Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma

YILDIZ, Gokhan

Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma

Gökhan YILDIZ (Karadeniz Teknik Üniversite, Tıp Fakültesi, Tıbbi Biyoloji Anabilim Dalı, Trabzon, TÜRKİYE)

Fırat Üniversitesi Sağlık Bilimleri Tıp Dergisi

10 2

Yıl: 2020 Cilt: 34 Sayı: 2 Sayfa Aralığı: 123 - 129 Metin Dili: İngilizce İndeks Tarihi: 28-06-2021

Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma

Öz:

Objective: Hepatocellular carcinoma (HCC) is a frequently diagnosed cancer type with low overallsurvival (OS) rates. Known prognostic biomarkers of HCC are inefficient to monitor diseaseprogression. Therefore, identification of novel patient OS time predictive biomarkers is needed.Materials and Methods: Cbioportal, OncoLnc, and dbDEMC tools were utilized to analyse DNAsequencing, mRNA-sequencing and miRNA-sequencing data of HCC patients in The CancerGenome Atlas (TCGA) database. Integrated molecular interactions network of the novel biomarkercandidates were generated using NetworkAnalyst and MiRNet tools.Results: Next generation sequencing data analyses revealed expression profiles of 11 frequentlymutated and differentially expressed genes as well as two differentially expressed miRNAs, whichpredict OS time. Transcriptional upregulation of GPATCH4 gene (P:0.009) and downregulation offour genes (PPARGC1A P:0.000013, PIK3R1 P:0.002, COL18A1 P:0.009, and A1BG P:0.01) werecorrelated with poor prognosis of HCC patients, for the first time. Integrated network of thesemolecules also revealed novel regulatory molecules and interactions associated with prognosis ofHCC.Conclusion: As a resul of this study, in silico data that can benefit the development of novelmolecularly targeted diagnostic and therapeutic applications specific to HCC have been obtained.

Anahtar Kelime:

Hepatoselüler Kansere Özgü Yeni Prognostik Biyobelirteç Adaylarının Biyoenformatik Veri Analizleriyle Belirlenmesi

Öz:

Amaç: Hepatoselüler kanser (HSK), en sık görülen ve sağkalım oranı düşük olan bir kanser tipidir. HSK’ya özgü bilinen prognostik biyobelirteçler hastalığın seyrinin izleminde yetersiz kalmaktadır. Bu nedenle, hastaların sağkalım sürelerinin tahmininde kullanılabilecek yeni biyobelirteçlerin belirlenmesine ihtiyaç duyulmaktadır. Gereç ve Yöntem: HSK hastalarının, Kanser Genom Atlası (TCGA) veri tabanındaki yeni nesil DNA, mRNA ve miRNA dizileme verilerinin analizleri cbioportal, OncoLnc ve dbDEMC araçları kullanılarak gerçekleştirilmiştir. Belirlenen yeni biyobelirteç adaylarının yaptıkları entegre moleküler etkileşimler ağı NetworkAnalyst ve MiRNet araçları kullanılarak oluşturulmuştur. Bulgular: Yeni nesil dizileme veri analizleriyle, HSK’da sıklıkla mutasyona uğrayan ve ekspresyon farklılığı gösteren 11 gen ile iki miRNA’nın ekspreyon örüntüleriyle hasta sağkalım süresinin tahmin edilebildiği belirlenmiştir. Bunlardan bir genin ifadesinin artışının HSK hastalarının kötü prognozuyla doğru orantılı (GPATCH4 P:0.009), dört genin ifadesindeki azalışın (PPARGC1A P:0.000013, PIK3R1 P:0.002, COL18A1 P:0.009 ve A1BG P: 0.01) ise ters orantılı olduğu ilk kez belirlenmiştir. Bu moleküllerin oluşturduğu entegre moleküler etkileşimler ağı da HSK’nın prognozuyla ilişkili yeni düzenleyici molekülleri ve etkileşimleri ortaya çıkarmıştır. Sonuç: HSK’ya özgü moleküler hedefli yeni tanı ve tedavi uygulamalarının geliştirilmesine fayda sağlayabilecek in silico veriler elde edilmiştir.

Anahtar Kelime:

Belge Türü: Makale Makale Türü: Araştırma Makalesi Erişim Türü: Erişime Açık

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APA	YILDIZ G (2020). Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma. , 123 - 129.
Chicago	YILDIZ Gokhan Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma. (2020): 123 - 129.
MLA	YILDIZ Gokhan Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma. , 2020, ss.123 - 129.
AMA	YILDIZ G Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma. . 2020; 123 - 129.
Vancouver	YILDIZ G Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma. . 2020; 123 - 129.
IEEE	YILDIZ G "Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma." , ss.123 - 129, 2020.
ISNAD	YILDIZ, Gokhan. "Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma". (2020), 123-129.

APA	YILDIZ G (2020). Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma. Fırat Üniversitesi Sağlık Bilimleri Tıp Dergisi, 34(2), 123 - 129.
Chicago	YILDIZ Gokhan Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma. Fırat Üniversitesi Sağlık Bilimleri Tıp Dergisi 34, no.2 (2020): 123 - 129.
MLA	YILDIZ Gokhan Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma. Fırat Üniversitesi Sağlık Bilimleri Tıp Dergisi, vol.34, no.2, 2020, ss.123 - 129.
AMA	YILDIZ G Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma. Fırat Üniversitesi Sağlık Bilimleri Tıp Dergisi. 2020; 34(2): 123 - 129.
Vancouver	YILDIZ G Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma. Fırat Üniversitesi Sağlık Bilimleri Tıp Dergisi. 2020; 34(2): 123 - 129.
IEEE	YILDIZ G "Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma." Fırat Üniversitesi Sağlık Bilimleri Tıp Dergisi, 34, ss.123 - 129, 2020.
ISNAD	YILDIZ, Gokhan. "Bioinformatics Data Analyses Revealed Novel Prognostic Biomarker Candidates For Hepatocellular Carcinoma". Fırat Üniversitesi Sağlık Bilimleri Tıp Dergisi 34/2 (2020), 123-129.