Biomarker Discovery and Verification of Esophageal Squamous Cell Carcinoma Using Integration of SWATH/MRM

Hou, Guixue; Lou, Xiaomin; Sun, Yulin; Xu, Shaohang; Zi, Jian; Wang, Quanhui; Zhou, Baojin; Han, Bo Hoon; Wu, Lin; Zhao, Xiaohang; Lin, Liang; Liu, Siqi

doi:10.1021/acs.jproteome.5b00438

Cited by 41 publications

(41 citation statements)

References 43 publications

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“…The MRM data structure is similar to that of SWATH-MS and the qualitative and quantitative information extracted from SWATH-MS are ideal to verify by MRM-MS assays (Hou et al, 2015). When the protein abundance ratios of 65 SWATH-MS quantified proteins (adequately representing the major groups of chloroplast proteins) were plotted against that those derived from MRM-MS, the Pearson correlation coefficient was 0.78 (Figure 1C; Supplementary Table 3).…”

Section: Resultsmentioning

confidence: 99%

The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation

et al. 2016

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Plant protoplasts are widely used for genetic manipulation and functional studies in transient expression systems. However, little is known about the molecular pathways involved in a cell response to the combined stress factors resulted from protoplast generation. Plants often face more than one type of stress at a time, and how plants respond to combined stress factors is therefore of great interest. Here, we used protoplasts of the moss Physcomitrella patens as a model to study the effects of short-term stress on the chloroplast proteome. Using label-free comparative quantitative proteomic analysis (SWATH-MS), we quantified 479 chloroplast proteins, 219 of which showed a more than 1.4-fold change in abundance in protoplasts. We additionally quantified 1451 chloroplast proteins using emPAI. We observed degradation of a significant portion of the chloroplast proteome following the first hour of stress imposed by the protoplast isolation process. Electron-transport chain (ETC) components underwent the heaviest degradation, resulting in the decline of photosynthetic activity. We also compared the proteome changes to those in the transcriptional level of nuclear-encoded chloroplast genes. Globally, the levels of the quantified proteins and their corresponding mRNAs showed limited correlation. Genes involved in the biosynthesis of chlorophyll and components of the outer chloroplast membrane showed decreases in both transcript and protein abundance. However, proteins like dehydroascorbate reductase 1 and 2-cys peroxiredoxin B responsible for ROS detoxification increased in abundance. Further, genes such as thylakoid ascorbate peroxidase were induced at the transcriptional level but down-regulated at the proteomic level. Together, our results demonstrate that the initial chloroplast reaction to stress is due changes at the proteomic level.

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Section: Resultsmentioning

confidence: 99%

The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation

et al. 2016

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“…In particular, N-acylethanolamine acid amidase and protein tyrosine kinase 7 were found to indicate distinct signatures for tumor aggressiveness [63], as a combined area under the ROC curve (AUROC = 0.801) score indicated from immunostained tissues. Biopsies from another type of cancer, esophageal squamous cell carcinoma, were analyzed with SWATH quantification to discover new biomarker candidates [64]. In addition to investigating biomarkers from biopsies, proteins from BALF hold great potential as lung cancer biomarkers due to new mildly invasive endoscopy-based collection techniques.…”

Section: Application Of Dia/swath Workflows To Clinically Relevantmentioning

confidence: 99%

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

Meyer

Schilling

2017

Expert Review of Proteomics

132

105

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Introduction While selected/multiple-reaction monitoring (SRM or MRM) is considered the gold standard for quantitative protein measurement, emerging data-independent acquisition (DIA) using high-resolution scans have opened a new dimension of high-throughput, comprehensive quantitative proteomics. These newer methodologies are particularly well suited for discovery of biomarker candidates from human disease samples, and for investigating and understanding human disease pathways. Areas covered This article reviews the current state of targeted and untargeted DIA mass spectrometry-based proteomic workflows, including SRM, parallel-reaction monitoring (PRM) and untargeted DIA (e.g., SWATH). Corresponding bioinformatics strategies, as well as application in biological and clinical studies are presented. Expert commentary Nascent application of highly-multiplexed untargeted DIA, such as SWATH, for accurate protein quantification from clinically relevant and disease-related samples shows great potential to comprehensively investigate biomarker candidates and understand disease.

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“…Hou et al applied a combination of sequential window acquisition of all theoretical fragment ion mass spectra (SWATH) and multiple‐reaction monitoring (MRM) to discover and verify ESCC‐related protein biomarkers in 10 ESCC tissues samples paired with adjacent non‐malignant tissue . The authors quantified 1758 proteins.…”

Section: Systematic Reviewmentioning

confidence: 99%

Proteomics biomarkers for solid tumors: Current status and future prospects

Belczacka

Latosinska

Metzger

et al. 2018

Mass Spectrometry Reviews

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Cancer is a heterogeneous multifactorial disease, which continues to be one of the main causes of death worldwide. Despite the extensive efforts for establishing accurate diagnostic assays and efficient therapeutic schemes, disease prevalence is on the rise, in part, however, also due to improved early detection. For years, studies were focused on genomics and transcriptomics, aiming at the discovery of new tests with diagnostic or prognostic potential. However, cancer phenotypic characteristics seem most likely to be a direct reflection of changes in protein metabolism and function, which are also the targets of most drugs. Investigations at the protein level are therefore advantageous particularly in the case of in-depth characterization of tumor progression and invasiveness. Innovative high-throughput proteomic technologies are available to accurately evaluate cancer formation and progression and to investigate the functional role of key proteins in cancer. Employing these new highly sensitive proteomic technologies, cancer biomarkers may be detectable that contribute to diagnosis and guide curative treatment when still possible. In this review, the recent advances in proteomic biomarker research in cancer are outlined, with special emphasis placed on the identification of diagnostic and prognostic biomarkers for solid tumors. In view of the increasing number of screening programs and clinical trials investigating new treatment options, we discuss the molecular connections of the biomarkers as well as their potential as clinically useful tools for diagnosis, risk stratification and therapy monitoring of solid tumors.

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Biomarker Discovery and Verification of Esophageal Squamous Cell Carcinoma Using Integration of SWATH/MRM

Cited by 41 publications

References 43 publications

The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation

The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

Proteomics biomarkers for solid tumors: Current status and future prospects

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