Cancer proteomics: developments in technology, clinical use and commercialization

Yeat, Nai Chien; Lin, Chih-Lung; Sager, Monica; Lin, Jimmy C.

doi:10.1586/14789450.2015.1051969

Cited by 9 publications

(2 citation statements)

References 97 publications

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“…Quantitative proteomics is the most promising technology in screening biomarkers for early diagnosis of diseases [16][17][18] . It has been widely used to analyze all protein levels expressed in a wide range of body uids and tissues obtained from patients in order to identify potential clinical biomarkers [19,20] .…”

Section: Introductionmentioning

confidence: 99%

Identification Novel Biomarker for Acute Aortic Dissection Using 4D-Label-Free Proteomics

wang

Wang

Maitusun

et al. 2021

Preprint

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Purpose: we aimed to identify potential candidate biomarkers in aorta tissue from AAD patients. Methods: We used 4D label-free quantification (4D-LFQ) mass spectrometry to screen differentially expressed proteins in aorta tissues of AAD patients. Then we performed protein annotation, unsupervised hierarchical clustering, functional classification, functional enrichment and cluster, and protein-protein interaction analyses. Parallel Reaction Monitoring (PRM) technology was used to accurately and quantitatively confirm the selected target proteins. Results: A total of 3350 proteins were identified. Taking 1.5 times as the differential expression threshold, 139 were upregulated and 108 were downregulated as compared to the control groups. Bioinformatics analysis showed that the differential proteins were mainly distributed in extracellular matrix and cytoplasm. And their functions mainly involve cell migration and proliferation, inflammatory cell activation, cell contraction, muscle organ development and other processes. PRM technology accurately quantified the selected 20 target proteins, and found SAA1, LBP, MPO, and ENG were confirmed to be enriched in the aorta tissue of AAD patients. Conclusions: This is the first application of a 4D-LFQ-PRM workflow to identify and validate biomarkers in AAD patients. SAA1, LBP, MPO, and ENG represent novel biomarkers for the pathogenesis of AAD and might be a therapeutic target in the future.

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Section: Introductionmentioning

confidence: 99%

Identification Novel Biomarker for Acute Aortic Dissection Using 4D-Label-Free Proteomics

wang

Wang

Maitusun

et al. 2021

Preprint

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“…Liquid Chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used technique in proteomic investigations allowing global analyses of samples of multiple biologic types and disease states, including cancer. [23][24] MS offers the ability to directly investigate altered signaling pathways and biologic anomalies found in the tumors. Generally, the utility of MS in the analysis of clinical tissue samples has been limited by the requirement for fresh or frozen samples, whereas the largest clinical resource of such tissues is in the form of archival tissues stored as formalin-fixed, paraffin-embedded (FFPE) blocks in biobanks.…”

Section: Introductionmentioning

confidence: 99%

Downregulation of antigen presentation-associated pathway proteins is linked to poor outcome in triple-negative breast cancer patient tumors

et al. 2017

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Triple-negative breast cancer (TNBC) is a heterogeneous subtype with varying disease outcomes. Tumor-infiltrating lymphocytes (TILs) are frequent in TNBC and have been shown to correlate with outcome, suggesting an immunogenic component in this subtype. However, other factors intrinsic to the cancer cells may also influence outcome. To identify proteins and molecular pathways associated with recurrence in TNBC, 34 formalin-fixed paraffin-embedded (FFPE) primary TNBC tumors were investigated by global proteomic profiling using mass spectrometry. Approximately, half of the patients were lymph node-negative and remained free of local or distant metastasis within 10 y follow-up, while the other half developed distant metastasis. Proteomic profiling identified >4,000 proteins, of which 63 exhibited altered expression in primary tumors of recurrence versus recurrence-free patients. Importantly, downregulation of proteins in the major histocompatibility complex (MHC) class I antigen presentation pathways were enriched, including TAP1, TAP2, CALR, HLA-A, ERAP1 and TAPBP, and were associated with significantly shorter recurrence-free and overall survival. In addition, proteins involved in cancer cell proliferation and growth, including GBP1, RAD23B, WARS and STAT1, also exhibited altered expression in primary tumors of recurrence versus recurrence-free patients. The association between the antigen-presentation pathway and outcome were validated in a second sample set of 10 primary TNBC tumors and corresponding metastases using proteomics and in a large public gene expression database of 249 TNBC and 580 basal-like breast cancer cases. Our study demonstrates that downregulation of antigen presentation is a key mechanism for TNBC cells to avoid immune surveillance, allowing continued growth and spread.

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Glycosaminoglycans and glycolipids as potential biomarkers in lung cancer

Joo

et al. 2017

Glycoconj J

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In this report, we used liquid chromatography-mass spectrometry and Western blotting to analyze the content and structure of glycosaminoglycans, glycolipids and selected proteins to compare differences between patient-matched normal and cancerous lung tissues obtained from lung cancer patients. The cancer tissue samples contained over twice as much chondroitin sulfate (CS)/dermatan sulfate (DS) as did the normal tissue samples, while the amount of heparan sulfate (HS) and hyaluronan (HA) in normal and cancer tissues were not significantly different. In HS, several minor disaccharide components, including NS6S, NS2S and 2S were significantly lower in cancer tissues, while the levels of major disaccharides, TriS, NS and 0S disaccharides were not significantly different in normal and cancer tissues. In regards to CS/DS, the level of 4S disaccharide (the major component of CS-type A and DS) decreased and the level of 6S disaccharide (the major component of CS- type C) increased in cancer tissues. We also compared the content and structure of GAGs in lung tissues from smoking and non-smoking patients. Analysis of the glycolipids showed all lipids present in these lung tissues, with the exception of sphingomyelin were higher in cancer tissues than in normal tissues. Western analysis showed that syndecan 1 and 2 proteoglycans displayed much higher expression in cancer tissue/biopsy samples. This investigation begins to provide an understanding of patho-physiological roles on glycosaminoglycans and glycolipids and might be useful in identifying potential biomarkers in lung cancer.

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Cancer proteomics: developments in technology, clinical use and commercialization

Cited by 9 publications

References 97 publications

Identification Novel Biomarker for Acute Aortic Dissection Using 4D-Label-Free Proteomics

Identification Novel Biomarker for Acute Aortic Dissection Using 4D-Label-Free Proteomics

Downregulation of antigen presentation-associated pathway proteins is linked to poor outcome in triple-negative breast cancer patient tumors

Glycosaminoglycans and glycolipids as potential biomarkers in lung cancer

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