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A recommended and verified procedure for in situ tryptic digestion of formalin-fixed paraffin-embedded tissues for analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry.
Judd AM, Gutierrez DB, Moore JL, Patterson NH, Yang J, Romer CE, Norris JL, Caprioli RM
(2019) J Mass Spectrom 54: 716-727
MeSH Terms: Formaldehyde, Humans, Paraffin Embedding, Proteins, Proteolysis, Specimen Handling, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Tissue Array Analysis, Tissue Fixation, Trypsin
Show Abstract · Added October 15, 2019
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a molecular imaging technology uniquely capable of untargeted measurement of proteins, lipids, and metabolites while retaining spatial information about their location in situ. This powerful combination of capabilities has the potential to bring a wealth of knowledge to the field of molecular histology. Translation of this innovative research tool into clinical laboratories requires the development of reliable sample preparation protocols for the analysis of proteins from formalin-fixed paraffin-embedded (FFPE) tissues, the standard preservation process in clinical pathology. Although ideal for stained tissue analysis by microscopy, the FFPE process cross-links, disrupts, or can remove proteins from the tissue, making analysis of the protein content challenging. To date, reported approaches differ widely in process and efficacy. This tutorial presents a strategy derived from systematic testing and optimization of key parameters, for reproducible in situ tryptic digestion of proteins in FFPE tissue and subsequent MALDI IMS analysis. The approach describes a generalized method for FFPE tissues originating from virtually any source.
© 2019 John Wiley & Sons, Ltd.
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Discerning the Primary Carcinoma in Malignant Peritoneal and Pleural Effusions Using Imaging Mass Spectrometry-A Feasibility Study.
Schwamborn K, Weirich G, Steiger K, Zimmermann G, Schmidmayr M, Weichert W, Caprioli RM
(2019) Proteomics Clin Appl 13: e1800064
MeSH Terms: Diagnosis, Differential, Feasibility Studies, Humans, Mass Spectrometry, Molecular Imaging, Peritoneal Neoplasms, Pleural Effusion, Malignant, Tissue Array Analysis
Show Abstract · Added March 3, 2020
PURPOSE - Malignant effusions challenge diagnostic accuracy due to cytomorphologic overlaps between various malignant primaries. Workup of this material to establish a correct diagnosis is time consuming and limited by the sparsity of material. In order to circumvent these drawbacks, the use of MALDI imaging MS (IMS) as a diagnostic platform has been explored.
EXPERIMENTAL DESIGN - Cytology cell blocks from malignant effusions (serous ovarian carcinoma and several non-ovarian carcinomas including gastric adenocarcinoma) containing at least 30% neoplastic cells are selected for generation of cytology microarrays (CMA). CMA sections are transferred to conductive glass slides, subjected to on-tissue tryptic digestion, and matrix application for MALDI-IMS analysis.
RESULTS - Supervised classification analysis identifies serous ovarian carcinomas as the source of malignant effusions with a sensitivity of 85.7% when compared to samples from all other included primary sites. When compared to gastric adenocarcinoma, serous ovarian carcinoma samples can be delineated with a sensitivity of 97.3%.
CONCLUSION AND CLINICAL RELEVANCE - These preliminary results highlight that MALDI-IMS allows subtyping of malignant effusions to identify the precise origin of neoplastic cells. While achieving similar results compared to classical approaches such as immunocytology, more material is conserved that will be available for further tests.
© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Identification of Proteomic Features To Distinguish Benign Pulmonary Nodules from Lung Adenocarcinoma.
