Role of COLCA1 and lncRNAs in Early-Stage Breast Cancer Progression: Insights from RNA Sequencing
Role of COLCA1 and lncRNAs in Early-Stage Breast Cancer Progression: Insights from RNA Sequencing
Roxana Tajdini,1Farinaz Behfarjam,2,*Maryam Shahhoseini2,3Mostafa rafiepour,4
1. Department of Genetics, Faculty of Science, Science and Culture University 2. Royan Institute of Reproductive Biomedicine 2. Department of Genetics, Faculty of Science, Danesh Alborz University 3. Royan Institute of Reproductive Biomedicine 4. 3. Department of Genetics, Faculty of Science, Danesh Alborz University
Introduction: Breast cancer is the most common cancer affecting women worldwide each year. It is a multifactorial disease caused by various factors such as gender, age, genetic mutations, and being overweight. Early detection of breast cancer can save lives. One method used for diagnosis is next-generation sequencing (NGS).In this research project, data from RNA sequencing of early-stage breast cancer tissue, obtained using the NGS method, is analyzed to identify lncRNAs (long non-coding RNA) involved in the development of breast cancer. These lncRNAs can serve as biomarkers for the prognosis and diagnosis of the disease.
Methods: Three RNA-seq data sets from early-stage breast cancer tissue (sample group) and three RNA-seq data sets from healthy breast tissue (control group) were extracted from the NCBI Sequence Read Archive (SRA) database. First, the data quality was assessed using FastQC software, ensuring its quality standards. Next, STAR software was used to compare and align the RNA-seq sequences from healthy and cancerous tissue to the human reference genome.
For data normalization and statistical analysis, the DESeq2 package in the R software environment was used, identifying genes with differential expression.
Results: By determining the biotype of these genes, potential lncRNAs involved in breast cancer development were identified. By applying thresholds of P-value < 0.05 and Log2 Fold Change > 2 on differentially expressed genes, 16 lncRNAs with increased expression were found. These include SNHG26, PAX8-AS1, SLC7A14-AS1, AQP5-AS1, and COLCA1.
Conclusion: Evidence shows that COLCA1 plays an important role in cancer progression pathways, such as the Wnt/β-catenin and mTORC1 pathways, which affect cell growth and angiogenesis, contributing to tumor growth and spread. Additionally, COLCA1 affects the expression of microRNAs, including miR-371a-5p, which regulates inflammation and immune responses. miR-371a-5p acts as a tumor suppressor, and COLCA1 likely helps tumors evade the immune system by inhibiting this function, promoting tumor growth.
Due to the complex role of COLCA1 in biological pathways, this lncRNA could be considered an important biomarker for diagnosing early-stage breast cancer.