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Comparison of methanol fixation versus cryopreservation of the placenta for metabolomics analysis. Sci Rep 2023; 13:4063. [PMID: 36906704 PMCID: PMC10008642 DOI: 10.1038/s41598-023-31287-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 03/09/2023] [Indexed: 03/13/2023] Open
Abstract
Methods for collection of placental tissue at room temperature for metabolic profiling are described. Specimens were excised from the maternal side of the placenta and immediately flash frozen or fixed and stored for 1, 6, 12, 24, or 48 h in 80% methanol. Untargeted metabolic profiling was performed on both the methanol-fixed tissue and the methanol extract. Data were analyzed using Gaussian generalized estimating equations, two sample t-tests with false discovery rate (FDR) corrections, and principal components analysis. Methanol-fixed tissue samples and methanol extracts had a similar number of metabolites (p = 0.45, p = 0.21 in positive vs. negative ion mode). In positive ion mode, when compared to flash frozen tissue, both the methanol extract and methanol-fixed tissue (6 h) had a higher number of metabolites detected (146 additional metabolites, pFDR = 0.020; 149 additional metabolites, pFDR = 0.017; respectively), but these associations were not found in negative ion mode (all pFDR ≥ 0.05). Principle components analysis demonstrated separation of the metabolite features in the methanol extract, but similarity between methanol-fixed tissue and flash frozen tissue. These results show that placental tissue samples collected in 80% methanol at room temperature can yield similar metabolic data to flash frozen specimens.
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2
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Pinto FG, Mahmud I, Harmon TA, Rubio VY, Garrett TJ. Rapid Prostate Cancer Noninvasive Biomarker Screening Using Segmented Flow Mass Spectrometry-Based Untargeted Metabolomics. J Proteome Res 2020; 19:2080-2091. [PMID: 32216312 DOI: 10.1021/acs.jproteome.0c00006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Spectrometric methods with rapid biomarker detection capacity through untargeted metabolomics are becoming essential in the clinical cancer research. Liquid chromatography-mass spectrometry (LC-MS) is a rapidly developing metabolomic-based biomarker technique due to its high sensitivity, reproducibility, and separation efficiency. However, its translation to clinical diagnostics is often limited due to long data acquisition times (∼20 min/sample) and laborious sample extraction procedures when employed for large-scale metabolomics studies. Here, we developed a segmented flow approach coupled with high-resolution mass spectrometry (SF-HRMS) for untargeted metabolomics, which has the capability to acquire data in less than 1.5 min/sample with robustness and reproducibility relative to LC-HRMS. The SF-HRMS results demonstrate the capability for screening metabolite-based urinary biomarkers associated with prostate cancer (PCa). The study shows that SF-HRMS-based global metabolomics has the potential to evolve into a rapid biomarker screening tool for clinical research.
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Affiliation(s)
- Frederico G Pinto
- Instituto de Ciências Exatas e Tecnológicas, Universidade Federal de Viçosa, Campus de Rio Paranaíba, Viçosa 36570-900, Brazil
| | - Iqbal Mahmud
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Taylor A Harmon
- Department of Chemistry, University of Florida, Gainesville, Florida 32603, United States
| | - Vanessa Y Rubio
- Department of Chemistry, University of Florida, Gainesville, Florida 32603, United States
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States.,Southeast Center for Integrated Metabolomics, Clinical and Translational Science Institute, University of Florida, Gainesville, Florida 32610, United States
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3
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Andersen MK, Krossa S, Høiem TS, Buchholz R, Claes BSR, Balluff B, Ellis SR, Richardsen E, Bertilsson H, Heeren RMA, Bathen TF, Karst U, Giskeødegård GF, Tessem MB. Simultaneous Detection of Zinc and Its Pathway Metabolites Using MALDI MS Imaging of Prostate Tissue. Anal Chem 2020; 92:3171-3179. [PMID: 31944670 PMCID: PMC7584334 DOI: 10.1021/acs.analchem.9b04903] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Levels
of zinc, along with its mechanistically related metabolites citrate
and aspartate, are widely reported as reduced in prostate cancer compared
to healthy tissue and are therefore pointed out as potential cancer
biomarkers. Previously, it has only been possible to analyze zinc
and metabolites by separate detection methods. Through matrix-assisted
laser desorption/ionization mass spectrometry imaging (MSI), we were
for the first time able to demonstrate, in two different sample sets
(n = 45 and n = 4), the simultaneous
spatial detection of zinc, in the form of ZnCl3–, together with citrate, aspartate, and N-acetylaspartate
on human prostate cancer tissues. The reliability of the ZnCl3– detection was validated by total zinc
determination using laser ablation inductively coupled plasma MSI
on adjacent serial tissue sections. Zinc, citrate, and aspartate were
correlated with each other (range r = 0.46 to 0.74)
and showed a significant reduction in cancer compared to non-cancer
epithelium (p < 0.05, log2 fold change
range: −0.423 to −0.987), while no significant difference
between cancer and stroma tissue was found. Simultaneous spatial detection
of zinc and its metabolites is not only a valuable tool for analyzing
the role of zinc in prostate metabolism but might also provide a fast
and simple method to detect zinc, citrate, and aspartate levels as
a biomarker signature for prostate cancer diagnostics and prognostics.
