Simulating the restoration of normal gene expression from different thyroid cancer stages using deep learning

Abstract

Background: Thyroid cancer (THCA) is the most common endocrine malignancy and incidence is increasing. There is an urgent need to better understand the molecular differences between THCA tumors at different pathologic stages so appropriate diagnostic, prognostic, and treatment strategies can be applied. Transcriptome State Perturbation Generator (TSPG) is a tool created to identify the changes in gene expression necessary to transform the transcriptional state of a source sample to mimic that of a target.

Methods: We used TSPG to perturb the bulk RNA expression data from various THCA tumor samples at progressive stages towards the transcriptional pattern of normal thyroid tissue. The perturbations produced were analyzed to determine if there are consistently up- or down-regulated genes or functions in certain stages of tumors.

Results: Some genes of particular interest were investigated further in previous research. SLC6A15 was found to be down-regulated in all stage 1-3 samples. This gene has previously been identified as a tumor suppressor. The up-regulation of PLA2G12B in all samples was notable because the protein encoded by this gene belongs to the PLA2 superfamily, which is involved in metabolism, a major function of the thyroid gland. REN was up-regulated in all stage 3 and 4 samples. The enzyme renin encoded by this gene, has a role in the renin-angiotensin system; this system regulates angiogenesis and may have a role in cancer development and progression. This is supported by the consistent up-regulation of REN only in later stage tumor samples. Functional enrichment analysis showed that olfactory receptor activities and similar terms were enriched for the up-regulated genes which supports previous research concluding that abundance and stimulation of olfactory receptors is linked to cancer.

Conclusions: TSPG can be a useful tool in exploring large gene expression datasets and extracting the meaningful differences between distinct classes of data. We identified genes that were characteristically perturbed in certain sample types, including only late-stage THCA tumors. Additionally, we provided evidence for potential transcriptional signatures of each stage of thyroid cancer. These are potentially relevant targets for future investigation into THCA tumorigenesis.

Keywords: Deep learning; TSPG; Thyroid cancer; Transcriptome.

Fig. 1

Expression profiles of 19,239 genes in THCA tumor and normal thyroid samples. (A) The t-SNE plot shows RNA expression profiles of normal thyroid tissue from GTEx, normal thyroid tissue from TCGA, THCA tumor samples from TCGA of various stages, and all the perturbed samples with GTEx normal thyroid tissue as the target. (B) The representative heatmap shows the expression vectors of one Stage 3 THCA tumor sample (X), the perturbations applied (P), the perturbed sample (X + P), and average for the target class of normal thyroid tissue from GTEx (mu_T). Missing values in the training and perturbed sample GEMs were imputed with the minimum value of the training GEM

Fig. 2

Number of genes found by TSPG to be significantly perturbed in samples within each sample type. Significantly tumor-downregulated genes, as indicated by positive perturbations toward normal thyroid tissue from GTEx, are shown in red. Significantly tumor-upregulated genes, as indicated by negative perturbations toward normal thyroid tissue from GTEx, are shown in blue. Error bars represent standard error

Fig. 3

Number of shared significantly perturbed genes within each sample type. Significantly tumor-downregulated genes, as indicated by positive perturbations toward normal thyroid tissue from GTEx, are shown in red. Significantly tumor-upregulated genes, as indicated by negative perturbations toward normal thyroid tissue from GTEx, are shown in blue. Error bars represent standard error

Fig. 4

Proportion of shared significantly perturbed genes between samples, out of their unique significantly perturbed genes, within each sample type. Significantly tumor-downregulated genes, as indicated by positive perturbations toward normal thyroid tissue from GTEx, are shown in red. Significantly tumor-upregulated genes, as indicated by negative perturbations toward normal thyroid tissue from GTEx, are shown in blue. Error bars represent standard error