Proteome Analysis of Isolated Perfused Organ Effluent as a Novel Model for Protein Biomarker Discovery

2006 ◽  
Vol 5 (1) ◽  
pp. 177-182 ◽  
Author(s):  
John M. Koomen ◽  
Christopher R. Wilson ◽  
Patrick Guthrie ◽  
Matthew J. Androlewicz ◽  
Ryuji Kobayashi ◽  
...  
Keyword(s):  
Biomarker Discovery ◽  
Proteome Analysis ◽  
Protein Biomarker ◽  
Novel Model

scholarly journals Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers

2018 ◽  
Vol 1 (2) ◽  
pp. e201800042 ◽  
Author(s):  
Tiannan Guo ◽  
Li Li ◽  
Qing Zhong ◽  
Niels J Rupp ◽  
Konstantina Charmpi ◽  
...  
Keyword(s):  
Biomarker Discovery ◽  
Specific Antigen ◽  
Proteome Analysis ◽  
Tissue Microarrays ◽  
Protein Biomarker ◽  
Pressure Cycling ◽  
Pressure Cycling Technology ◽  
New Perspective ◽  
High Degree ◽  
Independent Cohort

It remains unclear to what extent tumor heterogeneity impacts on protein biomarker discovery. Here, we quantified proteome intra-tissue heterogeneity (ITH) based on a multi-region analysis of prostate tissues using pressure cycling technology and Sequential Windowed Acquisition of all THeoretical fragment ion mass spectrometry. We quantified 6,873 proteins and analyzed the ITH of 3,700 proteins. The level of ITH varied depending on proteins and tissue types. Benign tissues exhibited more complex ITH patterns than malignant tissues. Spatial variability of 10 prostate biomarkers was validated by immunohistochemistry in an independent cohort (n = 83) using tissue microarrays. Prostate-specific antigen was preferentially variable in benign prostatic hyperplasia, whereas growth/differentiation factor 15 substantially varied in prostate adenocarcinomas. Furthermore, we found that DNA repair pathways exhibited a high degree of variability in tumorous tissues, which may contribute to the genetic heterogeneity of tumors. This study conceptually adds a new perspective to protein biomarker discovery: it suggests that recent technological progress should be exploited to quantify and account for spatial proteome variation to complement biomarker identification and utilization.

scholarly journals Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers

2018 ◽  
Author(s):  
Tiannan Guo ◽  
Li Li ◽  
Qing Zhong ◽  
Niels J Rupp ◽  
Konstantina Charmpi ◽  
...  
Keyword(s):  
Technological Progress ◽  
Biomarker Discovery ◽  
Proteome Analysis ◽  
Tissue Microarrays ◽  
Protein Biomarker ◽  
Pressure Cycling ◽  
Pressure Cycling Technology ◽  
New Perspective ◽  
High Degree ◽  
Independent Cohort

AbstractMany tumors are characterized by large genomic heterogeneity and it remains unclear to what extent this impacts on protein biomarker discovery. Here, we quantified proteome intra-tissue heterogeneity (ITH) based on a multi-region analysis of 30 biopsy-scale prostate tissues using pressure cycling technology and SWATH mass spectrometry. We quantified 8,248 proteins and analyzed the ITH of 3,700 proteins. The level of ITH varied significantly depending on proteins and tissue types. Benign tissues exhibited generally more complex ITH patterns than malignant tissues. Spatial variability of ten prostate biomarkers was further validated by immunohistochemistry in an independent cohort (n=83) using tissue microarrays. PSA was preferentially variable in benign prostatic hyperplasia, while GDF15 substantially varied in prostate adenocarcinomas. Further, we found that DNA repair pathways exhibited a high degree of variability in tumorous tissues, which may contribute to the genetic heterogeneity of tumors. This study conceptually adds a new perspective to protein biomarker discovery by quantifying spatial proteome variation and it demonstrates the feasibility by exploiting recent technological progress.