Codreanu SG, Hoeksema MD, Slebos RJC, Zimmerman LJ, Rahman SMJ, Li M, Chen SC, Chen H, Eisenberg R, Liebler DC, Massion PP
(2017) J Proteome Res 16: 3266-3276
MeSH Terms: 5-Lipoxygenase-Activating Proteins, Adenocarcinoma, Adenocarcinoma of Lung, Adult, Aged, Antigens, CD, Arachidonate 5-Lipoxygenase, Biomarkers, Tumor, CD11 Antigens, Cell Adhesion Molecules, Diagnosis, Differential, Female, GPI-Linked Proteins, Gene Expression Regulation, Neoplastic, Glucose Transporter Type 3, Humans, Integrin alpha Chains, Lung Neoplasms, Male, Middle Aged, Neoplasm Proteins, Proteomics, Respiratory Mucosa, Solitary Pulmonary Nodule, Tandem Mass Spectrometry, Tissue Array Analysis, Transcriptome
Show Abstract · Added January 29, 2018
We hypothesized that distinct protein expression features of benign and malignant pulmonary nodules may reveal novel candidate biomarkers for the early detection of lung cancer. We performed proteome profiling by liquid chromatography-tandem mass spectrometry to characterize 34 resected benign lung nodules, 24 untreated lung adenocarcinomas (ADCs), and biopsies of bronchial epithelium. Group comparisons identified 65 proteins that differentiate nodules from ADCs and normal bronchial epithelium and 66 proteins that differentiate ADCs from nodules and normal bronchial epithelium. We developed a multiplexed parallel reaction monitoring (PRM) assay to quantify a subset of 43 of these candidate biomarkers in an independent cohort of 20 benign nodules, 21 ADCs, and 20 normal bronchial biopsies. PRM analyses confirmed significant nodule-specific abundance of 10 proteins including ALOX5, ALOX5AP, CCL19, CILP1, COL5A2, ITGB2, ITGAX, PTPRE, S100A12, and SLC2A3 and significant ADC-specific abundance of CEACAM6, CRABP2, LAD1, PLOD2, and TMEM110-MUSTN1. Immunohistochemistry analyses for seven selected proteins performed on an independent set of tissue microarrays confirmed nodule-specific expression of ALOX5, ALOX5AP, ITGAX, and SLC2A3 and cancer-specific expression of CEACAM6. These studies illustrate the value of global and targeted proteomics in a systematic process to identify and qualify candidate biomarkers for noninvasive molecular diagnosis of lung cancer.
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27 MeSH Terms
Three-dimensional culture system identifies a new mode of cetuximab resistance and disease-relevant genes in colorectal cancer.
Li C, Singh B, Graves-Deal R, Ma H, Starchenko A, Fry WH, Lu Y, Wang Y, Bogatcheva G, Khan MP, Milne GL, Zhao S, Ayers GD, Li N, Hu H, Washington MK, Yeatman TJ, McDonald OG, Liu Q, Coffey RJ
(2017) Proc Natl Acad Sci U S A 114: E2852-E2861
MeSH Terms: Animals, Antineoplastic Agents, Immunological, Cell Culture Techniques, Cell Line, Tumor, Cetuximab, Colorectal Neoplasms, Crizotinib, Drug Resistance, Neoplasm, Gene Expression Regulation, Neoplastic, Humans, Hydroxyprostaglandin Dehydrogenases, Mice, Phosphorylation, Protein-Serine-Threonine Kinases, Proto-Oncogene Proteins c-akt, Pyrazoles, Pyridines, Receptor, Transforming Growth Factor-beta Type II, Receptors, Transforming Growth Factor beta, Tissue Array Analysis, Versicans, Xenograft Model Antitumor Assays
Show Abstract · Added May 3, 2017
We previously reported that single cells from a human colorectal cancer (CRC) cell line (HCA-7) formed either hollow single-layered polarized cysts or solid spiky masses when plated in 3D in type-I collagen. To begin in-depth analyses into whether clonal cysts and spiky masses possessed divergent properties, individual colonies of each morphology were isolated and expanded. The lines thus derived faithfully retained their parental cystic and spiky morphologies and were termed CC (cystic) and SC (spiky), respectively. Although both CC and SC expressed EGF receptor (EGFR), the EGFR-neutralizing monoclonal antibody, cetuximab, strongly inhibited growth of CC, whereas SC was resistant to growth inhibition, and this was coupled to increased tyrosine phosphorylation of MET and RON. Addition of the dual MET/RON tyrosine kinase inhibitor, crizotinib, restored cetuximab sensitivity in SC. To further characterize these two lines, we performed comprehensive genomic and transcriptomic analysis of CC and SC in 3D. One of the most up-regulated genes in CC was the tumor suppressor , and the most up-regulated gene in SC was () in 3D and xenografts. Analysis of a CRC tissue microarray showed that epithelial, but not stromal, VCAN staining strongly correlated with reduced survival, and combined epithelial VCAN and absent HPGD staining portended a poorer prognosis. Thus, with this 3D system, we have identified a mode of cetuximab resistance and a potential prognostic marker in CRC. As such, this represents a potentially powerful system to identify additional therapeutic strategies and disease-relevant genes in CRC and possibly other solid tumors.
