Mass Spectrometry Analyses of Multicellular Tumor Spheroids

Acland, Mitchell; Mittal, Parul; Lokman, Noor A.; Klingler‐Hoffmann, Manuela; Oehler, Martin K.; Hoffmann, Peter

doi:10.1002/prca.201700124

Cited by 23 publications

(20 citation statements)

References 130 publications

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“…These results are also congruent with metagenomes of particle-sized fractions compared to freeliving microbes in river and marine samples; the former, which are more likely to harbor multicellular communities, are associated with lower n H 2 O of the coded proteins (20). In addition, up-regulated proteins in 3D culture also tend to be more reduced (Table 2), which might be a reflection of the hypoxic conditions that develop in the interiors of spheroids (21,22,65).…”

Section: Discussionsupporting

confidence: 71%

“…Differential protein expression data for cell culture experiments and cancer compared to normal tissue were located through literature searches and include studies using any proteomics techniques. Several review articles were also consulted in order to locate experimental data for breast cancer (74), lung cancer (75,76) and 3D cell culture (65). In general, datasets were selected that have a minimum of 30 up-regulated and 30 downregulated proteins in order to reduce random variation associated with small sample sizes, but smaller datasets (at least ca.…”

Section: Methodsmentioning

confidence: 99%

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Water as a reactant in the differential expression of proteins in cancer

Dick¹

2020

Preprint

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The large amounts of proteomic data now available for cancer can used to investigate whether the physicochemical conditions of tumors are reflected in patterns of protein expression and chemical composition. Compositional analysis of more than 250 datasets for differentially expressed proteins compiled from the literature reveals a clear signal of higher stoichiometric hydration state (n H 2 O , derived from the theoretical formation reactions of proteins from particular basis species) in specific cancer types compared to normal tissue; this trend is also evident in pan-cancer transcriptomic and proteomic datasets from The Cancer Genome Atlas and Human Protein Atlas. In marked contrast to cancer, n H 2 O decreases for differentially expressed proteins in hyperosmotic stress (including high glucose) experiments and 3D cell culture compared to monolayer growth. Compositional analysis combined with gene ages (phylostrata) taken from the literature shows higher n H 2 O of human proteins earlier in evolution. Further analyses using amino acid biosynthetic reactions supports the conclusion that a net increase of water going into the reactions of protein synthesis is a biochemical characteristic shared by most cancer types. These findings raise the possibility of a basic physicochemical link between increased water content in tumors and the atavistic or embryonic patterns of gene and protein expression in cancer.

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Section: Discussionsupporting

confidence: 71%

Section: Methodsmentioning

confidence: 99%

Water as a reactant in the differential expression of proteins in cancer

Dick¹

2020

Preprint

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“…Although biomarker candidates were identified with G‐Met analysis using UHPLC/QTOFMS, their localized information was lost in the tissue sample. MSI can directly analyze small molecules in a tissue section and observe their localization . MSI has the potential to overcome the disadvantages of G‐Met and has already been widely applied for cancerous tissues using the traditional matrix‐assisted laser desorption ionization technique .…”

Section: Resultsmentioning

confidence: 99%

“…The CCS values of feature A and B obtained by HDMS were 338.7 and 326.1 and matched the values of TG (54:2) [M + NH 4 ] + and TG (52:2) [M + NH 4 ] + , respectively, in a previous report. 36 The acceptable difference in the CCS value (ΔCCS) has previously been defined at less than 2%, 37 40 MSI has the potential to overcome the disadvantages of G-Met and has already been widely applied for cancerous tissues using the traditional matrix-assisted laser desorption ionization technique. 41,42 Recently, DESI-MSI was also applied as a matrix-free approach to the imaging of small molecules in tissue samples, 39,43 and it might be possible to obtain similar corresponding profiles with UHPLC/QTOFMS analysis because of ESI-based ionization.…”

Section: Identification Of Metabolites By Hdmsmentioning

confidence: 99%

Identification of novel biomarkers of hepatocellular carcinoma by high‐definition mass spectrometry: Ultrahigh‐performance liquid chromatography quadrupole time‐of‐flight mass spectrometry and desorption electrospray ionization mass spectrometry imaging

