosis. TIIsno scores were seen to be negatively correlated with (I) the infiltration level of most immune cells, (II) the inhibitory immune checkpoints expression level, and (III) the immune score. These findings, taken together with the observation that TIIsno score is lower in MSI-H patients, suggests that patients with a low TIIsno score may have a better response to immunotherapy.Interpretation In conclusion, we successfully identified TIIsno and constructed a TIIsno score model, a new potential biomarker of immunotherapy response, which can effectively predict the prognosis of CC patients as well.

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Section: Discussionmentioning

confidence: 99%

Identification of tumour immune infiltration-associated snoRNAs (TIIsno) for predicting prognosis and immune landscape in patients with colon cancer via a TIIsno score model

et al. 2022

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“…With the discovery of high-throughput sequencing technology, more and more studies have shown that snoRNAs is closely related to the prognosis of cancers. Huang et al identi ed several snoRNAs signi cantly related to the prognosis of colon adenocarcinoma by analyzing the TCGA RNA-seq dataset, and constructed a prognosis signature consisting of two snoRNAs expressions [14]. Similar to the research by Huang et al, Xing et al identi ed snoRNAs of 113 snoRNAs signi cantly related to the prognosis of HNSC by using the RNA-seq dataset of the TCGA head and neck squamous cell carcinoma (HNSC) cohort, and used the least absolute shrinkage and selection operator (LASSO) regression to construct a prognostic signature that included 5 prognostic snoRNAs, which can signi cantly divide HNSC patients into high-and low-risk phenotypes [13].…”

Section: Discussionmentioning

confidence: 99%

“…As early studies found that snoRNA was mainly located in the nucleoli and was related to the processing and modi cation of rRNA, its function was relatively simple [9][10][11]. However, in recent years, more and more RNA sequencing (RNA-seq) dataset show that snoRNA shows a general trend of high expression in tumors, and some studies show that snoRNA is involved in the occurrence, progression and prognosis of tumors, and may be a kinds of new clinical biomarkers [12][13][14].…”

Section: Introductionmentioning

confidence: 99%

Identification of a novel small nucleolar RNAs prognostic signature for patients with acute myelocytic leukemia

Huang¹,

Liao²,

Li³

2020

Preprint

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Background: This study mainly used The Cancer Genome Atlas (TCGA) RNA sequencing dataset to screen prognostic snoRNAs of acute myeloid leukemia (AML), and used for the construction of prognostic snoRNAs signature for AML. Methods: A total of 130 AML patients with RNA sequencing dataset were used for prognostic snoRNAs screenning. SnoRNAs co-expressed genes and differentially expressed genes (DEGs) were used for functional annotation, as well as gene set enrichment analysis (GSEA). Connectivity Map (CMap) also used for potential targeted drugs screening. Results:Through genome-wide screening, we identified 30 snoRNAs that were significantly associated with the prognosis of AML. Then we used the step function to screen a prognostic signature composed of 14 snoRNAs (SNORD72, SNORD38, U3, SNORA73B, SNORD79, SNORA73, SNORD12B, SNORA74, SNORD116-12, SNORA65, SNORA14, snoU13, SNORA75, SNORA31), which can significantly divide AML patients into high- and low-risk groups. Through GSEA, snoRNAs co-expressed genes and DEGs functional enrichment analysis, we screened a large number of potential functional mechanisms of this prognostic signature in AML, such as phosphatidylinositol 3-kinase-Akt ,Wnt, epithelial to mesenchymal transition, T cell receptors, NF-kappa B, mTOR and other classic cancer-related signaling pathways. In the subsequent targeted drug screening using CMap, we also identified six drugs that can be used for AML targeted therapy, they were alimemazine, MG-262, fluoxetine, quipazine, naltrexone and oxybenzone. Conclusion: Our current study was constructed an AML prognostic signature based on the 14 prognostic snoRNAs, which may serve as a novel prognostic biomarker for AML.

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“…[2][3][4][5][6][7] Not only that, early diagnosis and treatment of CRC are difficult because CRC is asymptomatic in its early stages. 8 Currently, the effective therapeutic strategies for CRC include combinations of surgery, chemotherapy, molecular targeted therapy, and/or radiation. [9][10][11] Radiotherapy, which uses high-energy rays to irradiate tumors, is an important strategy for the treatment of CRC and can reduce local recurrence and improve patient survival.…”

Section: Introductionmentioning

confidence: 99%

Active Enhancer Assessment by H3K27ac ChIP-seq Reveals Claudin-1 as a Biomarker for Radiation Resistance in Colorectal Cancer

et al. 2021

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Background Colorectal cancer (CRC) represents the third most common malignant tumor in the worldwide. Radiotherapy is the common therapeutic treatment for CRC, but radiation resistance is often encountered. ChIP-seq of Histone H3K27 acetylation (H3K27ac) has revealed enhancers that play an important role in CRC. This study examined the relationship between an active CRC enhancer and claudin-1 (CLDN1), and its effect on CRC radiation resistance. Methods The target CRC genes of active enhancers were obtained from public H3K27ac ChIP-seq, and the genes highly expressed in radio-resistant CRC were screened and intersected with enhancer-driven genes. The clinical roles of CLDN1 in radiation resistance were examined using the t-test, standard mean deviation (SMD), summary receiver operating characteristic curve and Kaplan-Meier curves. The co-expressed genes of CLDN1 were calculated using Pearson Correlation analysis, and Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes and Gene Set Variation Analysis (GSVA) analyses were used to examine the molecular mechanisms of CLDN1. Results Total 13 703 CRC genes were regulated by enhancers using 58 H3K27ac ChIP-seq. Claudin-1 (CLDN1) was enhancer-driven and notably up-regulated in CRC tissues compared to non-CRC controls, with a SMD of 3.45 (95 CI % = .56-4.35). CLDN1 expression was increased in radiation-resistant CRC with a SMD of .42 (95% CI = .16-.68) and an area under the curve of .74 (95% CI = .70-.77). The cell cycle and immune macrophage levels were the most significant pathways associated with CLDN1. Conclusion CLDN1 as an enhancer-regulated gene that can boost radiation resistance in patients with CRC.

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Prognostic value of small nucleolar RNAs (snoRNAs) for colon adenocarcinoma based on RNA sequencing data

Cited by 23 publications

References 29 publications

Identification of tumour immune infiltration-associated snoRNAs (TIIsno) for predicting prognosis and immune landscape in patients with colon cancer via a TIIsno score model

Identification of tumour immune infiltration-associated snoRNAs (TIIsno) for predicting prognosis and immune landscape in patients with colon cancer via a TIIsno score model

Identification of a novel small nucleolar RNAs prognostic signature for patients with acute myelocytic leukemia

Active Enhancer Assessment by H3K27ac ChIP-seq Reveals Claudin-1 as a Biomarker for Radiation Resistance in Colorectal Cancer

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