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22 MeSH Terms
Larger core size has superior technical and analytical accuracy in bladder tissue microarray.
Eskaros AR, Egloff SA, Boyd KL, Richardson JE, Hyndman ME, Zijlstra A
(2017) Lab Invest 97: 335-342
MeSH Terms: Cell Proliferation, Fluorescent Antibody Technique, Humans, Ki-67 Antigen, Mitotic Index, Paraffin Embedding, Pilot Projects, Reproducibility of Results, Tissue Array Analysis, Urinary Bladder, Urinary Bladder Neoplasms
Show Abstract · Added April 6, 2017
The construction of tissue microarrays (TMAs) with cores from a large number of paraffin-embedded tissues (donors) into a single paraffin block (recipient) is an effective method of analyzing samples from many patient specimens simultaneously. For the TMA to be successful, the cores within it must capture the correct histologic areas from the donor blocks (technical accuracy) and maintain concordance with the tissue of origin (analytical accuracy). This can be particularly challenging for tissues with small histological features such as small islands of carcinoma in situ (CIS), thin layers of normal urothelial lining of the bladder, or cancers that exhibit intratumor heterogeneity. In an effort to create a comprehensive TMA of a bladder cancer patient cohort that accurately represents the tumor heterogeneity and captures the small features of normal and CIS, we determined how core size (0.6 vs 1.0 mm) impacted the technical and analytical accuracy of the TMA. The larger 1.0 mm core exhibited better technical accuracy for all tissue types at 80.9% (normal), 94.2% (tumor), and 71.4% (CIS) compared with 58.6%, 85.9%, and 63.8% for 0.6 mm cores. Although the 1.0 mm core provided better tissue capture, increasing the number of replicates from two to three allowed with the 0.6 mm core compensated for this reduced technical accuracy. However, quantitative image analysis of proliferation using both Ki67+ immunofluorescence counts and manual mitotic counts demonstrated that the 1.0 mm core size also exhibited significantly greater analytical accuracy (P=0.004 and 0.035, respectively, r=0.979 and 0.669, respectively). Ultimately, our findings demonstrate that capturing two or more 1.0 mm cores for TMA construction provides superior technical and analytical accuracy over the smaller 0.6 mm cores, especially for tissues harboring small histological features or substantial heterogeneity.
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11 MeSH Terms
PDX1 dynamically regulates pancreatic ductal adenocarcinoma initiation and maintenance.
