Experimental profiling and in silico validation of autophagy and apoptosis-related genes in murine lung cancer and fibroblast cells

Berrin Ozdil; Yasemin Adalı; Yasemin Berberoğlu; Irmak Tutak; Aylin Koseler; Hüseyin Aktuğ

doi:10.19161/etd.1763314

TR EN

Murin akciğer kanseri ve fibroblast hücrelerinde otofaji ve apoptoz genlerinin deneysel profilleme ve in silico validasyonu

Öz

Amaç: Otofaji ve apoptoz, hücresel homeostazın korunmasında kritik bir rol oynayan kritik programlanmış hücre ölüm yollarıdır. Bu süreçlerin düzensizliği genellikle kanser gelişimi ve ilerlemesinde rol oynar. Amacımız, murin akciğer karsinomu hücreleri ile malign olmayan fibroblastlar arasındaki anahtar otofaji ve apoptozla ilişkili genlerin ekspresyon profillerini karşılaştırmak ve in silico analizler kullanarak düzenleyici etkileşimlerini değerlendirmektir. Gereç ve Yöntem: KLN-205 murin akciğer karsinomu hücreleri ve fare derisi fibroblastları (MSF) standart koşullar altında kültüre edilmiştir. Atg7, SQSTM1, Beclin-1, Kaspaz-3, Kaspaz-8, Kaspaz-9, Bax ve Bcl-2'nin mRNA ekspresyon seviyeleri RT-qPCR ile ölçülmüştür. Normalize edilen veriler 2-ΔΔCT dönüşümü kullanılarak analiz edilmiş ve gruplar arasındaki istatistiksel farklılıklar eşleşmemiş t-testleri ile değerlendirilmiştir. Temel bileşen analizi (PCA) ve STRING veri tabanı kullanılarak protein-protein etkileşimi (PPI) ağlarının oluşturulması dahil olmak üzere daha geniş ekspresyon modellerini ve moleküler etkileşimleri keşfetmek için in silico analizler yapılmıştır. Bulgular: MSF'ye kıyasla KLN-205 hücrelerinde Atg7'de anlamlı bir aşağı regülasyon gözlenmiştir (p <0.05). PCA, iki hücre tipinin farklı kümelenmesini gösterirken, volkan grafikleri ve ısı haritaları transkripsiyonel farkın varlığını desteklemiştir. STRING ağ analizi, otofaji ve apoptoz düzenleyicileri arasında, Beclin-1 ve Kaspaz-3’ün ana ağ merkezleri olarak kompakt etkileşimleri ortaya çıkarmıştır. Zenginleştirme analizleri, ‘Otofaji’, ‘Apoptoz’, ‘p53 sinyali’ ve ‘Mitofaji’ gibi aşırı temsil edilen yolakları belirlenmiştir. Sonuç: Çalışmamız, murin akciğer karsinomu hücrelerinde otofaji ve apoptoz yolaklarının koordineli transkripsiyonel modülasyonunu vurgulamaktadır. Atg7'nin belirgin aşağı regülasyonu ve diğer anahtar genlerin değişmiş ekspresyonu, otofajik mekanizmanın fonksiyonel olarak baskılanmasını ve hücre ölümü regülasyonunun yeniden şekillenmesini önermektedir.

Anahtar Kelimeler

Experimental profiling and in silico validation of autophagy and apoptosis-related genes in murine lung cancer and fibroblast cells

Abstract

Aim: Autophagy and apoptosis are key programmed cell death pathways that play a critical role in cellular homeostasis. Dysregulation of these pathways is frequently associated with cancer development and progression. Comparing the molecular signatures of tumor and normal cells may provide novel insights into the survival mechanisms adopted by cancer cells. Objective: The objective of this study was to compare the expression profiles of key autophagy- and apoptosis-related genes between murine lung carcinoma cells and non-malignant fibroblasts and to assess their regulatory interactions using in silico analyses. Materials and Methods: KLN-205 murine lung carcinoma cells and mouse skin fibroblasts (MSF) were cultured under standard conditions. The mRNA expression levels of Atg7, SQSTM1, Beclin-1, Caspase-3, Caspase-8, Caspase-9, Bax, and Bcl-2 were quantified by RT-qPCR. Normalized data were analyzed using 2-ΔΔCT method, and statistical differences between groups were evaluated using unpaired t-tests. In silico analyses were performed to explore broader expression patterns and molecular interactions, including principal component analysis (PCA) and the construction of protein–protein interaction (PPI) networks using the STRING database. Results: A significant downregulation of Atg7 was observed in KLN-205 cells compared to MSF (p < 0.05). PCA demonstrated distinct clustering of the two cell types, while volcano plots and heatmaps supported the presence of transcriptional differences. STRING network analysis revealed compact interactions between autophagy and apoptosis regulators, with Beclin-1 and Caspase-3 as key network hubs. Enrichment analyses identified overrepresented pathways such as ‘Autophagy,’ ‘Apoptosis,’ ‘p53 signaling,’ and ‘Mitophagy.’ Conclusion: Our findings indicate that murine lung carcinoma cells exhibit coordinated transcriptional changes in autophagy and apoptosis pathways. In particular, the significant downregulation of Atg7 and altered expression of other key genes suggest a functional suppression of the autophagic machinery and a reprogramming of cell death regulation.

Keywords

Kaynakça

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Ayrıntılar

Birincil Dil

İngilizce

Konular

Kanser Hücre Biyolojisi

Bölüm

Araştırma Makalesi

Yazarlar

Berrin Ozdil
0000-0001-6081-2308
Türkiye

Yasemin Adalı
0000-0002-6314-4816
United Kingdom

Yasemin Berberoğlu
0000-0003-4226-674X
Türkiye

Irmak Tutak
0000-0001-5559-8650
Türkiye

Aylin Koseler
0000-0003-4832-0436
Türkiye

Hüseyin Aktuğ ^*
0000-0003-4150-8495
Türkiye

Yayımlanma Tarihi

9 Mart 2026

Gönderilme Tarihi

14 Ağustos 2025

Kabul Tarihi

28 Ekim 2025

Yayımlandığı Sayı

Yıl 2026 Cilt: 65 Sayı: 1

DOI

https://doi.org/10.19161/etd.1763314

IZ

https://izlik.org/JA96LC37DR

Kaynak Göster

RIS / Bibtex

Vancouver

1.Berrin Ozdil, Yasemin Adalı, Yasemin Berberoğlu, Irmak Tutak, Aylin Koseler, Hüseyin Aktuğ. Experimental profiling and in silico validation of autophagy and apoptosis-related genes in murine lung cancer and fibroblast cells. ETD. 01 Mart 2026;65(1):55-67. doi:10.19161/etd.1763314