Dynamics of the microbiome in pancreatic cancer from inception to invasion

Pfisterer, Nina

dc.contributor.advisor	Neeße, Albrecht Prof. Dr. Dr.
dc.contributor.author	Pfisterer, Nina
dc.date.accessioned	2023-10-23T17:29:32Z
dc.date.available	2023-10-30T00:52:56Z
dc.date.issued	2023-10-23
dc.identifier.uri	http://resolver.sub.uni-goettingen.de/purl?ediss-11858/14930
dc.identifier.uri	http://dx.doi.org/10.53846/goediss-10152
dc.format.extent	174	de
dc.language.iso	eng	de
dc.subject.ddc	610
dc.title	Dynamics of the microbiome in pancreatic cancer from inception to invasion	de
dc.type	doctoralThesis	de
dc.contributor.referee	Neeße, Albrecht Prof. Dr. Dr.
dc.date.examination	2023-09-11	de
dc.description.abstracteng	Recently, the microbiome was associated with hallmark features of pancreatic ductal adenocarcinoma (PDAC). This dismal human disease with one of the lowest survival rates of below 10% is characterized by clinical challenges such as unspecific symptoms, lack of biomarkers, late diagnosis, refractoriness against systemic therapies, and a high recurrence rate after surgery. The biology behind these difficulties has been approached in multiple ways, for instance by tackling the pronounced desmoplastic stroma or investigating chemotherapy-inactivating enzymes. To date, no significant progress with clinical usage was made. After being long known for its impact on a plethora of physiological and pathophysiological processes, studies of considerable impact have lately demonstrated the microbiome to be involved in all kinds of aspects of various cancer types. Moreover, the discovery of tumors and healthy organs to harbor differential microbiota was groundbreaking. These findings were also and most notably shown in PDAC. Being one of the deadliest cancers, PDAC would benefit immensely from systematic, reliable microbiome research. Being convinced that third generation sequencing is the most effective technology for precise and reproducible microbiome studies, a sequencing platform by Oxford Nanopore Technologies (ONT) together with a comprehensive workflow for DNA extraction, library preparation and bioinformatic analysis was established as a major project within the scope of this thesis. This comprised testing seven different DNA isolation protocols and benchmarking several other parameters. Further, the pipeline was optimized for murine high (feces) and low microbial biomass (pancreatic) samples. Ensuing successful establishment of ONT sequencing, the presence of bacterial material in murine KPC tumor and human PDAC tissue was shown via IHC targeting lipopolysaccharide and FISH targeting the 16s rRNA gene. The occurrence of both components was visualized and, for KPC tumors, also quantified demonstrating a significantly higher abundance in diseased tissue as compared to healthy controls. The characterization of the fecal microbiome at various time points during disease progression as well as the end stage tumor microbiome in the KPC mouse model via ONT sequencing impressively showed significant differences in beta diversity metrics compared to their healthy counterparts. Furthermore, the similarity with recently published human stool and PDAC microbiomes could be ascertained via regression models. Finally, first experiments involving FFPE tissue material as most commonly available sample source in the clinical setting were performed aiming at evaluating the impact of PDAC subtypes on their intratumoral microbiomes. Therefore, samples from tumors derived from orthotopically transplanted human PDAC cell lines of the classical and basal-like subtype, as well as xenografted classical tumors treated with TNFα causing lineage reprogramming, and resected human PDAC which was subtyped via IHC were employed. In the course of these experiments, contamination issues were encountered and are explicitly discussed in the following. The results were not as conclusive as the KPC data, however, first evidence for the PDAC subtype to impinge on the microbiome is given. Taken together, new sequencing technology by ONT was installed in a customized way, distinct local microbiomes of the KPC model were characterized and found to be similar to the situation in humans, and PDAC subtypes seem to influence the microbiome.	de
dc.contributor.coReferee	Dobbelstein, Matthias Prof. Dr.
dc.subject.eng	pancreatic ductal adenocarcinoma	de
dc.subject.eng	PDAC	de
dc.subject.eng	pancreas	de
dc.subject.eng	tumor	de
dc.subject.eng	KPC mouse model	de
dc.subject.eng	microbiome	de
dc.subject.eng	orthotopic transplantation	de
dc.subject.eng	Oxford Nanopore Technologies	de
dc.subject.eng	ONT sequencing	de
dc.subject.eng	third generation sequencing	de
dc.subject.eng	alpha diversity	de
dc.subject.eng	beta diversity	de
dc.subject.eng	cell lines	de
dc.subject.eng	feces	de
dc.subject.eng	subtypes	de
dc.subject.eng	16S rRNA	de
dc.identifier.urn	urn:nbn:de:gbv:7-ediss-14930-7
dc.affiliation.institute	Medizinische Fakultät
dc.subject.gokfull	Gastroenterologie (PPN61987578X)	de
dc.description.embargoed	2023-10-30	de
dc.identifier.ppn	1870496930
dc.notes.confirmationsent	Confirmation sent 2023-10-23T19:45:02	de

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