Roy N, Takeuchi KK, Ruggeri JM, Bailey P, Chang D, Li J, Leonhardt L, Puri S, Hoffman MT, Gao S, Halbrook CJ, Song Y, Ljungman M, Malik S, Wright CV, Dawson DW, Biankin AV, Hebrok M, Crawford HC
(2016) Genes Dev 30: 2669-2683
MeSH Terms: Acinar Cells, Animals, Carcinoma, Pancreatic Ductal, Cell Transformation, Neoplastic, Gene Deletion, Gene Expression Regulation, Neoplastic, Homeodomain Proteins, Humans, Mice, Pancreatic Neoplasms, Tissue Array Analysis, Trans-Activators, Tumor Cells, Cultured
Show Abstract · Added February 7, 2017
Aberrant activation of embryonic signaling pathways is frequent in pancreatic ductal adenocarcinoma (PDA), making developmental regulators therapeutically attractive. Here we demonstrate diverse functions for pancreatic and duodenal homeobox 1 (PDX1), a transcription factor indispensable for pancreas development, in the progression from normal exocrine cells to metastatic PDA. We identify a critical role for PDX1 in maintaining acinar cell identity, thus resisting the formation of pancreatic intraepithelial neoplasia (PanIN)-derived PDA. Upon neoplastic transformation, the role of PDX1 changes from tumor-suppressive to oncogenic. Interestingly, subsets of malignant cells lose PDX1 expression while undergoing epithelial-to-mesenchymal transition (EMT), and PDX1 loss is associated with poor outcome. This stage-specific functionality arises from profound shifts in PDX1 chromatin occupancy from acinar cells to PDA. In summary, we report distinct roles of PDX1 at different stages of PDA, suggesting that therapeutic approaches against this potential target need to account for its changing functions at different stages of carcinogenesis. These findings provide insight into the complexity of PDA pathogenesis and advocate a rigorous investigation of therapeutically tractable targets at distinct phases of PDA development and progression.
© 2016 Roy et al.; Published by Cold Spring Harbor Laboratory Press.
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13 MeSH Terms
Utility of [F]FSPG PET to Image Hepatocellular Carcinoma: First Clinical Evaluation in a US Population.
Kavanaugh G, Williams J, Morris AS, Nickels ML, Walker R, Koglin N, Stephens AW, Washington MK, Geevarghese SK, Liu Q, Ayers D, Shyr Y, Manning HC
(2016) Mol Imaging Biol 18: 924-934
MeSH Terms: Acetates, Adult, Aged, Amino Acid Transport System y+, Carbon Radioisotopes, Carcinoma, Hepatocellular, Female, Glutamates, Glutamic Acid, Humans, Liver Neoplasms, Male, Middle Aged, Positron-Emission Tomography, Radiopharmaceuticals, Sequence Analysis, RNA, Tissue Array Analysis
Show Abstract · Added April 6, 2017
PURPOSE - Non-invasive imaging is central to hepatocellular carcinoma (HCC) diagnosis; however, conventional modalities are limited by smaller tumors and other chronic diseases that are often present in patients with HCC, such as cirrhosis. This pilot study evaluated the feasibility of (4S)-4-(3-[F]fluoropropyl)-L-glutamic acid ([F]FSPG) positron emission tomography (PET)/X-ray computed tomography (CT) to image HCC. [F]FSPG PET/CT was compared to standard-of-care (SOC) magnetic resonance imaging (MRI) and CT, and [C]acetate PET/CT, commonly used in this setting. We report the largest cohort of HCC patients imaged to date with [F]FSPG PET/CT and present the first comparison to [C]acetate PET/CT and SOC imaging. This study represents the first in a US HCC population, which is distinguished by different underlying comorbidities than non-US populations.
PROCEDURES - x transporter RNA and protein levels were evaluated in HCC and matched liver samples from The Cancer Genome Atlas (n = 16) and a tissue microarray (n = 83). Eleven HCC patients who underwent prior MRI or CT scans were imaged by [F]FSPG PET/CT, with seven patients also imaged with [C]acetate PET/CT.
RESULTS - x transporter RNA and protein levels were elevated in HCC samples compared to background liver. Over 50 % of low-grade HCCs and ~70 % of high-grade tumors exceeded background liver protein expression. [F]FSPG PET/CT demonstrated a detection rate of 75 %. [F]FSPG PET/CT also identified an HCC devoid of typical MRI enhancement pattern. Patients scanned with [F]FSPG and [C]acetate PET/CT exhibited a 90 and 70 % detection rate, respectively. In dually positive tumors, [F]FSPG accumulation consistently resulted in significantly greater tumor-to-liver background ratios compared with [C]acetate PET/CT.
