Identification of TIG1 Associated Molecular Targets for Breast Cancer Using Bioinformatic Approach

Tuğcan Korak; Merve Gulsen Bal Albayrak; Gürler Akpınar; Murat Kasap

Makale detayları

Identification of TIG1 Associated Molecular Targets for Breast Cancer Using Bioinformatic Approach

Yazarlar:

Tuğcan Korak | Merve Gulsen Bal Albayrak | Gürler Akpınar | Murat Kasap

Yayıncı:

Gumushane University

Ana Başlıklar:

Biyokimya ve Hücre Biyolojisi (Diğer)

Dergi:

Gümüşhane Üniversitesi Sağlık Bilimleri Dergisi Vol.13 Issue 4, pp.1807-1817

Belge Tipi:

Makale

Yayın Tarihi:

12/2024

Belge Dili:

İngilizce

Document ID (Org No.):

2001335103

pISSN:

2146-9954

Anahtar kelimeler:

Özet:

 e-postae-mail: tugcankorakgmail.comtugcan.korakkocaeli.edu.tr Kabul TarihiAccepted: Tazarotene-induced gene 1 TIG1 is involved in modulating the α-tubulin modification and effectively inhibiting tumor growth. In this bioinformatics study, we aim to propose novel therapeutic targets in breast cancer by utilizing differentially expressed genes DEGs of TIG1 in inflammatory breast cancer IBC and examining their correlation with the molecular and immune subtypes. Using the GEO2R tool, we analyzed DEGs in the GSE30543 dataset, specifically comparing suppressed TIG1 groups with control samples from SUM149 cells. Functional annotation analysis of DEGs were explored using SRplot with data from STRING log2FC 2 and p0,05. Cytoscape software was used to construct intersected protein-protein interaction PPI network and define central genes. Subsequently, the molecular and immune subtype analysis were performed in TISIDB utilizing the identified hub genes. A total of 19 upregulated DEGs and 3 downregulated DEGs were identified in IBC and utilized to construct the STRING PPI network. GO analysis revealed that the biological functions of the identified DEGs primarily centered around the regulation of cell adhesion and migration. KEGG pathway analysis demonstrated their significant involvement in regulation of cell adhesion-related signaling pathways. Hub genes were identified as STAT3, PXDNL, FN1, CTNNB1, CD44, TNF, TP53, MMP9, SRC and INS. TISIDB analysis revealed significant correlations between all hub gene expressions and both the molecular subtypes except for TP53 and immune subtypes of breast cancer p0,05. This study identified potential prognostic biomarkers for breast cancer based on the hub genes derived from TIG1-associated DEGs, indicating their potential use in targeted therapeutic approaches.

 e-postae-mail: tugcankorakgmail.comtugcan.korakkocaeli.edu.tr Kabul TarihiAccepted: Tazarotene-induced gene 1 TIG1 is involved in modulating the α-tubulin modification and effectively inhibiting tumor growth. In this bioinformatics study, we aim to propose novel therapeutic targets in breast cancer by utilizing differentially expressed genes DEGs of TIG1 in inflammatory breast cancer IBC and examining their correlation with the molecular and immune subtypes. Using the GEO2R tool, we analyzed DEGs in the GSE30543 dataset, specifically comparing suppressed TIG1 groups with control samples from SUM149 cells. Functional annotation analysis of DEGs were explored using SRplot with data from STRING log2FC 2 and p0,05. Cytoscape software was used to construct intersected protein-protein interaction PPI network and define central genes. Subsequently, the molecular and immune subtype analysis were performed in TISIDB utilizing the identified hub genes. A total of 19 upregulated DEGs and 3 downregulated DEGs were identified in IBC and utilized to construct the STRING PPI network. GO analysis revealed that the biological functions of the identified DEGs primarily centered around the regulation of cell adhesion and migration. KEGG pathway analysis demonstrated their significant involvement in regulation of cell adhesion-related signaling pathways. Hub genes were identified as STAT3, PXDNL, FN1, CTNNB1, CD44, TNF, TP53, MMP9, SRC and INS. TISIDB analysis revealed significant correlations between all hub gene expressions and both the molecular subtypes except for TP53 and immune subtypes of breast cancer p0,05. This study identified potential prognostic biomarkers for breast cancer based on the hub genes derived from TIG1-associated DEGs, indicating their potential use in targeted therapeutic approaches.

 e-postae-mail: tugcankorakgmail.comtugcan.korakkocaeli.edu.tr Kabul TarihiAccepted: Tazarotene-induced gene 1 TIG1 is involved in modulating the α-tubulin modification and effectively inhibiting tumor growth. In this bioinformatics study, we aim to propose novel therapeutic targets in breast cancer by utilizing differentially expressed genes DEGs of TIG1 in inflammatory breast cancer IBC and examining their correlation with the molecular and immune subtypes. Using the GEO2R tool, we analyzed DEGs in the GSE30543 dataset, specifically comparing suppressed TIG1 groups with control samples from SUM149 cells. Functional annotation analysis of DEGs were explored using SRplot with data from STRING log2FC 2 and p0,05. Cytoscape software was used to construct intersected protein-protein interaction PPI network and define central genes. Subsequently, the molecular and immune subtype analysis were performed in TISIDB utilizing the identified hub genes. A total of 19 upregulated DEGs and 3 downregulated DEGs were identified in IBC and utilized to construct the STRING PPI network. GO analysis revealed that the biological functions of the identified DEGs primarily centered around the regulation of cell adhesion and migration. KEGG pathway analysis demonstrated their significant involvement in regulation of cell adhesion-related signaling pathways. Hub genes were identified as STAT3, PXDNL, FN1, CTNNB1, CD44, TNF, TP53, MMP9, SRC and INS. TISIDB analysis revealed significant correlations between all hub gene expressions and both the molecular subtypes except for TP53 and immune subtypes of breast cancer p0,05. This study identified potential prognostic biomarkers for breast cancer based on the hub genes derived from TIG1-associated DEGs, indicating their potential use in targeted therapeutic approaches.

