Personalized Proteome Profiles of Healthy and Tumor Human Colon Organoids Reveal Both Individual Diversity and Basic Features of Colorectal Cancer

Abstract

Diseases at the molecular level are complex and patient dependent, necessitating development of strategies that enable precision treatment to optimize clinical outcomes. Organoid technology has recently been shown to have the potential to recapitulate the in vivo characteristics of the original individual's tissue in a three-dimensional in vitro culture system. Here, we present a quantitative mass-spectrometry-based proteomic analysis and a comparative transcriptomic analysis of human colorectal tumor and healthy organoids derived, in parallel, from seven patients. Although gene and protein signatures can be derived to distinguish the tumor organoid population from healthy organoids, our data clearly reveal that each patient possesses a distinct organoid signature at the proteomic level. We demonstrate that a personalized patient-specific organoid proteome profile can be related to the diagnosis of a patient and with future development contribute to the generation of personalized therapies.

Phenotypic Analysis of Organoids by Proteomics

“…A different approach for the quantification that also uses a shift in mass measured at the MS level can be done following enzymatic digestion of proteins, and then labeling the resulting peptides using labels of different masses, with the possibility of adding an affinity tag to further purify the labeled peptides . For example, peptides obtained from human colon organoids were tagged by stable isotope dimethyl labeling . The advantage of this method is that it greatly reduces the time necessary for in vivo incorporation of isotopes and does not require the preparation of complex media in comparison to SILAC, but it does introduce variations due to differences in preparation from mixing the samples at later steps.…”

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“…Clinical trials are currently ongoing to determine whether this approach can prognosticate treatment outcome of pancreatic, liver and colorectal cancer patients [5,6]. Interestingly, tumoroid cultures also maintain the tumor heterogeneity of the tumor-of-origin and since normal surrounding tissues can be established in addition with little modification to the culture media, a patient disease-specific genomic or proteomic tumor profile can be established in relation to the normal tissue from which the tumor arose [5,7]. Tumoroid cultures can also be implanted orthotopically in immunodeficient mice to address the impact of diseasespecific driver genes and their impact on the tumoroid's capacity to metastasize to distant organs [8].…”

Take a deep breath and digest the material: organoids and biomaterials of the respiratory and digestive systems

“…[5,[14][15][16][17][18][19][20][21][22] Intestinal organoids have been used to model epithelial barrier function, interactions with microbes, infectious diseases and cancer. [23][24][25][26][27][28][29][30][31][32] Intestinal organoids derived from human samples were first grown from isolated small intestinal or colonic crypts, which are localized at the base of the intestinal and colonic epithelium, respectively. In the crypt, an adult stem cell population can be found with the capacity to replenish all intestinal epithelial cells, including absorptive and secretory cells (goblet cells, enterocytes/colonocyte, enteroendocrine cells and Paneth cells in the small intestine).…”

“…In addition to healthy crypts, patient tissue with specific mutations and cancer tissue has been used to derive organoid models in order to conduct drug screens. [14,[27][28][29][30][34][35][36] Both the healthy and diseased organoids were maintained in Matrigel, [14][15][16]33] yet was also shown that intestinal organoids derived from primary crypts can be maintained in ECM protein, Collagen I. [17] Matrigel is the most common ECM scaffold used for the culture and transplantation of organoids including intestinal organoids (Table I).…”