Samenvatting
Pancreatic cancer is known as a lethal disease with poor treatment responses. This is partly attributed to the complex and heterogeneous landscape of the tumours.
Transcriptomic studies on bulk tumours defined two consensus molecular subtypes in human pancreatic ductal adenocarcinoma (PDAC): GATA6-expressing classical tumours and deltaNp63/p40-driven basal-like tumours, with the latter having reportedly higher levels of KRAS dosage and a worse prognosis. Adenosquamous cancer of the pancreas (ASCP) is another rare tumor with a large component of deltaNp63/p40 expressing cells and an even worse prognosis.
When single-cell omics came into practice, the two-classification system in PDAC was considered an oversimplification. More recent studies reported the coexistence of both subtypes within a single tumour leading to the hypothesis of plastic tumour cells on a transcriptomic spectrum, rather than distinct cell populations. At the onset of this PhD, there were no specific markers to detect different subtypes in situ, except for GATA6 that is a marker of the classical subtype.
To better understand the spatial context of transcriptomic subtypes and the related expression of mutant KRAS, we aimed to apply RNAScope™ as a method to quantify
classical and basal-like tumour cells in paraffin sections of human resected PDAC, along with BaseScope™ assay to detect KRAS-specific point mutations in situ. In addition, we wanted to explore spatial transcriptomics methods to better profile P40-expressing cells in pancreatic tumours.
Informed by bulk transcriptomic signatures, we developed and optimised novel subtypespecific gene panels for multiplex RNAScope™ in combination with in situ mutation detection of mutant KRAS. We observed an intra-tumour subtype heterogeneity with different levels of mutant KRAS expression up until the level of single PDAC ducts. We
managed to measure tumour heterogeneity and we identified the dominant subtype. Additionally, we applied the method to an in vitro system where matched cancer-associated fibroblasts were co-cultured with PDAC organoids, showing the spatial relevance of stromal cell populations in shaping tumour subtypes. In addition, we
collected preliminary data demonstrating a heterogeneity in deltaNp63/p40 tumour cells, with a distinct spatial and functional organisation within ASCP.
Altogether, this thesis dissertation presented novel methods for spatial subtyping of pancreatic tumours, that is applicable in (pre-)clinical research studies. We believe that
these novel technologies will provide significant insights into understanding subtype plasticity, paving the way for stratified (plasticity-targeted) therapies in pancreatic cancer.
Transcriptomic studies on bulk tumours defined two consensus molecular subtypes in human pancreatic ductal adenocarcinoma (PDAC): GATA6-expressing classical tumours and deltaNp63/p40-driven basal-like tumours, with the latter having reportedly higher levels of KRAS dosage and a worse prognosis. Adenosquamous cancer of the pancreas (ASCP) is another rare tumor with a large component of deltaNp63/p40 expressing cells and an even worse prognosis.
When single-cell omics came into practice, the two-classification system in PDAC was considered an oversimplification. More recent studies reported the coexistence of both subtypes within a single tumour leading to the hypothesis of plastic tumour cells on a transcriptomic spectrum, rather than distinct cell populations. At the onset of this PhD, there were no specific markers to detect different subtypes in situ, except for GATA6 that is a marker of the classical subtype.
To better understand the spatial context of transcriptomic subtypes and the related expression of mutant KRAS, we aimed to apply RNAScope™ as a method to quantify
classical and basal-like tumour cells in paraffin sections of human resected PDAC, along with BaseScope™ assay to detect KRAS-specific point mutations in situ. In addition, we wanted to explore spatial transcriptomics methods to better profile P40-expressing cells in pancreatic tumours.
Informed by bulk transcriptomic signatures, we developed and optimised novel subtypespecific gene panels for multiplex RNAScope™ in combination with in situ mutation detection of mutant KRAS. We observed an intra-tumour subtype heterogeneity with different levels of mutant KRAS expression up until the level of single PDAC ducts. We
managed to measure tumour heterogeneity and we identified the dominant subtype. Additionally, we applied the method to an in vitro system where matched cancer-associated fibroblasts were co-cultured with PDAC organoids, showing the spatial relevance of stromal cell populations in shaping tumour subtypes. In addition, we
collected preliminary data demonstrating a heterogeneity in deltaNp63/p40 tumour cells, with a distinct spatial and functional organisation within ASCP.
Altogether, this thesis dissertation presented novel methods for spatial subtyping of pancreatic tumours, that is applicable in (pre-)clinical research studies. We believe that
these novel technologies will provide significant insights into understanding subtype plasticity, paving the way for stratified (plasticity-targeted) therapies in pancreatic cancer.
| Originele taal-2 | English |
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| Toekennende instantie |
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| Begeleider(s)/adviseur |
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| Status | Published - 2025 |