scholarly journals Cerebrospinal fluid extracellular vesicle enrichment for protein biomarker discovery in neurological disease; multiple sclerosis

2017 ◽  
Vol 6 (1) ◽  
pp. 1369805 ◽  
Author(s):  
Joanne L. Welton ◽  
Samantha Loveless ◽  
Timothy Stone ◽  
Chris von Ruhland ◽  
Neil P. Robertson ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Cerebrospinal Fluid ◽  
Neurological Disease ◽  
Biomarker Discovery ◽  
Extracellular Vesicle ◽  
Protein Biomarker

scholarly journals Transcriptome and Proteome Research in Veterinary Science: What Is Possible and What Questions Can Be Asked?

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Robert Klopfleisch ◽  
Achim D. Gruber
Keyword(s):  
Sequential Analysis ◽  
Biomarker Discovery ◽  
Expression Patterns ◽  
Proteome Analysis ◽  
Shotgun Proteomics ◽  
Complete Analysis ◽  
Biological Research ◽  
Veterinary Research ◽  
Gene Sets ◽  
2D Gel

In recent years several technologies for the complete analysis of the transcriptome and proteome have reached a technological level which allows their routine application as scientific tools. The principle of these methods is the identification and quantification of up to ten thousands of RNA and proteins species in a tissue, in contrast to the sequential analysis of conventional methods such as PCR and Western blotting. Due to their technical progress transcriptome and proteome analyses are becoming increasingly relevant in all fields of biological research. They are mainly used for the explorative identification of disease associated complex gene expression patterns and thereby set the stage for hypothesis-driven studies. This review gives an overview on the methods currently available for transcriptome analysis, that is, microarrays, Ref-Seq, quantitative PCR arrays and discusses their potentials and limitations. Second, the most powerful current approaches to proteome analysis are introduced, that is, 2D-gel electrophoresis, shotgun proteomics, MudPIT and the diverse technological concepts are reviewed. Finally, experimental strategies for biomarker discovery, experimental settings for the identification of prognostic gene sets and explorative versus hypothesis driven approaches for the elucidation of diseases associated genes and molecular pathways are described and their potential for studies in veterinary research is highlighted.

scholarly journals Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation

2021 ◽  
Author(s):  
Ernesto S. Nakayasu ◽  
Marina Gritsenko ◽  
Paul D. Piehowski ◽  
Yuqian Gao ◽  
Daniel J. Orton ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Best Practices ◽  
Biomarker Discovery ◽  
Protein Biomarker

Protein biomarker discovery for head and neck cancer

2010 ◽  
Vol 73 (10) ◽  
pp. 1790-1803 ◽  
Author(s):  
Tieneke B.M. Schaaij-Visser ◽  
Ruud H. Brakenhoff ◽  
C. René Leemans ◽  
Albert J.R. Heck ◽  
Monique Slijper
Keyword(s):  
Head And Neck Cancer ◽  
Head And Neck ◽  
Neck Cancer ◽  
Biomarker Discovery ◽  
Protein Biomarker

Proteome analysis for 3T3-L1 adipocyte differentiation and biomarker discovery in adipogenesis

2008 ◽  
Vol 136 ◽  
pp. S441-S442
Author(s):  
Kim Hyun Ah ◽  
Md. Atiar Rahman ◽  
Suresh G. Kumar ◽  
Lee Sung Hak ◽  
Hwang Hee Sun ◽  
...  
Keyword(s):  
Adipocyte Differentiation ◽  
Biomarker Discovery ◽  
Proteome Analysis

Proteome analysis of body fluids for amyotrophic lateral sclerosis biomarker discovery

2013 ◽  
Vol 7 (1-2) ◽  
pp. 123-135 ◽  
Author(s):  
Thomas Krüger ◽  
Janin Lautenschläger ◽  
Julian Grosskreutz ◽  
Heidrun Rhode
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Biomarker Discovery ◽  
Proteome Analysis ◽  
Body Fluids ◽  
Lateral Sclerosis
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