Dataset Information

Building a spectral library to analyze colorectal cancer organoids

ABSTRACT: The goal of this project was to build SWATH Spectral libraries to analyze colorectal cancer organoids.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Colon

DISEASE(S): Colon Cancer

SUBMITTER: Peter Blattmann

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD018835 | Pride | 2023-12-10

REPOSITORIES: Pride

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Publications

Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer.

Plattner Christina C Lamberti Giorgia G Blattmann Peter P Kirchmair Alexander A Rieder Dietmar D Loncova Zuzana Z Sturm Gregor G Scheidl Stefan S Ijsselsteijn Marieke M Fotakis Georgios G Noureen Asma A Lisandrelli Rebecca R Böck Nina N Nemati Niloofar N Krogsdam Anne A Daum Sophia S Finotello Francesca F Somarakis Antonios A Schäfer Alexander A Wilflingseder Doris D Gonzalez Acera Miguel M Öfner Dietmar D Huber Lukas A LA Clevers Hans H Becker Christoph C Farin Henner F HF Greten Florian R FR Aebersold Ruedi R de Miranda Noel F C C NFCC Trajanoski Zlatko Z

iScience 20231104 12

Precision oncology approaches for patients with colorectal cancer (CRC) continue to lag behind other solid cancers. Functional precision oncology-a strategy that is based on perturbing primary tumor cells from cancer patients-could provide a road forward to personalize treatment. We extend this paradigm to measuring proteome activity landscapes by acquiring quantitative phosphoproteomic data from patient-derived organoids (PDOs). We show that kinase inhibitors induce inhibitor- and patient-speci ...[more]

PMID: 38047086

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Project description:Fomitiporia mediterranea (Fmed) is one of the main fungal species found in grapevine wood rot, also called “amadou”, one of the most typical symptoms of grapevine trunk disease Esca. This fungus is functionally classified as a white-rot, able to degrade all wood structure polymers, i.e., hemicelluloses, cellulose, and the most recalcitrant component, lignin. Specific enzymes are secreted by the fungus to degrade those components, namely carbohydrate active enzymes for hemicelluloses and cellulose, which can be highly specific for given polysaccharide, and peroxidases, which enable white-rot to degrade lignin, with specificities relating to lignin composition as well. Furthermore, besides polymers, a highly diverse set of metabolites often associated with antifungal activities is found in wood, this set differing among the various wood species. Wood decayers possess the ability to detoxify these specific extractives and this ability could reflect the adaptation of these fungi to their specific environment. The aim of this study is to better understand the molecular mechanisms used by Fmed to degrade wood structure, and in particular its potential adaptation to grapevine wood. To do so, Fmed was cultivated on sawdust from different origins: grapevine, beech, and spruce. Carbon mineralization rate, mass loss, wood structure polymers contents, targeted metabolites and secreted proteins were measured. We used the well-known white-rot model Trametes versicolor for comparison. Whereas no significant degradation was observed with spruce, a higher mass loss was measured on Fmed grapevine culture compared to beech culture. Moreover, on both substrates, a simultaneous degradation pattern and the degradation of wood extractives were demonstrated, and proteomic analyses identified a relative overproduction of oxidoreductases involved in lignin and extractive degradation on grapevine cultures, and only few differences in carbohydrate active enzymes. These results could explain at least partially the adaptation of Fmed to grapevine wood structural composition compared to other wood species and suggest that other biotic and abiotic factors should be considered to fully understand the potential adaptation of Fmed to its ecological niche.

			Action	DRS
	180813_Swissprot_human_iRT.fasta	Fasta
	PB_200413_CRC_TL.kit	Other
	PB_200413_CRC_TL.xls	Xls
	andromeda.zip	Other
	aschaefe_D1908_209.raw	Raw