Identification of Ferroptosis-Related Genes in Laryngeal Carcinoma Using an Integrated Bioinformatics Approach

Year 2022, Issue: 17, 351 - 368, 29.08.2022

Çağdaş Aktan

https://doi.org/10.38079/igusabder.1128423

Abstract

Aim: Ferroptosis, which is characterized by intracellular iron accumulation and lipid peroxidation, is a newly described form of regulated cell death that may play a key role in tumour suppression. There is still a lack of knowledge regarding the association between laryngeal squamous cell carcinoma (LSCC) and ferroptosis. The aim of this study is finding ferroptosis-related markers in LSCC to explore new directions for LSCC diagnosis and treatment using in silico methods.

Method: The ferroptosis-related genes were obtained from FerrDb database. mRNA expression data from LSCC patients from The Cancer Genome Atlas (TCGA) datasets were used to screen for some genes related to ferroptosis. GSE143224 and GSE84957 microarray datasets about LSCC were obtained from the GEO database. Overlapping data was used to obtain genes associated with ferroptosis and LSHK using all datasets. The differentially expressed genes (DEGs) and ferroptosis-related DEGs between the LSCC group and normal controls were analyzed using bioinformatics methods. Then the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and the protein-protein interaction (PPI) network analyses were performed using STRING and Cytoscape softwares.

Results: 259 ferroptosis-related genes were fetched from FerrDb database and intersected them with TCGA-HNSC (523 samples), GSE143224 (25 samples) and GSE84957 (18 samples) to identify ferroptosis DEGs. Finally, it was found that 13 upregulated (NOX4, BID, ABCC1, TNFAIP3, PANX1, SLC1A4, SLC3A2, FTL, TFRC, AURKA, HSF1, PML, CA9; p<0.05) and 3 downregulated genes (CHAC1, LPIN1, MUC1; p<0.05). The result of the enrichment gene dataset analysis (cellular stress, inflammation, oxidative stress and carcinogenesis; p<0.05) indicated that the genes significantly enriched were involved in progression of LSCC.

Conclusions: In conclusion, 16 potential genes that are closely associated with ferroptosis in LSCC and may differentiate LSCC patients from controls. Our study may provide a broader idea for exploring the molecular mechanism and therapeutic targets of LSCC.

Keywords

Laringeal carcinoma, ferroptosis, bioinformatics

Laringeal Karsinomda Ferroptoz ile İlişkili Genlerin Biyoinformatik Yöntemler Kullanılarak Belirlenmesi

Abstract

Amaç: Hücre içi demir birikimi ve lipid peroksidasyonu ile karakterize edilen ferroptoz, tümör baskılanmasında önemli rol oynayabilen yeni tanımlanmış bir hücre ölüm şeklidir. Larengeal skuamöz hücreli karsinom (LSHK) ve ferroptozis arasındaki ilişki hakkında yapılan çalışmalar sınırlıdır. Bu çalışmanın amacı, LSHK' nin tanı, tedavisinde ve ferroptozis ile ilgili belirteçleri in siliko yöntemleri kullanarak saptamaktır.

Yöntem: Ferroptoz ile ilgili genler, FerrDb veri tabanından elde edildi. The Cancer Genome Atlas (TCGA) veri setlerinden LSHK hastalarının mRNA ekspresyon verileri ve ferroptoz ile ilgili bazı genleri taramak için kullanıldı. LSHK ile ilgili GSE143224 ve GSE84957 mikrodizi veri setleri GEO veri tabanından elde edilmiştir. Tüm veri setleri kullanılarak ferroptoz ve LSHK ile ilişkili genleri elde etmek için örtüşen veriler kullanılmıştır. LSHK grubu ve normal kontroller arasındaki diferansiyel olarak eksprese edilen genler (DEG'ler) ve ferroptoz ile ilgili DEG'ler, biyoinformatik yöntemler kullanılarak analiz edildi. Daha sonra STRING ve Cytoscape yazılımları kullanılarak Gene Ontology (GO), KEGG ve protein-protein etkileşimi (PPE) ağı analizleri gerçekleştirilmiştir.

Bulgular: Ferroptoz ile ilgili 259 gen, FerrDb veri tabanından alındı ve ferroptoz DEG'lerini tanımlamak için bunları TCGA-HNSC (523 örnek), GSE143224 (25 örnek) ve GSE84957 (18 örnek) ile analizleri yapıldı. Analiz sonrasında 13 adet yukarı regüle edilmiş (NOX4, BID, ABCC1, TNFAIP3, PANX1, SLC1A4, SLC3A2, FTL, TFRC, AURKA, HSF1, PML, CA9; p<0.05) ve 3 adet aşağı regüle edilmiş gen (CHAC1, LPIN1, MUC1; p<0.05) saptanmıştır. GO, KEGG ve PPE analizleri ile elde edilen hücresel stres, inflamasyon, oksidatif stres ve karsinogenez süreçlerine benzer sonuçlar (p<0.05) ile bu genlerin LSHK' nin ilerlemesinde rol oynayabileceğini göstermektedir.

Sonuç: Sonuç olarak, bu çalışmada LSHK'de ferroptoz ile yakından ilişkili olan ve LSHK hastalarını sağlıklı kontrollerden ayırt edebilen 16 potansiyel gen saptanmıştır. Çalışmamız, LSHK’nin moleküler mekanizmasını ve terapötik hedeflerini keşfetmek için daha geniş bir fikir sağlayabilir.

Keywords

laringeal kanser, ferroptoz, biyoinformatik

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