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

Yıl 2022, , 351 - 368, 29.08.2022

Çağdaş Aktan

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

Öz

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.

Anahtar Kelimeler

Laringeal carcinoma, ferroptosis, bioinformatics

Laringeal Karsinomda Ferroptoz ile İlişkili Genlerin Biyoinformatik Yöntemler Kullanılarak Belirlenmesi

Öz

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.

Anahtar Kelimeler

laringeal kanser, ferroptoz, biyoinformatik

Kaynakça

• Tamaki A, Miles BA, Lango M, Kowalski L, Zender CA. AHNS Series: Do you know your guidelines? Review of current knowledge on laryngeal cancer. Head Neck. 2018;40(1):170-181.
• Steuer CE, El-Deiry M, Parks JR, Higgins KA, Saba NF. An update on larynx cancer. CA Cancer J Clin. 2017;67(1):31-50.
• Belcher R, Hayes K, Fedewa S, Chen AY. Current treatment of head and neck squamous cell cancer. J Surg Oncol. 2014;110(5):551-574.
• Salvador-Coloma C, Cohen E. Multidisciplinary Care of Laryngeal Cancer. J Oncol Pract. 2016;12(8):717-724.
• Zhang Y, Lu X, Tai B, Li W, Li T. Ferroptosis and Its Multifaceted Roles in Cerebral Stroke. Frontiers in Cellular Neuroscience. 2021;15:615372.
• Bu ZQ, Yu HY, Wang J, et al. Emerging Role of Ferroptosis in the Pathogenesis of Ischemic Stroke: A New Therapeutic Target? ASN Neuro. 2021;13:17590914211037505.
• Guan Q, Zhou LL, Dong YB. Ferroptosis in cancer therapeutics: a materials chemistry perspective. Journal of Materials Chemistry. 2021;9(43):8906-8936.
• Hu X, Xu Y, Xu H, et al. Progress in Understanding Ferroptosis and Its Targeting for Therapeutic Benefits in Traumatic Brain and Spinal Cord Injuries. Frontiers in Cell and Developmental Biology. 2021;9:705786.
• Ye F, Chai W, Xie M, et al. HMGB1 regulates erastin-induced ferroptosis via RAS-JNK/p38 signaling in HL-60/NRAS(Q61L) cells. American Journal of Cancer Research. 2019;9(4):730-739.
• Nishizawa H, Matsumoto M, Chen G, et al. Lipid peroxidation and the subsequent cell death transmitting from ferroptotic cells to neighboring cells. Cell Death & Disease. 2021;12(4):332.
• Li J, Cao F, Yin HL, et al. Ferroptosis: Past, present and future. Cell Death Dis. 2020;11(2):88.
• Lin R, Zhang Z, Chen L, et al. Dihydroartemisinin (DHA) induces ferroptosis and causes cell cycle arrest in head and neck carcinoma cells. Cancer Lett. 2016;381(1):165-175.
• Kim EH, Shin D, Lee J, Jung AR, Roh JL. CISD2 inhibition overcomes resistance to sulfasalazine-induced ferroptotic cell death in head and neck cancer. Cancer Lett. 2018;432:180-190.
• Han F, Li W, Chen T, et al. Ferroptosis-related genes for predicting prognosis of patients with laryngeal squamous cell carcinoma. Eur Arch Otorhinolaryngol. 2021;278(8):2919-2925.
• Wu F, Xiong G, Chen Z, Lei C, Liu Q, Bai Y. SLC3A2 inhibits ferroptosis in laryngeal carcinoma via mTOR pathway. Hereditas. 2022;159(1):6.
• Huang T, Yin L, Wu J, et al. TNFAIP3 inhibits migration and invasion in nasopharyngeal carcinoma by suppressing epithelial mesenchymal transition. Neoplasma. 2017;64(3):389-394.
• Catrysse L, Vereecke L, Beyaert R, van Loo G. A20 in inflammation and autoimmunity. Trends in Immunology. 2014;35(1):22-31.
• Meng Z, Zhao T, Zhou K, et al. A20 Ameliorates Intracerebral Hemorrhage-Induced Inflammatory Injury by Regulating TRAF6 Polyubiquitination. Journal of Immunology. Jan 15 2017;198(2):820-831.
• Xiao FJ, Zhang D, Wu Y, et al. miRNA-17-92 protects endothelial cells from erastin-induced ferroptosis through targeting the A20-ACSL4 axis. Biochemical and Biophysical Research Communications. 2019;515(3):448-454.
