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Turkish Journal of Biochemistry

Türk Biyokimya Dergisi


IMPACT FACTOR 2018: 0.329

CiteScore 2018: 0.28

SCImago Journal Rank (SJR) 2018: 0.138
Source Normalized Impact per Paper (SNIP) 2018: 0.169

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1303-829X
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Volume 44, Issue 5

Issues

Identification of immune-related genes in thymus of breast cancer mouse model exposed to different calorie restriction

Farklı Kalori Kısıtlaması Uygulanmış Meme Kanseri Model Farenin Timusundaki İmmün Sistem İlişkili Genlerin Belirlenmesi

Zehra Omeroglu Ulu / Salih Ulu / Soner Dogan / Bilge Guvenc Tuna / Nehir Ozdemir OzgenturkORCID iD: https://orcid.org/0000-0003-3809-6303
Published Online: 2018-11-14 | DOI: https://doi.org/10.1515/tjb-2018-0121

Abstract

Introduction

In the present study, RNA sequencing-mediated transcriptome analysis was performed in order to elucidate the molecular mechanisms of the immune response for different types of calorie restriction (CR) application using MMTV-TGF-α breast cancer mouse model.

Methods

Animals were applied to three different dietary regiments; ad libitum (AL), chronic calorie restriction (CCR) and intermittent calorie restriction (ICR). Using thymus tissues, 6091 differentially expressed genes (DEGs) were identified in three dietary groups. After clustering of total of 6091 DEGs using Gene Ontology (GO) categories, a total of 400 genes were identified to be involved in immune system process (GO:0002376) GO categories. KEGG pathway and gene co-expression network analysis of these immune-related DEGs were done using String database. The results were confirmed with measuring mRNA expression levels of four selected immune-related DEGs genes (Casp3, Thy1, IL-16 and CD4) using quantitative real-time PCR (qPCR).

Results

The expression levels of immune-related genes were different in three RNA-seq data.

Conclusion

The results provide useful information to investigate the immune-related transcriptional profiling in thymus tissue of breast cancer mouse model applied to two different types of CR and to identify the specific functional immune related genes in response to CR during cancer development.

Öz

Amaç

Bu çalışmada, MMTV-TGF-a meme kanseri fare modeli kullanılarak, farklı kalori kısıtlaması (KK) uygulamaları için immün yanıtın moleküler mekanizmalarını açıklamak amacıyla RNA sekanslama aracılıklı transkriptom analizi yapılmıştır.

Gereç ve Yöntem

Farelere üç farklı beslenme uygulanmıştır; ad libitum (AL), kronik kalorili kısıtlama (KKK) ve aralıklı kalori kısıtlaması (AKK). Timus dokuları alınarak üç beslenmedeki diferansiyel eksprese olan genlerin toplamda 6091 tane olduğu tanımlanmıştır. Bu genler genler Gen Ontolojisi (GO) kategorileri kullanılarak sınıflandırılmıştır. İmmün sistem proses (GO: 0002376) GO kategorisinde toplam 400 gen tespit edilmiştir. Bu genler için KEGG yolak ve ortak ifade ağ analizi, String veritabanı kullanılarak yapılmıştır. Daha sonra, kantitatif gerçek zamanlı PCR kullanılarak seçilmiş dört immün sistemde görevli geninin (Casp3, Thy1, IL-16 ve CD4) mRNA ekspresyon seviyeleri ölçülmüştür.

Sonuç

Üç RNA-seq datasında immün sistemle ilişkili genlerin ekspresyon seviyelerinin farklı olduğu gözlemlenmiştir.

Tartışma

Sonuçlar, iki farklı kalori kısıtlaması uygulanan meme kanseri fare modelinin timus dokusunda immün sistem ile ilgili transkripsiyonel profili araştırmak için ve kanser gelişimi sırasında kalori kısıtlamasına yanıt olarak spesifik fonksiyonel immün sistem ilişkili genleri tanımlamamıza yardımcı olacak bilgiler sağlamaktadır.

Keywords: Intermittent calorie restriction; Chronic calorie restriction; Thymus; RNA-seq; Immune-related genes

Anahtar kelimeler: Aralıklı kalori kısıtlaması; Kronik kalori kısıtlaması; Timus; RNA sekanslama; İmmün sistem ilişkili genler

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About the article

Received: 2018-04-16

Accepted: 2018-10-02

Published Online: 2018-11-14

Published in Print: 2019-10-25


Conflicts of interest statement: The authors declare that they have no conflicts of interest.


Citation Information: Turkish Journal of Biochemistry, Volume 44, Issue 5, Pages 635–645, ISSN (Online) 1303-829X, DOI: https://doi.org/10.1515/tjb-2018-0121.

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