Discovery of New Targets to Control Metastasis in Pancreatic Cancer by Single-cell Transcriptomics Analysis of Circulating Tumor Cells

Abstract

◥Metastasis development is the leading cause of cancer-related mortality in pancreatic ductal adenocarcinoma (PDAC) and yet, few preclinical systems to recapitulate its full spreading process are available. Thus, modeling of tumor progression to metastasis is urgently needed. In this work, we describe the generation of highly metastatic PDAC patient-derived xenograft (PDX) mouse models and subsequent single-cell RNA-sequencing (RNA-seq) of circulating tumor cells (CTC), isolated by human HLA sorting, to identify altered signaling and metabolic pathways, as well as potential therapeutic targets. The mouse models developed liver and lung metastasis with a high reproducibility rate. Isolated CTCs were highly tumorigenic, had metastatic potential, and single-cell RNAseq showed that their expression profiles clustered separately from those of their matched primary and metastatic tumors and were characterized by low expression of cell-cycle and extracellular matrix-associated genes. CTC transcriptomics identified survivin (BIRC5), a key regulator of mitosis and apoptosis, as one of the highest upregulated genes during metastatic spread. Pharmacologic inhibition of survivin with YM155 or survivin knockdown promoted cell death in organoid models as well as anoikis, suggesting that survivin facilitates cancer cell survival in circulation. Treatment of metastatic PDX models with YM155 alone and in combination with chemotherapy hindered the metastatic development resulting in improved survival. Metastatic PDX mouse model development allowed the identification of survivin as a promising therapeutic target to prevent the metastatic dissemination in PDAC.

Investigating epithelial‐mesenchymal heterogeneity of tumors and circulating tumor cells with transcriptomic analysis and biophysical modeling

“…First, we consider the case where the EMT score of the tumor is known; this is a typical scenario if gene expression from a tumor sample is analyzed, either at a single‐cell or bulk resolution. For instance, we calculate the MLR scores of several samples from a pancreatic ductal patient‐derived xenograpt model [43]; on average, the samples are predicted to be hybrid E/M (1.13 0.14). In the model, constraining the tumor EMT score to a fixed value is equivalent to selecting a contour line on the two‐dimensional (k, c) parameter space (Figure 5B, left).…”

Application of single-cell sequencing technologies in pancreatic cancer

“…These makers are found to be distinct subpopulation and are used to navigate management of cancer [ 27 ]. Dimitrov et al [ 28 ] isolated CTCs from the PC mouse models having liver and lung metastasis. They clustered the single-cell RNA sequencing as per their expressing profile including cell cycle molecules and extracellular matrix-associated genes taken from both primary and metastatic samples.…”

The Single-Cell Sequencing: A Dazzling Light Shining on the Dark Corner of Cancer

“…Another meaningful study using scRNA-seq identified heterogeneity between primary and metastatic lesions, confirming that BIRC5 expression was massively upregulated in metastatic CTCs. YM155 administration in a model with BIRC5 deletion shrank the metastatic foci in SW1990-bearing mice, thus indicating that BIRC5 in CTCs is a key coordinator of the metastasis of pancreatic cancer ( 71 ).…”