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Affiliation(s)
- Maria K Andersen
- Department of Circulation and Medical Imaging , Norwegian University of Science and Technology (NTNU) , 7491 Trondheim , Norway
| | - Sebastian Krossa
- Department of Circulation and Medical Imaging , Norwegian University of Science and Technology (NTNU) , 7491 Trondheim , Norway
| | - Therese S Høiem
- Department of Circulation and Medical Imaging , Norwegian University of Science and Technology (NTNU) , 7491 Trondheim , Norway
| | - Rebecca Buchholz
- Institute of Inorganic and Analytical Chemistry , University of Münster , D-48149 Münster , Germany
| | - Britt S R Claes
- Maastricht MultiModal Molecular Imaging Institute (M4I) , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute (M4I) , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Shane R Ellis
- Maastricht MultiModal Molecular Imaging Institute (M4I) , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Elin Richardsen
- Department of Medical Biology , The Arctic University of Norway (UIT) , 9037 Tromsø , Norway.,Department of Clinical Pathology , University Hospital of North Norway, UNN , 9019 Tromsø , Norway
| | - Helena Bertilsson
- Department of Clinical and Molecular Medicine , Norwegian University of Science and Technology (NTNU) , 7491 Trondheim , Norway.,Clinic of Surgery, St. Olavs Hospital , Trondheim University Hospital , 7030 Trondheim , Norway
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging Institute (M4I) , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Tone F Bathen
- Department of Circulation and Medical Imaging , Norwegian University of Science and Technology (NTNU) , 7491 Trondheim , Norway
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry , University of Münster , D-48149 Münster , Germany
| | - Guro F Giskeødegård
- Department of Circulation and Medical Imaging , Norwegian University of Science and Technology (NTNU) , 7491 Trondheim , Norway
| | - May-Britt Tessem
- Department of Circulation and Medical Imaging , Norwegian University of Science and Technology (NTNU) , 7491 Trondheim , Norway.,Clinic of Surgery, St. Olavs Hospital , Trondheim University Hospital , 7030 Trondheim , Norway
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4
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Kdadra M, Höckner S, Leung H, Kremer W, Schiffer E. Metabolomics Biomarkers of Prostate Cancer: A Systematic Review. Diagnostics (Basel) 2019; 9:E21. [PMID: 30791464 PMCID: PMC6468767 DOI: 10.3390/diagnostics9010021] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 12/27/2022] Open
Abstract
Prostate cancer (PCa) diagnosis with current biomarkers is difficult and often results in unnecessary invasive procedures as well as over-diagnosis and over-treatment, highlighting the need for novel biomarkers. The aim of this review is to provide a summary of available metabolomics PCa biomarkers, particularly for clinically significant disease. A systematic search was conducted on PubMed for publications from July 2008 to July 2018 in accordance with PRISMA guidelines to report biomarkers with respect to their application in PCa diagnosis, progression, aggressiveness, recurrence, and treatment response. The vast majority of studies report biomarkers with the ability to distinguish malignant from benign prostate tissue with a few studies investigating biomarkers associated with disease progression, treatment response or tumour recurrence. In general, these studies report high dimensional datasets and the number of analysed metabolites often significantly exceeded the number of available samples. Hence, observed multivariate differences between case and control samples in the datasets might potentially also be associated with pre-analytical, technical, statistical and confounding factors. Giving the technical and methodological hurdles, there are nevertheless a number of metabolites and pathways repeatedly reported across various technical approaches, cohorts and sample types that appear to play a predominant role in PCa tumour biology, progression and recurrence.
