Proteomics analysis of bodily fluids in pancreatic cancer

Pan, Sheng; Brentnall, Teresa A.; Chen, Ru

doi:10.1002/pmic.201400476

Cited by 53 publications

(58 citation statements)

References 132 publications

(143 reference statements)

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“…Proteomics is an emerging technology to quickly survey altered cellular functions through a large‐scale gene determination and, therefore has been employed in a variety of clinical studies . However, potential biomarker proteins in body fluids are often present at low levels, requiring sensitive techniques.…”

mentioning

confidence: 99%

In‐Depth Proteomic Analysis of Human Bronchoalveolar Lavage Fluid toward the Biomarker Discovery for Lung Cancers

Sim

Choi

Lee

et al. 2019

Proteomics Clinical Apps

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Purpose Lung cancer is among the most common cancers. Bronchoalveolar lavage fluid (BALF) can be easily obtained from patients with lung cancers. The aim is to develop a novel proteomic method of the molecule‐based sensitive detection of biomarkers from BALF. Experimental Design BALF samples are collected from segmental bronchus of 14 patients with lung cancers from Kyung Hee University Hospital. First, BALF proteome is depleted using a depletion column, and then peptides are prepared from the enriched low abundant proteins and fractionated by high pH reverse phase liquid chromatography prior to LC‐MS/MS. Data are available via ProteomeXchange with identifier PXD012645. Results A novel method is developed for in‐depth proteomic analysis of BALF by combining antibody‐based depletion of high abundant proteins from BALF with high pH peptide fractionation. Peptides are analyzed on a high resolution Orbitrap Fusion mass spectrometer. MaxQuant search result in the identification of 4615 protein groups mapped to 4534 genes. Conclusions and Clinical Relevance It is found that the method outperformed conventional BALF proteomic methods and it is believed that this method will facilitate the biomarker research for lung cancer. In addition, it is shown that BALF will be a great source of biomarkers of lung diseases.

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mentioning

confidence: 99%

In‐Depth Proteomic Analysis of Human Bronchoalveolar Lavage Fluid toward the Biomarker Discovery for Lung Cancers

Sim

Choi

Lee

et al. 2019

Proteomics Clinical Apps

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“…Proteomics approach has been widely adopted in studies of human diseases including cancer (Frantzi et al, 2015; S. Pan, Brentnall, & Chen, 2015; Petricoin et al, 2002; Tsai et al, 2015), multiple sclerosis (Farias, Pradella, Schmitt, Santos, & Martins-de-Souza, 2014) and schizophrenia (Al Awam et al, 2015; Nascimento & Martins-de-Souza, 2015).…”

Section: Overview Of Omics Technologies and Association Studiesmentioning

confidence: 99%

“…However, these studies have found many protein candidates, which can potentially improve prognosis, diagnosis, and effectiveness of treatment. More recent proteomic studies also used body fluid samples to identify protein markers for bladder cancer (Frantzi et al, 2015), pancreatic cancer (S. Pan et al, 2015) and hepatocellular carcinoma (Tsai et al, 2015).…”

Section: Overview Of Omics Technologies and Association Studiesmentioning

confidence: 99%

Integrative Analysis of Multi-omics Data for Discovery and Functional Studies of Complex Human Diseases

Sun

2016

Advances in Genetics

352

222

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Complex and dynamic networks of molecules are involved in human diseases. High-throughput technologies enable omics studies interrogating thousands to millions of makers with similar biochemical properties (e.g. transcriptomics for RNA transcripts). However, a single layer of ‘omics’ can only provide limited insights into the biological mechanisms of a disease. In the case of GWAS, although thousands of SNPs have been identified for complex diseases and traits, the functional implications and mechanisms of the associated loci are largely unknown. Additionally, the genomic variants alone are not able to explain the changing disease risk across the life span. DNA, RNA, protein, and metabolite often have complementary roles to jointly perform a certain biological function. Such complementary effects and synergistic interactions between omic layers in the life-course can only be captured by integrative study of multiple molecular layers. Building upon the success in single-omics discovery research, population studies started adopting the multi-omics approach to better understanding the molecular function and disease etiology. Multi-omics approaches integrate data obtained from different omic levels to understand their interrelation and combined influence on the disease processes. Here, we summarize major omics approaches available in population research, and review integrative approaches and methodologies interrogating multiple omic layers, which enhance the gene discovery and functional analysis of human diseases. We seek to provide analytical recommendations for different types of multi-omics data and study designs to guide the emerging multi-omic research, and to suggest improvement of the existing analytical methods.

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“…As TDSFs are diagnostically more important than the elements within the liver niche, it would not be necessary to access liver tissue in premetastatic phases. In fact, it was recently demonstrated for pancreatic cancer [66] that it should be feasible to detect TDSFs in body fluids during niche-creating inflammation or premalignant phases in a proteomic approach. Regarding the premetastatic niche in the liver, it will be important also to demonstrate the metastasis-promoting activation of specific liver cells by TDSFs in patients.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Premetastatic niche formation in the liver: emerging mechanisms and mouse models

Krüger

2015

J Mol Med

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The liver is recognized as the target organ of metastases of almost all prominent malignancies. Its unique biology renders this organ particularly susceptible to circulating disseminated tumour cells (DTCs), and it can be assumed that very early metastasis occurs in the liver. The premetastatic niche concept may explain very early metastasis, as it defines priming of a future target organ of metastasis by factors that may already be secreted from premalignant lesions. This review shows that comprehensive knowledge on mechanisms of premetastatic niche formation in the liver is based on pre-clinical models only and still rather rare, mostly due to the scarcity of mouse liver metastasis models displaying a tumour cell-free period in the liver or lack of liver-tropic syngeneic tumour cells to probe for the niche. Attentive re-assessment of previous studies and reviews was undertaken revealing only two clearly identified tumour-derived secreted factors (TDSFs), both inducing infiltration of the liver by bone marrow-derived cells and increased liver metastasis, namely tissue inhibitor of metalloproteinases-1 (TIMP-1) and macrophage-inducing factor (MIF). Future directions of this research area will comprise elucidation of the impact of TDSFs on regulation and activity of myeloid-derived suppressor cells and/or the specific architecture and homeostasis of the liver, as well as development of prognostic TDSF detection in patients at risk of liver metastasis.

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Proteomics analysis of bodily fluids in pancreatic cancer

Cited by 53 publications

References 132 publications

In‐Depth Proteomic Analysis of Human Bronchoalveolar Lavage Fluid toward the Biomarker Discovery for Lung Cancers

In‐Depth Proteomic Analysis of Human Bronchoalveolar Lavage Fluid toward the Biomarker Discovery for Lung Cancers

Integrative Analysis of Multi-omics Data for Discovery and Functional Studies of Complex Human Diseases

Premetastatic niche formation in the liver: emerging mechanisms and mouse models

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