Background : Uncontrolled proliferation of tumor cells leads to hypoxia. Hypoxia can cause changes in hypoxia responsive genes transcriptions as an adaptation to limited oxygen. RNA sequencing in breast cancer cells is still varied and is known to change with the duration of treatment. The aim of this project was to compare the mRNA profiles between normoxia and hypoxia of T47D breast cancer cells using RNA-seq.
Methods : T47D breast cancer cell cultured under hypoxic conditions (0.5% oxygen) for 6, 24 and 48 h. RNA was extracted using the Qiagen allprep DNA/RNA/Protein Mini kit. Total RNA with RNA Integrity Number >7 will be sequenced to reveal gene expression profiles.
Results: 143,875,430 out of 169,314,448 reads (85%) were passed filtering. Of those, 26.684,288 reads (18.45%) are from 6 hours hypoxia, 29,178,225 reads (20.28%) from hypoxia 24 hours, 27,615,450 reads (19.19%) from hypoxia 48 hours. While 24,514,359 reads (17.94%) are from the normoxia group. During treatment, 23 genes were differentially expressed between groups; three genes are downregulated, and the rest are upregulated. Three genes (TAF1C, CD63, TM7SF2) were upregulated in the normoxia group, two genes (CYP1A1 and VCP) were upregulated in 6 hours of hypoxia. Two genes (NEBL and KDM3A) were upregulated in 24 hours hypoxia, while six genes (ERBB3, PIKP1, Ro60, ESRP1, KLF6, MKRN2) were upregulated in 48 hours hypoxia group.
Conclusion: Gene expression profiles between treatment and control group are different. Modulation of gene expression during hypoxia plays a role in glycolysis, proliferation, growth, and migration.