Bioinformatics role of the WGCNA analysis and co-expression network identifies of prognostic marker in lung cancer

Chengcheng, Liang; Raza, Sayed Haidar Abbas; Shengchen, Yu; Mohammedsaleh, Zuhair M.; Shater, Abdullah F.; Saleh, Fayez M.; Alamoudi, Muna O.; Aloufi, Bandar Hamad; Alshammari, Ahmed Mohajja; Schreurs, Nicola M.; Liu, Zan

doi:10.1016/j.sjbs.2022.02.016

Cited by 11 publications

(4 citation statements)

References 34 publications

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“…Recently, a study revealed that MRPL17 was identi ed as an important prognostic factor for lung cancer patients 14 . Miao et al revealed that MRPL17 considered as one of the shared gene signatures for endometrial cancer and polycystic ovary syndrome 16 .…”

Section: Discussionmentioning

confidence: 99%

A multidimensional analysis of MRPL17 protein in human tumors

Li,

Xie,

Zhang

et al. 2024

Preprint

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MRPL17 is one of mitochondrial ribosome protein (MRP) family proteins, which have oncogenic effects in several malignant tumors. However, it is unclear that the relationship between MRPL17 expression pattern and prognosis across different cancer types. Also, the biological function or effects on the immune microenvironment of MRPL17 is unknown. In this study, we parsed multiple public databases to explore the potential tumorigenic actions of MRPL17, including correlations with prognosis, microsatellite instability (MSI), tumor mutational burden (TMB), immune checkpoint genes, immune cell infiltration, and immunotherapy response in pan-cancer. Moreover, we validated MRPL17 expression in a tissue microarray by immunohistochemistry. The results showed that MRPL17 was upregulated in 19 cancer types and correlated with poor prognosis in many cancers. The correlation between MRPL17 and TMB was found in 10 cancers as well as MSI in five. The expression level of MRPL17 was found to be notably correlated with immune cell infiltration, showing a negative correlation with CD4 T cells infiltration and a positive correlation with dendritic cells (DC). MRPL17 expression levels were positively associated with drug sensitivity in certain cancers. In addition, we discovered that MRPL17 participated in the DNA repair at the single-cell level for most cancers. These findings provides a promising candidate for therapeutic targets and a new direction for future research.

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Section: Discussionmentioning

confidence: 99%

A multidimensional analysis of MRPL17 protein in human tumors

Li,

Xie,

Zhang

et al. 2024

Preprint

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“…Additionally, their association with carotenoid dioxygenase activity underscores their potential in carotenoid cleavage reactions. The high enrichment of OsCCO gene in the chloroplast stroma suggests their crucial participation in diverse metabolic processes within this organelle, particularly related to photosynthesis and pigment biosynthesis (Chengcheng et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress

Haider,

Sami,

Shafiq

et al. 2023

Front. Plant Sci.

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Rice constitutes a foundational cereal and plays a vital role in the culinary sector. However, the detriments of abiotic stress on rice quality and productivity are noteworthy. Carotenoid cleavage oxygenases (CCO) hold vital importance as they enable the particular breakdown of carotenoids and significantly contribute towards the growth and response to abiotic stress in rice. Due to the insufficient information regarding rice CCOs and their potential role in abiotic stress, their utilization in stress-resistant genetic breeding remains limited. The current research identified 16 CCO genes within the Oryza sativa japonica group. These OsCCO genes can be bifurcated into three categories based on their conserved sequences: NCEDs (9-Cis-epoxycarotenoid dioxygenases), CCDs (Carotenoid cleavage dioxygenases) and CCD-like (Carotenoid cleavage dioxygenases-like). Conserved motifs were found in the OsCCO gene sequence via MEME analysis and multiple sequence alignment. Stress-related cis-elements were detected in the promoter regions of OsCCOs genes, indicating their involvement in stress response. Additionally, the promoters of these genes had various components related to plant light, development, and hormone responsiveness, suggesting they may be responsive to plant hormones and involved in developmental processes. MicroRNAs play a pivotal role in the regulation of these 16 genes, underscoring their significance in rice gene regulation. Transcriptome data analysis suggests a tissue-specific expression pattern for rice CCOs. Only OsNCED6 and OsNCED10 significantly up-regulated during salt stress, as per RNA seq analyses. CCD7 and CCD8 levels were also higher in the CCD group during the inflorescence growth stage. This provides insight into the function of rice CCOs in abiotic stress response and identifies possible genes that could be beneficial for stress-resistant breeding.

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“…Their potential in carotenoid cleavage reactions is further highlighted by their relationship with carotenoid dioxygenase activity. The significant involvement of CsCCO genes in many metabolic activities inside the chloroplast stroma, especially those pertaining to photosynthesis and pigment production, is indicated by the high enrichment of these genes in this organelle [ 51 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana

Akram,

Siddique,

Shafiq

et al. 2023

BMC Plant Biol

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Carotenoid cleavage oxygenase (CCO) is an enzyme capable of converting carotenoids into volatile, aromatic compounds and it plays an important role in the production of two significant plant hormones, i.e., abscisic acid (ABA) and strigolactone (SL). The cucumber plant genome has not been mined for genomewide identification of the CCO gene family. In the present study, we conducted a comprehensive genome-wide analysis to identify and thoroughly examine the CCO gene family within the genomic sequence of Cucumis sativus L. A Total of 10 CCO genes were identified and mostly localized in the cytoplasm and chloroplast. The CCO gene is divided into seven subfamilies i.e. 3 NCED, 3 CCD, and 1 CCD-like (CCDL) subfamily according to phylogenetic analysis. Cis-regulatory elements (CREs) analysis revealed the elements associated with growth and development as well as reactions to phytohormonal, biotic, and abiotic stress conditions. CCOs were involved in a variety of physiological and metabolic processes, according to Gene Ontology annotation. Additionally, 10 CCO genes were regulated by 84 miRNA. The CsCCO genes had substantial purifying selection acting upon them, according to the synteny block. In addition, RNAseq analysis indicated that CsCCO genes were expressed in response to phloem transportation and treatment of chitosan oligosaccharides. CsCCD7 and CsNCED2 showed the highest gene expression in response to the exogenous application of chitosan oligosaccharides to improve cold stress in cucumbers. We also found that these genes CsCCD4a and CsCCDL-a showed the highest expression in different plant organs with respect to phloem content. The cucumber CCO gene family was the subject of the first genome-wide report in this study, which may help us better understand cucumber CCO proteins and lay the groundwork for the gene family's future cloning and functional investigations.

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Bioinformatics role of the WGCNA analysis and co-expression network identifies of prognostic marker in lung cancer

Cited by 11 publications

References 34 publications

A multidimensional analysis of MRPL17 protein in human tumors

A multidimensional analysis of MRPL17 protein in human tumors

Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress

Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana

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