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Affiliation(s)
| | | | - Hing Leung
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK.
- CRUK Beatson Institute, Bearsden, Glasgow G61 1BD, UK.
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93053 Regensburg, Germany.
| | - Eric Schiffer
- Numares AG, Am BioPark 9, 93053 Regensburg, Germany.
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5
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Zang X, Monge ME, Gaul DA, Fernández FM. Flow Injection–Traveling-Wave Ion Mobility–Mass Spectrometry for Prostate-Cancer Metabolomics. Anal Chem 2018; 90:13767-13774. [DOI: 10.1021/acs.analchem.8b04259] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Xiaoling Zang
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, Ciudad de Buenos Aires C1425FQD, Argentina
| | - David A. Gaul
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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6
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Wang Z, Gao K, Xu C, Gao J, Yan Y, Wang Y, Li Z, Chen J. Metabolic effects of Hedyotis diffusa on rats bearing Walker 256 tumor revealed by NMR-based metabolomics. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:5-17. [PMID: 28847040 DOI: 10.1002/mrc.4658] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/19/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
Hedyotis diffusa, a traditional Chinese herbal medicine, is widely used for oncotherapy and shows a positive effect in the clinical treatment. But its mechanism of anticancer activities is complicated and unclear. This study was undertaken to assess the therapeutic effects and reveal detailed mechanisms of H. diffusa for oncotherapy. A Walker 256 tumor-bearing rat model was established, and metabolomic profiles of plasma and urine were obtained from 1 H NMR technique. Multivariate statistical analysis methods were used to characterize the discriminating metabolites between control (C), Walker 256 tumor-bearing rats model (M), and H. diffusa treatment (H) groups. Finally, 13 and 10 metabolomic biomarkers in urine and plasma samples were further identified as characteristic metabolites in M group, whereas H group showed a partial metabolic balance recovered, such as ornithine, N-acetyl-l-aspartate, l-aspartate, and creatinine in urine samples, and acetate, lactate, choline, l-glutamine, and 3-hydroxybutyrate in plasma samples. On the basis of the methods above, we hypothesized H. diffusa treatment reduced the injury caused by Walker 256 tumor and maintained a metabolic balance. Our study demonstrated that this method provided new insights into metabolic alterations in tumor-bearing biosystems and researching on the effects of H. diffusa on the endogenous metabolism in tumor-bearing rats.
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Affiliation(s)
- Zhiyong Wang
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
- Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Kuo Gao
- Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Can Xu
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Jian Gao
- Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yujing Yan
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Yingfeng Wang
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Zhongfeng Li
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Jianxin Chen
- Beijing University of Chinese Medicine, Beijing, 100029, China
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7
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Kurreck A, Vandergrift LA, Fuss TL, Habbel P, Agar NYR, Cheng LL. Prostate cancer diagnosis and characterization with mass spectrometry imaging. Prostate Cancer Prostatic Dis 2017; 21:297-305. [PMID: 29209003 PMCID: PMC5988647 DOI: 10.1038/s41391-017-0011-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/15/2017] [Indexed: 02/06/2023]
Abstract
Background Prostate cancer (PCa), the most common cancer and second leading cause of cancer death in American men, presents the clinical challenge of distinguishing between indolent and aggressive tumors for proper treatment. PCa presents significant alterations in metabolic pathways that can potentially be measured using techniques like mass spectrometry (MS) or mass spectrometry imaging (MSI) and used to characterize PCa aggressiveness. MS quantifies metabolomic, proteomic, and lipidomic profiles of biological systems that can be further visualized for their spatial distributions through MSI. Methods PubMed was queried for all publications relating to MS and MSI in human prostate cancer from April 2007 to April 2017. With the goal of reviewing the utility of MSI in diagnosis and prognostication of human PCa, MSI articles that reported investigations of PCa-specific metabolites or metabolites indicating PCa aggressiveness were selected for inclusion. Articles were included that covered MS and MSI principles, limitations, and applications in PCa. Results We identified nine key studies on MSI in intact human prostate tissue specimens that determined metabolites which could either differentiate between benign and malignant prostate tissue or indicate prostate cancer aggressiveness. These MSI-detected biomarkers show promise in reliably identifying PCa and determining disease aggressiveness. Conclusions MSI represents an innovative technique with the ability to interrogate cancer biomarkers in relation to tissue pathologies and investigate tumor aggressiveness. We propose MSI as a powerful adjuvant histopathology imaging tool for prostate tissue evaluations, where clinical translation of this ex vivo technique could make possible the use of MSI for personalized medicine in diagnosis and prognosis of prostate cancer. Moreover, the knowledge provided from this technique can majorly contribute to the understanding of molecular pathogenesis of PCa and other malignant diseases.
