Title: Evolution of the Research Question
The approach to developing the research question was iterative, starting with a broad question and progressively refining it based on the available literature and data.
1- The broad research question:
The Primary research question guiding this study was, "Which shared characteristics among homogeneous studies can be utilized to distinguish between non-aggressive and aggressive breast cancer samples through gene expression profiling?"
The research question development process began with a broad interest in gene expression profiling in relation to breast cancer differentiation. Initially, with the aim of identifying biomarkers that could be utilized in the industry, a general research topic emerged, focusing on identifying common features across homogenous studies that could differentiate between non-aggressive and aggressive breast cancer samples through gene expression profiling. To ensure consistency and reliability, the selected studies included the use of the same platform (Affymetrix Human Genome U133A Array), technology (microarray), and biological specimens (tissue).
2- Utilizing Molecular Subtypes and Grading Systems for Breast Cancer Differentiation
After discovering the availability of grading systems and molecular subtypes in the homogenous datasets, we conducted a comprehensive literature review. The review revealed that Grade 1 was indicative of non-aggressiveness, while Grade 3 represented aggressiveness. In terms of molecular subtypes, Luminal A and Normal-like subtypes were associated with non-aggressive breast cancer, while Luminal B, Basal-like, and HER2-enriched subtypes were linked to more aggressive forms. Based on these findings, we developed two classification approaches: a grade-based classification and a molecular-based classification, each encompassing non-aggressive and aggressive groups. Consequently, the research question emerged as follows: "Can molecular subtypes and grading systems be used to differentiate between non-aggressive and aggressive breast cancer samples in microarray gene expression profiling?"
3- Distinguishing Non-Aggressive and Aggressive Breast Cancer Samples through Grade-Based Classification and Gene Expression Profiling
Further narrowing down the research question, the focus was specifically placed on examining whether the grading system (grade 1 vs. grade 3) and gene expression signatures, along with functional analysis, could be employed to distinguish between non-aggressive and aggressive breast cancer samples in microarray gene expression profiling. This research question served as the foundation for the subsequent analysis conducted in this study. The objective was to identify biomarkers that could accurately differentiate between these two groups using microarray gene expression profiling. The identified biomarkers would provide valuable information about the aggressiveness of the disease and aid in assessing the risk of distant metastasis.
4- Future Investigation: Comparative Analysis of Differentiating Breast Cancer Samples through Molecular Subtype-based and Grade-based approaches:
As a future research question, the research query will be further refined to investigate whether molecular subtypes and gene expression signatures, along with functional analysis, can be used to differentiate between non-aggressive and aggressive breast cancer samples in microarray gene expression profiling, while also comparing the obtained results with those derived from the grade-based classification. This comparative analysis will aim to evaluate the differential expression outcomes of the grade-based and molecular subtype-based classification approaches.