CONCLUSIONS - [F]FSPG PET/CT is a promising modality for HCC imaging, and larger studies are warranted to examine [F]FSPG PET/CT impact on diagnosis and management of HCC. [F]FSPG PET/CT may also be useful for phenotyping HCC tumor metabolism as part of precision cancer medicine.
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17 MeSH Terms
MAGI-2 Is a Sensitive and Specific Marker of Prostatic Adenocarcinoma:  A Comparison With AMACR.
Goldstein J, Goyal R, Roland JT, Gellert LL, Clark PE, Hameed O, Giannico GA
(2016) Am J Clin Pathol 146: 294-302
MeSH Terms: Adenocarcinoma, Biomarkers, Tumor, Carrier Proteins, Diagnosis, Differential, Humans, Male, Prostate, Prostatectomy, Prostatic Hyperplasia, Prostatic Intraepithelial Neoplasia, Prostatic Neoplasms, Racemases and Epimerases, Sensitivity and Specificity, Tissue Array Analysis
Show Abstract · Added June 27, 2017
OBJECTIVES - We compared the utility of membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 (MAGI-2) and α-methylacyl CoA (AMACR) by immunohistochemistry in diagnosing prostatic adenocarcinoma.
METHODS - Seventy-eight radical prostatectomies were used to construct three tissue microarrays with 512 cores, including benign prostatic tissue, benign prostatic hyperplasia, high-grade prostatic intraepithelial neoplasia (HGPIN), and adenocarcinoma. AMACR and MAGI-2 immunohistochemistry were evaluated by visual and image analysis.
RESULTS - MAGI-2 and AMACR were significantly higher in adenocarcinoma and HGPIN compared with benign tissue. At H-score cutoffs of 300 and 200, MAGI-2 was more accurate in distinguishing benign from malignant glands than AMACR. Areas under the curve by image and visual analysis were 0.846 and 0.818 for MAGI-2 and 0.937 and 0.924 for AMACR, respectively. The accuracy of MAGI-2 in distinguishing benign from malignant glands on the same core was higher (95% vs 88%).
CONCLUSIONS - MAGI-2 could represent a useful adjunct for diagnosis of prostatic adenocarcinoma, especially when AMACR is not discriminatory.
© American Society for Clinical Pathology, 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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14 MeSH Terms
Rictor/mTORC2 Drives Progression and Therapeutic Resistance of HER2-Amplified Breast Cancers.
Morrison Joly M, Hicks DJ, Jones B, Sanchez V, Estrada MV, Young C, Williams M, Rexer BN, Sarbassov dos D, Muller WJ, Brantley-Sieders D, Cook RS
(2016) Cancer Res 76: 4752-64
MeSH Terms: Animals, Blotting, Western, Breast Neoplasms, Carrier Proteins, Disease Progression, Drug Resistance, Neoplasm, Female, Heterografts, Humans, Kaplan-Meier Estimate, Mechanistic Target of Rapamycin Complex 2, Mice, Mice, Inbred BALB C, Mice, Nude, Multiprotein Complexes, Rapamycin-Insensitive Companion of mTOR Protein, Receptor, ErbB-2, Signal Transduction, TOR Serine-Threonine Kinases, Tissue Array Analysis
Show Abstract · Added April 15, 2019
HER2 overexpression drives Akt signaling and cell survival and HER2-enriched breast tumors have a poor outcome when Akt is upregulated. Akt is activated by phosphorylation at T308 via PI3K and S473 via mTORC2. The importance of PI3K-activated Akt signaling is well documented in HER2-amplified breast cancer models, but the significance of mTORC2-activated Akt signaling in this setting remains uncertain. We report here that the mTORC2 obligate cofactor Rictor is enriched in HER2-amplified samples, correlating with increased phosphorylation at S473 on Akt. In invasive breast cancer specimens, Rictor expression was upregulated significantly compared with nonmalignant tissues. In a HER2/Neu mouse model of breast cancer, genetic ablation of Rictor decreased cell survival and phosphorylation at S473 on Akt, delaying tumor latency, penetrance, and burden. In HER2-amplified cells, exposure to an mTORC1/2 dual kinase inhibitor decreased Akt-dependent cell survival, including in cells resistant to lapatinib, where cytotoxicity could be restored. We replicated these findings by silencing Rictor in breast cancer cell lines, but not silencing the mTORC1 cofactor Raptor (RPTOR). Taken together, our findings establish that Rictor/mTORC2 signaling drives Akt-dependent tumor progression in HER2-amplified breast cancers, rationalizing clinical investigation of dual mTORC1/2 kinase inhibitors and developing mTORC2-specific inhibitors for use in this setting. Cancer Res; 76(16); 4752-64. ©2016 AACR.