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Affiliation(s)
- Annika Kurreck
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Hematology and Oncology, Charité Medical University of Berlin, Berlin, Germany
| | - Lindsey A Vandergrift
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor L Fuss
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Piet Habbel
- Department of Hematology and Oncology, Charité Medical University of Berlin, Berlin, Germany
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Leo L Cheng
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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8
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Lin D, Ettinger SL, Qu S, Xue H, Nabavi N, Chuen Choi SY, Bell RH, Mo F, Haegert AM, Gout PW, Fleshner N, Gleave ME, Pollak M, Collins CC, Wang Y. Metabolic heterogeneity signature of primary treatment-naïve prostate cancer. Oncotarget 2017; 8:25928-25941. [PMID: 28460430 PMCID: PMC5432227 DOI: 10.18632/oncotarget.15237] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 01/25/2017] [Indexed: 02/06/2023] Open
Abstract
To avoid over- or under-treatment of primary prostate tumours, there is a critical need for molecular signatures to discriminate indolent from aggressive, lethal disease. Reprogrammed energy metabolism is an important hallmark of cancer, and abnormal metabolic characteristics of cancers have been implicated as potential diagnostic/prognostic signatures. While genomic and transcriptomic heterogeneity of prostate cancer is well documented and associated with tumour progression, less is known about metabolic heterogeneity of the disease. Using a panel of high fidelity patient-derived xenograft (PDX) models derived from hormone-naïve prostate cancer, we demonstrated heterogeneity of expression of genes involved in cellular energetics and macromolecular biosynthesis. Such heterogeneity was also observed in clinical, treatment-naïve prostate cancers by analyzing the transcriptome sequencing data. Importantly, a metabolic gene signature of increased one-carbon metabolism or decreased proline degradation was identified to be associated with significantly decreased biochemical disease-free patient survival. These results suggest that metabolic heterogeneity of hormone-naïve prostate cancer is of biological and clinical importance and motivate further studies to determine the heterogeneity in metabolic flux in the disease that may lead to identification of new signatures for tumour/patient stratification and the development of new strategies and targets for therapy of prostate cancer.
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Affiliation(s)
- Dong Lin
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Susan L. Ettinger
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sifeng Qu
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Hui Xue
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Noushin Nabavi
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Stephen Yiu Chuen Choi
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Robert H. Bell
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Fan Mo
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Anne M. Haegert
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter W. Gout
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Neil Fleshner
- Division of Urology, University of Toronto, Department of Urology, University Health Network, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Martin E. Gleave
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael Pollak
- Lady Davis Research Institute and McGill University, Montreal, Quebec, Canada
| | - Colin C. Collins
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuzhuo Wang
- The Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, British Columbia, Canada
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9
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Metabolite Analysis and Histology on the Exact Same Tissue: Comprehensive Metabolomic Profiling and Metabolic Classification of Prostate Cancer. Sci Rep 2016; 6:32272. [PMID: 27578275 PMCID: PMC5006072 DOI: 10.1038/srep32272] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/04/2016] [Indexed: 12/15/2022] Open
Abstract
We report a method of metabolomic profiling of intact tissue based on molecular preservation by extraction and fixation (mPREF) and high-performance chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS). mPREF extracts metabolites by aqueous methanol from tissue biopsies without altering tissue architecture and thus conventional histology can be performed on the same tissue. In a proof-of-principle study, we applied dansylation LC-MS to profile the amine/phenol submetabolome of prostate needle biopsies from 25 patient samples derived from 16 subjects. 2900 metabolites were consistently detected in more than 50% of the samples. This unprecedented coverage allowed us to identify significant metabolites for differentiating tumor and normal tissues. The panel of significant metabolites was refined using 36 additional samples from 18 subjects. Receiver Operating Characteristic (ROC) analysis showed area-under-the-curve (AUC) of 0.896 with sensitivity of 84.6% and specificity of 83.3% using 7 metabolites. A blind study of 24 additional validation samples gave a specificity of 90.9% at the same sensitivity of 84.6%. The mPREF extraction can be readily implemented into the existing clinical workflow. Our method of combining mPREF with CIL LC-MS offers a powerful and convenient means of performing histopathology and discovering or detecting metabolite biomarkers in the same tissue biopsy.
