Gene chips, as a high-throughput gene detection technology, have been widely used in research fields such as basic medicine, disease diagnosis, and therapeutic targeting15. Gene chips can simultaneously detect the abundance of splicing, expression, and transcription of tens of thousands of genes in human samples, and the theories and methods for data analysis are still constantly evolving. At present, a large amount of publicly available gene chip research data related to diseases has accumulated, providing researchers with convenient research materials. Researchers can reanalyze public data from new scientific perspectives to quickly study new scientific problems. Given that clinical studies have shown that both anaplasia and laterality affect the clinical decision and prognosis of RB16, this study examined publicly available high-throughput gene expression data that were not fully analyzed, reorganized the samples, and compared gene expression related to anaplasia and laterality.
Analysis of the public GSE141209 dataset revealed that compared to those of unilateral patients, the tumor tissues of bilateral patients with RB were enriched in vision-related functions, and the expression of multiple related genes was increased. However, the impact of anaplasia on gene expression has not been explored9. This study compared the gene expression of negative and severe anaplasia samples in the GSE141209 dataset and revealed that the expression of functional genes related to sensory perception was inhibited in severe anaplasia samples, indicating that both anaplasia and laterality are important factors affecting clinical conditions. There were only 8 GSE141209 samples, which has certain limitations. Therefore, we further conducted research with the public dataset GSE110811.
GSE110811 revealed that different degrees of anaplasia were associated with various gene expression characteristics, and functional genes related to visual perception, such as light perception, exhibited significantly reduced expression in severe anaplasia patients. However, lateral effects have not been explored10. This study included 28 patients in the GSE110811 dataset for further analysis of the relationship between anaplasia/laterality and gene expression. Samples with the same laterality or grading of anaplasia were selected in the study to minimize the mutual interference between the two factors:
1) We compared gene expression between the bilateral and unilateral groups of 13 moderate anaplasia patients and found that the expression of multiple genes affecting eye conjugation movement and lipid metabolism was enhanced in the unilateral group, while the expression of genes inhibiting cell proliferation was enhanced in the bilateral group. This finding is different from the lateral comparison results of the public dataset GSE141209, indicating an objective difference between the two public datasets.
2) We compared the gene expression of 17 unilateral patients in the severe and moderate anaplasia groups and found a statistically significant decrease in the expression of genes related to sensory perception and light perception in the severe anaplasia group. This finding is similar to the results of the entire GSE110811 sample, as well as our analysis of anaplasia in the public dataset GSE141209. However, the related genes were not completely consistent. Notably, the expression of the RGS9 gene was significantly decreased in the severe anaplasia group according to both sets of public data, suggesting that RGS9 may have important functions in severe anaplasia patients.
3) We compared the gene expression of 9 bilateral patients in the moderate and mild anaplasia groups and did not detect any vision-related genes or functional changes. This may be related to the small difference in anaplasia between the two groups.
The results above indicate that different anaplasias and lateralities are regulated by different vision-related tumor genes in the pathogenesis of RB. This study suggested the possibility of unique functional gene features related to anaplasia and laterality, which may jointly affect the clinical development of RB. Future research with larger clinical samples is essential to elucidate the full impact of these genetic differences on diagnosis and treatment strategies. In addition, although public data can provide research materials for new research ideas, they also have certain sample limitations. For example, in this study, we can only choose a fixed research factor to study another factor; otherwise, it is difficult to rule out the mutual influence between the two factors. However, this has important significance for the next step of research, suggesting that attention should be given to avoiding interference between anaplasia and lateral factors when collecting self-owned samples and designing experiments.