©2016 American Association for Cancer Research.
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MAGI-2 in prostate cancer: an immunohistochemical study.
Goldstein J, Borowsky AD, Goyal R, Roland JT, Arnold SA, Gellert LL, Clark PE, Hameed O, Giannico GA
(2016) Hum Pathol 52: 83-91
MeSH Terms: Adenocarcinoma, Adult, Aged, Aged, 80 and over, Area Under Curve, Biomarkers, Tumor, Biopsy, Carrier Proteins, Humans, Immunohistochemistry, In Situ Hybridization, Fluorescence, Male, Middle Aged, Neoplasm Grading, PTEN Phosphohydrolase, Predictive Value of Tests, Prostatic Hyperplasia, Prostatic Intraepithelial Neoplasia, Prostatic Neoplasms, ROC Curve, Tissue Array Analysis, Transcription Factors, Tumor Suppressor Proteins, Up-Regulation
Show Abstract · Added April 18, 2017
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 (MAGI-2) is a scaffolding protein that links cell adhesion molecules, receptors, and signaling molecules to the cytoskeleton and maintains the architecture of cell junctions. MAGI-2 gene rearrangements have recently been described in prostate cancer. We studied the immunohistochemical expression of MAGI-2 protein in prostate tissue. Seventy-eight radical prostatectomies were used to construct 3 tissue microarrays consisting of 512 cores, including benign tissue, benign prostatic hyperplasia, high-grade prostatic intraepithelial neoplasia (HGPIN), and adenocarcinoma, Gleason patterns 3 to 5. Immunohistochemistry for phosphatase and tensin homologue (PTEN) and double-stain MAGI-2/p63 was performed and analyzed by visual and image analysis, the latter as percent of analyzed area (%AREA), and mean optical density multiplied by %AREA (STAIN). By visual and image analysis, MAGI-2 was significantly higher in adenocarcinoma and HGPIN compared with benign (benign versus HGPIN P < .001; benign versus adenocarcinoma, P < .001). HGPIN and adenocarcinoma did not significantly differ by either modality. Using visual intensity to distinguish benign tissue and adenocarcinoma, a receiver operating curve yielded an area under the curve of 0.902. A STAIN threshold of 1470 yielded a sensitivity of 0.66 and specificity of 0.96. There was a significant correlation between PTEN and MAGI-2 staining for normal and benign prostatic hyperplasia, but this was lost in HGPIN and cancer. We conclude that MAGI-2 immunoreactivity is elevated in prostate cancer and HGPIN compared with normal tissue, and suggest that MAGI-2 may contribute to prostate carcinogenesis. This is the first report of MAGI-2 staining by immunohistochemistry in prostate cancer.
Copyright © 2016 Elsevier Inc. All rights reserved.
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24 MeSH Terms