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10
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Kelly RS, Vander Heiden MG, Giovannucci E, Mucci LA. Metabolomic Biomarkers of Prostate Cancer: Prediction, Diagnosis, Progression, Prognosis, and Recurrence. Cancer Epidemiol Biomarkers Prev 2016; 25:887-906. [PMID: 27197278 DOI: 10.1158/1055-9965.epi-15-1223] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/23/2016] [Indexed: 02/07/2023] Open
Abstract
Metabolite profiling is being increasing employed in the study of prostate cancer as a means of identifying predictive, diagnostic, and prognostic biomarkers. This review provides a summary and critique of the current literature. Thirty-three human case-control studies of prostate cancer exploring disease prediction, diagnosis, progression, or treatment response were identified. All but one demonstrated the ability of metabolite profiling to distinguish cancer from benign, tumor aggressiveness, cases who recurred, and those who responded well to therapy. In the subset of studies where biomarker discriminatory ability was quantified, high AUCs were reported that would potentially outperform the current gold standards in diagnosis, prognosis, and disease recurrence, including PSA testing. There were substantial similarities between the metabolites and the associated pathways reported as significant by independent studies, and important roles for abnormal cell growth, intensive cell proliferation, and dysregulation of lipid metabolism were highlighted. The weight of the evidence therefore suggests metabolic alterations specific to prostate carcinogenesis and progression that may represent potential metabolic biomarkers. However, replication and validation of the most promising biomarkers is currently lacking and a number of outstanding methodologic issues remain to be addressed to maximize the utility of metabolomics in the study of prostate cancer. Cancer Epidemiol Biomarkers Prev; 25(6); 887-906. ©2016 AACR.
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Affiliation(s)
- Rachel S Kelly
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts. Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts. Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts. Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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11
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Ren J, Yuan L, Wen G, Yang J. The value of anti-1-amino-3-18F-fluorocyclobutane-1-carboxylic acid PET/CT in the diagnosis of recurrent prostate carcinoma: a meta-analysis. Acta Radiol 2016; 57:487-93. [PMID: 25907118 DOI: 10.1177/0284185115581541] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 03/20/2015] [Indexed: 12/26/2022]
Abstract
BACKGROUND Anti-1-amino-3-[18F]fluorocyclobutane-1-carboxylic acid (anti-3-18F-FACBC) positron emission tomography/computed tomography (PET/CT), 11 C-choline PET/CT, 111In-capromab pendetide, and T2-weighted magnetic resonance imaging (MRI) have been used for detecting prostate carcinoma relapse. PURPOSE To systematically review and perform a meta-analysis of published data regarding the performance of 18F-FACBC PET/CT in the diagnosis of recurrent prostate carcinoma. MATERIAL AND METHODS A comprehensive review of the literature regarding the role of 18F-FACBC PET/CT in the diagnosis of recurrent prostate carcinoma was performed. Pooled sensitivity, specificity, and the area under the receiver-operating characteristic of 18F-FACBC PET/CT in the diagnosis of recurrent prostate carcinoma were calculated based on the included studies. RESULTS Six studies comprising 251 patients, suspicious of prostate carcinoma recurrence, were included in this meta-analysis. 18F-FACBC PET/CT had an 87% pooled sensitivity, 66% pooled specificity, 0.93 the area under the receiver-operating characteristic curve on a per patient-based analysis in detecting prostate carcinoma recurrence. CONCLUSION 18F-FACBC PET/CT was a non-invasive, metabolic imaging technique in the diagnosis of prostate carcinoma relapse.