• Ye J, Wang Z, Chen X, et al. YTHDF1-enhanced iron metabolism depends on TFRC m(6)A methylation. Theranostics. 2020;10(26):12072-12089.
• Jiang XP, Elliott RL, Head JF. Manipulation of iron transporter genes results in the suppression of human and mouse mammary adenocarcinomas. Anticancer Research. 2010;30(3):759-765.
• Takahashi M, Shibutani M, Woo GH, et al. Cellular distributions of molecules with altered expression specific to the tumor promotion process from the early stage in a rat two-stage hepatocarcinogenesis model. Carcinogenesis. 2008;29(11):2218-2226.
• Huang Y, Huang J, Huang Y, et al. TFRC promotes epithelial ovarian cancer cell proliferation and metastasis via up-regulation of AXIN2 expression. American Journal of Cancer Research. 2020;10(1):131-147.
• Yang C, Li J, Guo Y, et al. Role of TFRC as a Novel Prognostic Biomarker and in Immunotherapy for Pancreatic Carcinoma. Frontiers in Molecular Biosciences. 2022;9:756895.
• Kazan HH, Urfali-Mamatoglu C, Gunduz U. Iron metabolism and drug resistance in cancer. Biometals. 2017;30(5):629-641.
• Min YH, Kim W, Kim JE. The Aurora kinase A inhibitor TC-A2317 disrupts mitotic progression and inhibits cancer cell proliferation. Oncotarget. 2016;7(51):84718-84735.
• Heo SK, Noh EK, Jeong YK, et al. Radotinib inhibits mitosis entry in acute myeloid leukemia cells via suppression of Aurora kinase a expression. Tumour biology : The Journal of The International Society for Oncodevelopmental Biology and Medicine. 2019;41(5):1010428319848612.
• Yuan CX, Zhou ZW, Yang YX, et al. Inhibition of mitotic Aurora kinase A by alisertib induces apoptosis and autophagy of human gastric cancer AGS and NCI-N78 cells. Drug Design, Development and Therapy. 2015;9:487-508.
• Xie CM, Lin XT, Wu D, Tan Y, Cheng CHK, Zhang J. Cardiac glycoside bufalin blocks cancer cell growth by inhibition of Aurora A and Aurora B activation via PI3K-Akt pathway. Oncotarget. 2018;9(17):13783-13795.
• Fu Y, Zhang Y, Gao M, Quan L, Gui R, Liu J. Alisertib induces apoptosis and autophagy through targeting the AKT/mTOR/AMPK/p38 pathway in leukemic cells. Molecular Medicine Reports. 2016;14(1):394-398.
• Dawei H, Honggang D, Qian W. AURKA contributes to the progression of oral squamous cell carcinoma (OSCC) through modulating epithelial-to-mesenchymal transition (EMT) and apoptosis via the regulation of ROS. Biochemical and Biophysical Research Communications. 2018;507(1-4):83-90.
• Lai CH, Huang YC, Lee JC, et al. Translational upregulation of Aurora-A by hnRNP Q1 contributes to cell proliferation and tumorigenesis in colorectal cancer. Cell Death & Disease. 2017;8(1):e2555.
• Maimaiti Y, Jie T, Jing Z, et al. Aurora kinase A induces papillary thyroid cancer lymph node metastasis by promoting cofilin-1 activity. Biochemical and Biophysical Research Communications. 2016;473(1):212-218.
• Bertolin G, Bulteau AL, Alves-Guerra MC, et al. Aurora kinase A localises to mitochondria to control organelle dynamics and energy production. eLife. 2018;7.
• Ma Y, Yang J, Wang R, et al. Aurora-A affects radiosenstivity in cervical squamous cell carcinoma and predicts poor prognosis. Oncotarget. 2017;8(19):31509-31520.
• Willems E, Dedobbeleer M, Digregorio M, et al. Aurora A plays a dual role in migration and survival of human glioblastoma cells according to the CXCL12 concentration. Oncogene. 2019;38(1):73-87.
• Moretti L, Niermann K, Schleicher S, et al. MLN8054, a small molecule inhibitor of aurora kinase a, sensitizes androgen-resistant prostate cancer to radiation. International Journal of Radiation Oncology, Biology, Physics. 2011;80(4):1189-1197.