Exploring novel immunotherapy biomarker candidates induced by cancer deformation

Abstract

Triple-negative breast cancer (TNBC) demands urgent attention for the development of effective treatment strategies due to its aggressiveness and limited therapeutic options [1]. This research is primarily focused on identifying new biomarkers vital for immunotherapy, with the aim of developing tailored treatments specifically for TNBC, such as those targeting the PD-1/PD-L1 pathway. To achieve this, the study places a strong emphasis on investigating Ig genes, a characteristic of immune checkpoint inhibitors, particularly genes expressing Ig-like domains with altered expression levels induced by "cancer deformation," a condition associated with cancer malignancy. Human cells can express approximately 800 Ig family genes, yet only a few Ig genes, including PD-1 and PD-L1, have been developed into immunotherapy drugs thus far. Therefore, we investigated the Ig genes that were either upregulated or downregulated by the artificial metastatic environment in TNBC cell line. As a result, we confirmed the upregulation of approximately 13 Ig genes and validated them using qPCR. In summary, our study proposes an approach for identifying new biomarkers applicable to future immunotherapies aimed at addressing challenging cases of TNBC where conventional treatments fall short.

Fig 1

A, Schematic Illustration Showing the Sample Preparation Process B, Heatmap illustrating variations in differentially expressed genes C, The top 5 genes among the 148 upregulated genes. D, The top 5 genes among the 148 downregulated genes.

Fig 2

A, Schematic diagram for distinguishing the extracellular Ig domain. B, RNA Sequencing-Derived Heatmap of Genes with Distinct Ig-Like Domains. C, List of genes with increased expression having Ig-like domains. D, List of genes with decreased expression having Ig-like domains.

Fig 3

A, Violin plot constructed based on RNA sequencing results for genes with increased expression containing Ig-like domains. B, Based on the results of the Violin plot, gene expression changes were validated through qRT-PCR in Ori, TW1, and TW2 samples.

Fig 4

A, Violin plot generated using RNA sequencing data to visualize genes with reduced expression that contain Ig-like domains. B, Based on the results from the Violin plot, the reduction in gene expression was confirmed through qRT-PCR in the Ori, TW1, and TW2 samples.

Fig 5

A, Schematic illustration depicting the structure of extracellular domains of genes analyzed as upregulated in RNA sequencing. B, List of genes with confirmed increases or decreases between Ori and TW1, validated through RNA sequencing and qRT-PCR.