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Affiliation(s)
- Jingyun Ren
- Department of Nuclear Medicine, Beijing Friendship Hospital of Capital Medical University, Beijing, PR China
| | - Leilei Yuan
- Department of Nuclear Medicine, Beijing Friendship Hospital of Capital Medical University, Beijing, PR China
| | - Guanghua Wen
- Department of Nuclear Medcine, Jin Hua Municipal Central Hospital, Zhe Jiang, PR China
| | - Jigang Yang
- Department of Nuclear Medicine, Beijing Friendship Hospital of Capital Medical University, Beijing, PR China
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12
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Determination of Optimum Formalin Fixation Duration for Prostate Needle Biopsies for Immunohistochemistry and Quantum Dot FISH Analysis. Appl Immunohistochem Mol Morphol 2016; 23:364-73. [PMID: 25265431 DOI: 10.1097/pai.0000000000000085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Prostate biopsy is the key clinical specimen for disease diagnosis. However, various conditions used during biopsy processing for histologic analysis may affect the performance of diagnostic tests, such as hematoxylin and eosin (H&E) staining, immunohistochemistry (IHC), or in situ hybridization (ISH). One such condition that may affect diagnostic test performance is fixation duration in 10% neutral buffered formalin (NBF). For example, prostate needle biopsies are often <1 mm in diameter and thus overfixed. It is important to understand the impact of tissue fixation duration on diagnostic test performance to enable optimized assay procedures. This study was designed to study the effect of 10% NBF fixation duration of prostate needle biopsy on multiplexed quantum dot (QD) ISH assay of ERG and PTEN, 2 genes commonly altered in prostate cancer. The samples were also evaluated for H&E staining and ERG and PTEN IHC. H&E staining and ERG and PTEN IHC were acceptable for all the durations of fixation tested. For QD ISH, we observed good signals with biopsy samples fixed from 4 to 120 hours. Biopsy specimens fixed between 8 and 72 hours gave the best signal as scored by the study pathologist. In a separate cohort of 18 routinely processed prostate biopsy cores, all cores were stained successfully with the QD ISH assay, and results were 100% concordant to ERG and PTEN IHC. We conclude that 8 to 72 hours duration of fixation for prostate needle biopsies in 10% NBF results in optimal QD ISH assay performance.
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Lou TF, Sethuraman D, Dospoy P, Srivastva P, Kim HS, Kim J, Ma X, Chen PH, Huffman KE, Frink RE, Larsen JE, Lewis C, Um SW, Kim DH, Ahn JM, DeBerardinis RJ, White MA, Minna JD, Yoo H. Cancer-Specific Production of N-Acetylaspartate via NAT8L Overexpression in Non-Small Cell Lung Cancer and Its Potential as a Circulating Biomarker. Cancer Prev Res (Phila) 2016; 9:43-52. [PMID: 26511490 PMCID: PMC4774047 DOI: 10.1158/1940-6207.capr-14-0287] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/18/2015] [Indexed: 01/14/2023]
Abstract
In order to identify new cancer-associated metabolites that may be useful for early detection of lung cancer, we performed a global metabolite profiling of a non-small cell lung cancer (NSCLC) line and immortalized normal lung epithelial cells from the same patient. Among several metabolites with significant cancer/normal differences, we identified a unique metabolic compound, N-acetylaspartate (NAA), in cancer cells-undetectable in normal lung epithelium. NAA's cancer-specific detection was validated in additional cancer and control lung cells as well as selected NSCLC patient tumors and control tissues. NAA's cancer specificity was further supported in our analysis of NAA synthetase (gene symbol: NAT8L) gene expression levels in The Cancer Genome Atlas: elevated NAT8L expression in approximately 40% of adenocarcinoma and squamous cell carcinoma cases (N = 577), with minimal expression in all nonmalignant lung tissues (N = 74). We then showed that NAT8L is functionally involved in NAA production of NSCLC cells through siRNA-mediated suppression of NAT8L, which caused selective reduction of intracellular and secreted NAA. Our cell culture experiments also indicated that NAA biosynthesis in NSCLC cells depends on glutamine availability. For preliminary evaluation of NAA's clinical potential as a circulating biomarker, we developed a sensitive NAA blood assay and found that NAA blood levels were elevated in 46% of NSCLC patients (N = 13) in comparison with age-matched healthy controls (N = 21) among individuals aged 55 years or younger. Taken together, these results indicate that NAA is produced specifically in NSCLC tumors through NAT8L overexpression, and its extracellular secretion can be detected in blood. Cancer Prev Res; 9(1); 43-52. ©2015 AACR.