 Tazaroten-indüklü gen 1 TIG1, α-tubulin tirosinasyon döngüsünü modüle etmek ve tümör büyümesini etkili bir şekilde inhibe etmekle ilişkilidir. Bu biyoinformatik çalışmada, TIG1in inflamatuar meme kanserindeki IBC farklı olarak ifade edilen genlerinin DEGler moleküler ve immün alt tiplerle olan korelasyonlarını inceleyerek meme kanserinde yeni terapötik hedefler önermeyi amaçlamaktayız. GEO2R aracını kullanarak, GSE30543 veri setindeki DEGler analiz edildi ve özellikle baskılanmış TIG1 grupları SUM149 hücrelerinden kontrol örnekleriyle karşılaştırıldı. DEGlerin fonksiyonel annotasyon analizi, SRplot aracılığıyla STRING verileri log2FC 2 ve p0,05 kullanılarak gerçekleştirildi. Cytoscape yazılımı, kesişen protein-protein etkileşim PPI ağını oluşturmak ve merkezi genleri belirlemek için kullanıldı. Ardından, moleküler ve immün alt tip analizleri, belirlenen merkezi genleri kullanılarak TISIDBde gerçekleştirildi. IBCde toplamda 19 yukarı regüle DEG ve 3 aşağı regüle DEG belirlendi ve bunlar yardımıyla STRING PPI ağı oluşturuldu. GO analizi, belirlenen DEGlerin biyolojik işlevlerinin başlıca olarak hücre adezyonu ve göçünün düzenlenmesine odaklandığını ortaya koydu. KEGG yolak analizi ise DEGlerin hücre adezyonu ile ilişkili sinyal yollarının düzenlenmesinde önemli bir rol oynadığını gösterdi. Merkezi genler STAT3, PXDNL, FN1, CTNNB1, CD44, TNF, TP53, MMP9, SRC ve INS olarak belirlendi. TISIDB analizi, tüm merkezi gen ekspresyonları ile meme kanserinin hem moleküler alt tipleri TP53 hariç hem de immün alt tipleri arasında anlamlı korelasyonlar olduğunu ortaya koydu p0,05. Bu çalışma ile TIG1 ile ilişkili DEGlerden elde edilen merkezi genlerden yola çıkarak meme kanseri için hedefe yönelik terapötik yaklaşımlarda kullanılabilecek potansiyel prognostik biyobelirteçlerin belirlenmesini sağlandı.

Makale detayları

Identification of TIG1 Associated Molecular Targets for Breast Cancer Using Bioinformatic Approach

Yazarlar:

Tuğcan Korak | Merve Gulsen Bal Albayrak | Gürler Akpınar | Murat Kasap

Yayıncı:

Gumushane University

Ana Başlıklar:

Biyokimya ve Hücre Biyolojisi (Diğer)

Dergi:

Gümüşhane Üniversitesi Sağlık Bilimleri Dergisi Vol.13 Issue 4, pp.1807-1817

Belge Tipi:

Makale

Yayın Tarihi:

12/2024

Belge Dili:

İngilizce

Document ID (Org No.):

2001335103

pISSN:

2146-9954

Biomarker

Breast cancer

GEO

TIG1Biyobelirteç

GEO

Meme kanseri

TIG1

Sayı

Makale detayları

Yazarlar: Tuğcan Korak | Merve Gulsen Bal Albayrak | Gürler Akpınar | Murat Kasap

Yayıncı: Gumushane University

Ana Başlıklar: Biyokimya ve Hücre Biyolojisi (Diğer)

Dergi: Gümüşhane Üniversitesi Sağlık Bilimleri Dergisi Vol.13 Issue 4, pp.1807-1817

Belge Tipi: Makale

Yayın Tarihi: 12/2024

Belge Dili: İngilizce

Document ID (Org No.): 2001335103

pISSN: 2146-9954

Sayı

Yazarlar:

Tuğcan Korak | Merve Gulsen Bal Albayrak | Gürler Akpınar | Murat Kasap

Yayıncı:

Gumushane University

Ana Başlıklar:

Biyokimya ve Hücre Biyolojisi (Diğer)

Dergi:

Gümüşhane Üniversitesi Sağlık Bilimleri Dergisi Vol.13 Issue 4, pp.1807-1817

Belge Tipi:

Makale

Yayın Tarihi:

12/2024

Belge Dili:

İngilizce

Document ID (Org No.):

2001335103

pISSN:

2146-9954