Nagai

Uranbileg

Chen

et al. 2019

Rapid Comm Mass Spectrometry

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Rationale Hepatocellular carcinoma (HCC) is a highly malignant disease for which the development of prospective or prognostic biomarkers is urgently required. Although metabolomics is widely used for biomarker discovery, there are some bottlenecks regarding the comprehensiveness of detected features, reproducibility of methods, and identification of metabolites. In addition, information on localization of metabolites in tumor tissue is needed for functional analysis. Here, we developed a wide‐polarity global metabolomics (G‐Met) method, identified HCC biomarkers in human liver samples by high‐definition mass spectrometry (HDMS), and demonstrated localization in cryosections using desorption electrospray ionization MS imaging (DESI‐MSI) analysis. Methods Metabolic profiling of tumor (n = 38) and nontumor (n = 72) regions in human livers of HCC was performed by an ultrahigh‐performance liquid chromatography quadrupole time‐of‐flight MS (UHPLC/QTOFMS) instrument equipped with a mixed‐mode column. The HCC biomarker candidates were extracted by multivariate analyses and identified by matching values of the collision cross section and their fragment ions on the mass spectra obtained by HDMS. Cryosections of HCC livers, which included both tumor and nontumor regions, were analyzed by DESI‐MSI. Results From the multivariate analysis, m/z 904.83 and m/z 874.79 were significantly high and low, respectively, in tumor samples and were identified as triglyceride (TG) 16:0/18:1(9Z)/20:1(11Z) and TG 16:0/18:1(9Z)/18:2(9Z,12Z) using the synthetic compounds. The TGs were clearly localized in the tumor or nontumor areas of the cryosection. Conclusions Novel biomarkers for HCC were identified by a comprehensive and reproducible G‐Met method with HDMS using a mixed‐mode column. The combination analysis of UHPLC/QTOFMS and DESI‐MSI revealed that the different molecular species of TGs were associated with tumor distribution and were useful for characterizing the progression of tumor cells and discovering prospective biomarkers.

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“…To monitor the response of spheroids to cancer therapeutics, a number of techniques such as flow cytometry, western blot, 2D PAGE, SILAC, and LC–MS/MS have been utilized, however these techniques require homogenization of spheroids, causing loss of spatial information as recently reviewed by us …”

mentioning

confidence: 99%

Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI MSI) for Monitoring of Drug Response in Primary Cancer Spheroids

et al. 2019

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Malignant ascites is a fluid, which builds up in the abdomen and contains cancer cells in the form of single cells or multicellular clusters called spheroids. Malignant ascites has been observed in patients suffering from ovarian, cervical, gastric, colorectal, pancreatic, endometrial, or primary liver cancer. The spheroids are believed to play a major role in chemo resistance and metastasis of the cancer. To ease the discomfort of patients, malignant ascites (MA) is often drained from the abdomen using a procedure called paracentesis. MA retrieved via this minimal invasive procedure is a great source for cancer spheroids, which can be used for testing chemotherapeutic drugs and drug combinations. Herein, the existing workflow is adapted to make concurrent monitoring of drug accumulation, drug response, and drug metabolites feasible using primary spheroids or spheroids grown without a scaffolding matrix. To achieve this, those spheroids are embedded in matrigel, before fixing them with formalin. This makes it possible to process, store, and ship samples at room temperature. This new approach might be used to choose the best targeted therapy for each patient and thereby facilitate personalized medicine.

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Mass Spectrometry Analyses of Multicellular Tumor Spheroids

Cited by 23 publications

References 130 publications

Water as a reactant in the differential expression of proteins in cancer

Water as a reactant in the differential expression of proteins in cancer

Identification of novel biomarkers of hepatocellular carcinoma by high‐definition mass spectrometry: Ultrahigh‐performance liquid chromatography quadrupole time‐of‐flight mass spectrometry and desorption electrospray ionization mass spectrometry imaging

Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI MSI) for Monitoring of Drug Response in Primary Cancer Spheroids

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