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Affiliation(s)
- Tzu-Fang Lou
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas. Center for Systems Biology, University of Texas at Dallas, Richardson, Texas
| | - Deepa Sethuraman
- Center for Systems Biology, University of Texas at Dallas, Richardson, Texas. Department of Bioengineering, University of Texas at Dallas, Richardson, Texas
| | - Patrick Dospoy
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Pallevi Srivastva
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas. Center for Systems Biology, University of Texas at Dallas, Richardson, Texas
| | - Hyun Seok Kim
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Joongsoo Kim
- Department of Chemistry, University of Texas at Dallas, Richardson, Texas
| | - Xiaotu Ma
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas
| | - Pei-Hsuan Chen
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kenneth E Huffman
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Robin E Frink
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jill E Larsen
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Cheryl Lewis
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Sang-Won Um
- Division of Pulmonary and Critical Care Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jung-Mo Ahn
- Department of Chemistry, University of Texas at Dallas, Richardson, Texas
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Michael A White
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hyuntae Yoo
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas. Center for Systems Biology, University of Texas at Dallas, Richardson, Texas. Department of Bioengineering, University of Texas at Dallas, Richardson, Texas.
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Jung K, Reszka R, Kamlage B, Bethan B, Stephan C, Lein M, Kristiansen G. Tissue metabolite profiling identifies differentiating and prognostic biomarkers for prostate carcinoma. Int J Cancer 2013; 133:2914-24. [PMID: 23737455 DOI: 10.1002/ijc.28303] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 04/22/2013] [Indexed: 12/17/2022]
Abstract
Metabolomic research offers a deeper insight into biochemical changes in cancer metabolism and is a promising tool for identifying novel biomarkers. We aimed to evaluate the diagnostic and prognostic potential of metabolites in prostate cancer (PCa) tissue after radical prostatectomy. In matched malignant and nonmalignant prostatectomy samples from 95 PCa patients, aminoadipic acid, cerebronic acid, gluconic acid, glycerophosphoethanolamine, 2-hydroxybehenic acid, isopentenyl pyrophosphate, maltotriose, 7-methylguanine and tricosanoic acid were determined within a global metabolite profiling study using gas chromatography/liquid chromatography-mass spectrometry. The data were related to clinicopathological variables like prostate volume, tumor stage, Gleason score, preoperative prostate-specific antigen and disease recurrence in the follow-up. All nine metabolites showed higher concentrations in malignant than in nonmalignant samples except for gluconic acid and maltotriose, which had lower levels in tumors. Receiver -operating characteristics analysis demonstrated a significant discrimination for all metabolites between malignant and nonmalignant tissue with a maximal area under the curve of 0.86 for tricosanoic acid, whereas no correlation was observed between the metabolite levels and the Gleason score or tumor stage except for gluconic acid. Univariate Cox regression and Kaplan-Meier analyses showed that levels of aminoadipic acid, gluconic acid and maltotriose were associated with the biochemical tumor recurrence (prostate-specific antigen > 0.2 ng/mL). In multivariate Cox regression analyses, aminoadipic acid together with tumor stage and Gleason score remained in a model as independent marker for prediction of biochemical recurrence. This study proved that metabolites in PCa tissue can be used, in combination with traditional clinicopathological factors, as promising diagnostic and prognostic tools.
