“Reprogram Enablement” as an Assay for Identifying Early Oncogenic Pathways by Their Ability to Allow Neoplastic Cells to Reacquire an Epiblast State

Abstract

Summary One approach to understanding how tissue-specific cancers emerge is to determine the requirements for “reprograming” such neoplastic cells back to their developmentally normal primordial pre-malignant epiblast-like pluripotent state and then scrutinizing their spontaneous reconversion to a neoplasm, perhaps rendering salient the earliest pivotal oncogenic pathway(s) (before other aberrations accumulate in the adult tumor). For the prototypical malignancy anaplastic thyroid carcinoma (ATC), we found that tonic RAS reduction was obligatory for reprogramming cancer cells to a normal epiblast-emulating cells, confirmed by changes in their transcriptomic and epigenetic profiles, loss of neoplastic behavior, and ability to derive normal somatic cells from their “epiblast organoids.” Without such suppression, ATCs re-emerged from the clones. Hence, for ATC, RAS inhibition was its “reprogram enablement” (RE) factor. Each cancer likely has its own RE factor; identifying it may illuminate pre-malignant risk markers, better classifications, therapeutic targets, and tissue-specification of a previously pluripotent, now neoplastic, cell.

Predicting the Reprogrammability of Human Cells Based on Transcriptome Data and SGD Classifier with Elastic-Net Regularization

“…In order to achieve a higher sample number to establish ML-based algorithms, we accessed transcriptome data of various reprogramming studies from the literature that resulted in either success or failure. Transcriptome reads that have been downloaded included that of melanoma cells from Castro-Perez et al 29 , human CD34+ cells from Friedli et al 30 , human fibroblast cells from different studies [31][32][33][34][35][36] , human acute myeloid leukemia cells from Chao et al 37 , human thyroid-carcinoma cell-lines from Kong et al 38 . Out of these 18 cell lines (consisting of 38 replicate (cells) ), 12 cell lines (26 replicates) have been reported to be successfully reprogrammed whereas 6 (12 replicates) of them failed to generate iPSC colonies [29][30][31][32][33][34][35][36] .…”

A review of dynamical systems approaches for the detection of chaotic attractors in cancer networks

“…(i.e., normal iPSC states). Kong et al 64 demonstrated that suppression of the RAS-pathway can reprogram anaplastic thyroid tumors-aggressive, fast-growing lethal cancers-into transient iPSCs.…”

“…Sendai virus-mediated transduction of the OSKM factors enabled the generation of transient iPSCs only from tumor cells bearing a Ras mutation. 64 At the transcriptional and epigenetic level, the cancer-derived iPSCs clustered closely to human embryonic stem cells and lost many of their malignant markers. The genes upregulated in the cancer-derived pluripotent stem cells (SOX2, LIN28A, and SALL4) showed a decrease in DNA methylation surrounding their promoters, indicative of reprogrammed epigenetic landscapes and a loss of neoplastic potential.…”

“…The genes upregulated in the cancer-derived pluripotent stem cells (SOX2, LIN28A, and SALL4) showed a decrease in DNA methylation surrounding their promoters, indicative of reprogrammed epigenetic landscapes and a loss of neoplastic potential. 64 While CD133+/CD44+ enriched CSCs may have been present in the starting tumor population, they were undetected post-reprogramming to epiblast-like states. Key molecular patterns regulated by the RAS-signaling cascade, such as NF-κB, were downregulated to levels seen in embryogenesis, as observed via the heatmaps constructed from gene set enrichment analysis.…”

“…When a reversible pharmacological RAS-MEK inhibitor, PD0325901, was withdrawn, the reprogramming was blocked and the cancer-derived iPSCs converted back to their parental lineage-specific neoplastic cells. 64 The risks of these methods, such as the possibility of tumor regression/formation, teratoma formation, and other possibilities are ignored here, and only the ability to reprogram tumor plasticity is put into context.…”