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Affiliation(s)
- Klaus Jung
- Department of Urology, University Hospital Charité, Schumannstraß 20/21, 10117 Berlin, Germany; Berlin Institute for Urologic Research, Schumannstraße 20/21, 10117 Berlin, Germany
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Nanni C, Schiavina R, Boschi S, Ambrosini V, Pettinato C, Brunocilla E, Martorana G, Fanti S. Comparison of 18F-FACBC and 11C-choline PET/CT in patients with radically treated prostate cancer and biochemical relapse: preliminary results. Eur J Nucl Med Mol Imaging 2013; 40 Suppl 1:S11-7. [DOI: 10.1007/s00259-013-2373-3] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 11/28/2022]
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Spur EM, Decelle EA, Cheng LL. Metabolomic imaging of prostate cancer with magnetic resonance spectroscopy and mass spectrometry. Eur J Nucl Med Mol Imaging 2013; 40 Suppl 1:S60-71. [PMID: 23549758 DOI: 10.1007/s00259-013-2379-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 02/18/2013] [Indexed: 12/14/2022]
Abstract
Metabolomic imaging of prostate cancer (PCa) aims to improve in vivo imaging capability so that PCa tumors can be localized noninvasively to guide biopsy and evaluated for aggressiveness prior to prostatectomy, as well as to assess and monitor PCa growth in patients with asymptomatic PCa newly diagnosed by biopsy. Metabolomics studies global variations of metabolites with which malignancy conditions can be evaluated by profiling the entire measurable metabolome, instead of focusing only on certain metabolites or isolated metabolic pathways. At present, PCa metabolomics is mainly studied by magnetic resonance spectroscopy (MRS) and mass spectrometry (MS). With MRS imaging, the anatomic image, obtained from magnetic resonance imaging, is mapped with values of disease condition-specific metabolomic profiles calculated from MRS of each location. For example, imaging of removed whole prostates has demonstrated the ability of metabolomic profiles to differentiate cancerous foci from histologically benign regions. Additionally, MS metabolomic imaging of prostate biopsies has uncovered metabolomic expression patterns that could discriminate between PCa and benign tissue. Metabolomic imaging offers the potential to identify cancer lesions to guide prostate biopsy and evaluate PCa aggressiveness noninvasively in vivo, or ex vivo to increase the power of pathology analysis. Potentially, this imaging ability could be applied not only to PCa, but also to different tissues and organs to evaluate other human malignancies and metabolic diseases.
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Affiliation(s)
- Eva-Margarete Spur
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, CNY-6, 149 13th Street, Charlestown, Boston, MA 02129, USA
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Brown MV, McDunn JE, Gunst PR, Smith EM, Milburn MV, Troyer DA, Lawton KA. Cancer detection and biopsy classification using concurrent histopathological and metabolomic analysis of core biopsies. Genome Med 2012; 4:33. [PMID: 22546470 PMCID: PMC3446261 DOI: 10.1186/gm332] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 03/21/2012] [Accepted: 04/30/2012] [Indexed: 12/22/2022] Open
Abstract
Background Metabolomics, the non-targeted interrogation of small molecules in a biological sample, is an ideal technology for identifying diagnostic biomarkers. Current tissue extraction protocols involve sample destruction, precluding additional uses of the tissue. This is particularly problematic for high value samples with limited availability, such as clinical tumor biopsies that require structural preservation to histologically diagnose and gauge cancer aggressiveness. To overcome this limitation and increase the amount of information obtained from patient biopsies, we developed and characterized a workflow to perform metabolomic analysis and histological evaluation on the same biopsy sample. Methods Biopsies of ten human tissues (muscle, adrenal gland, colon, lung, pancreas, small intestine, spleen, stomach, prostate, kidney) were placed directly in a methanol solution to recover metabolites, precipitate proteins, and fix tissue. Following incubation, biopsies were removed from the solution and processed for histology. Kidney and prostate cancer tumor and benign biopsies were stained with hemotoxylin and eosin and prostate biopsies were subjected to PIN-4 immunohistochemistry. The methanolic extracts were analyzed for metabolites on GC/MS and LC/MS platforms. Raw mass spectrometry data files were automatically extracted using an informatics system that includes peak identification and metabolite identification software. Results Metabolites across all major biochemical classes (amino acids, peptides, carbohydrates, lipids, nucleotides, cofactors, xenobiotics) were measured. The number (ranging from 260 in prostate to 340 in colon) and identity of metabolites were comparable to results obtained with the current method requiring 30 mg ground tissue. Comparing relative levels of metabolites, cancer tumor from benign kidney and prostate biopsies could be distinguished. Successful histopathological analysis of biopsies by chemical staining (hematoxylin, eosin) and antibody binding (PIN-4, in prostate) showed cellular architecture and immunoreactivity were retained. Conclusions Concurrent metabolite extraction and histological analysis of intact biopsies is amenable to the clinical workflow. Methanol fixation effectively preserves a wide range of tissues and is compatible with chemical staining and immunohistochemistry. The method offers an opportunity to augment histopathological diagnosis and tumor classification with quantitative measures of biochemicals in the same tissue sample. Since certain biochemicals have been shown to correlate with disease aggressiveness, this method should prove valuable as an adjunct to differentiate cancer aggressiveness.
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Affiliation(s)
- Meredith V Brown
- Metabolon, Inc,, 617 Davis Drive, Suite 400, Durham, NC 27713, USA.
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