Quantitative pattern analysis of the N‐terminally processed isoforms of platelet factor‐4 in serum

Kim, Jin Young; Lee, Jae-Ryoung; Choi, Sunkyu; Kim, Eun-Min; Jung, Nak-Kyun; Kim, Young Hwan; Yoo, Jong Shin; Lee, Seungwon

doi:10.1002/rcm.6480

Cited by 10 publications

(8 citation statements)

References 33 publications

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“…The last identified biomarker is an isoform of PF-4 with 4 additional amino acids at the N-terminal part of the sequence (up-regulated in ALS patients). N-terminally isoforms of a variant of PF4 were characterized by Struyf et al in 2004 [25], and more recently, seven N-terminally processed PF4 isoforms were identified in serum from healthy volunteers, including the isoform identified in our study [26]. To our knowledge, the isoform of PF4 identified in our study had never been mentioned as potential biomarker in any published study.…”

Section: Discussionsupporting

confidence: 52%

Plasma Peptide Biomarker Discovery for Amyotrophic Lateral Sclerosis by MALDI –TOF Mass Spectrometry Profiling

et al. 2013

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The diagnostic of Amyotrophic lateral sclerosis (ALS) remains based on clinical and neurophysiological observations. The actual delay between the onset of the symptoms and diagnosis is about 1 year, preventing early inclusion of patients into clinical trials and early care of the disease. Therefore, finding biomarkers with high sensitivity and specificity remains urgent. In our study, we looked for peptide biomarkers in plasma samples using reverse phase magnetic beads (C18 and C8) and MALDI-TOF mass spectrometry analysis. From a set of ALS patients (n=30) and healthy age-matched controls (n=30), C18- or C8-SVM-based models for ALS diagnostic were constructed on the base of the minimum of the most discriminant peaks. These two SVM-based models end up in excellent separations between the 2 groups of patients (recognition capability overall classes > 97%) and classify blinded samples (10 ALS and 10 healthy age-matched controls) with very high sensitivities and specificities (>90%). Some of these discriminant peaks have been identified by Mass Spectrometry (MS) analyses and correspond to (or are fragments of) major plasma proteins, partly linked to the blood coagulation.

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Section: Discussionsupporting

confidence: 52%

Plasma Peptide Biomarker Discovery for Amyotrophic Lateral Sclerosis by MALDI –TOF Mass Spectrometry Profiling

et al. 2013

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“…The LMW proteins including cystatin-A (CSTA, P01040, 10868.63 Da), CXCL7 (10255.38 Da), and the cleaved product of plasma serine protease inhibitor (IPSP, P05154, AA 374–406, 3888.15 Da) were only identified from HC plasma sample, whereas PF4 (AA 28–101, 8136.36 Da) and hemoglobin subunit alpha (HBA, Q9BX83, AA 2–100, 10133.18 Da) and a cleaved product of hemoglobin subunit beta (HBB, P68871, AA 2–93 9911.20 Da) were only identified from the CRC plasma sample. In the case of the PF4, the mature form was originally found to be composed of 70 amino acids (AA 32–101) with cleavage of signal peptide (AA 1–31); however, it was recently reported that the proteoform with AA 28–101 was also found as one of the N-terminally processed proteoforms in human plasma or serum sample . Although there were LMW proteoforms that were only identified from either HC or CRC plasma sample, most of the proteoforms were detected in the other sample when peak signals were manually extracted for the most abundant isotopic peaks with an identical charge state within 10 ppm tolerance in Xcalibur.…”

Section: Results and Discussionmentioning

confidence: 99%

“…In the case of the PF4, the mature form was originally found to be composed of 70 amino acids (AA 32−101) with cleavage of signal peptide (AA 1−31); 55 however, it was recently reported that the proteoform with AA 28−101 was also found as one of the N-terminally processed proteoforms in human plasma or serum sample. 56 Although there were LMW proteoforms that were only identified from either HC or CRC plasma sample, most of the proteoforms were detected in the other sample when peak signals were manually extracted for the most abundant isotopic peaks with an identical charge state within 10 ppm tolerance in Xcalibur. This indicates that there are few proteoforms specifically present in either HC or CRC plasma sample without removal of high-abundance plasma proteins.…”

Section: Lmw Cleaved Products Identified From the Four Types Of Plasm...mentioning

confidence: 99%

Comprehensive Analysis of Low-Molecular-Weight Human Plasma Proteome Using Top-Down Mass Spectrometry

et al. 2015

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While human plasma serves as a great source for disease diagnosis, low-molecular-weight (LMW) proteome (<30 kDa) has been shown to contain a rich source of diagnostic biomarkers. Here we employ top-down mass spectrometry to analyze the LMW proteoforms present in four types of human plasma samples pooled from three healthy controls (HCs) without immunoaffinity depletion and with depletion of the top two, six, and seven high-abundance proteins. The LMW proteoforms were first fractionated based on molecular weight using gel-eluted liquid fraction entrapment electrophoresis (GELFrEE). Then, the GELFrEE fractions containing up to 30 kDa were subjected to nanocapillary-LC-MS/MS, and the high-resolution MS and MS/MS data were processed using ProSightPC 3.0. As a result, a total of 442 LMW proteins and cleaved products, including those with post-translational modifications and single amino acid variations, were identified. From additional comparative analysis of plasma samples without immunoaffinity depletion between HCs and colorectal cancer (CRC) patients via top-down approach, tens of LMW proteoforms, including platelet factor 4, were found to show >1.5-fold changes between the plasma samples of HCs and CRC patients, and six of the LMW proteins were verified by Western blot analysis.

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“…A nine‐step salt gradient was performed using 2 μL of 0–500 mM ammonium acetate with 0.1% formic acid in H 2 O and then a 3‐step gradient of 2–5 μL of 500 mM ammonium acetate with 0.1% formic acid in 30% ACN. Mobile phases A and B contained 0.1% formic acid in 0 and 100% ACN, with an initial gradient of 5% B and then a ramp up to 15% B over 10 min, 55% B over the next 60 min, then 95% B over 20 min, and maintenance at 95% B for 5 min . Electrospray voltage was set at 2.1 kV.…”

Section: Methodsmentioning

confidence: 99%

Differential protein expression and basal lamina remodeling in human heart failure

et al. 2016

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Purpose A goal of this study was to identify and investigate previously unrecognized components of the remodeling process in the progression to heart failure by comparing protein expression in ischemic failing (F) and nonfailing (NF) human hearts. Experimental design Protein expression differences were investigated using multidimensional protein identification and validated by Western analysis. This approach detected basal lamina (BL) remodeling, and further studies analyzed samples for evidence of structural BL remodeling. A rat model of pressure overload (PO) was studied to determine whether nonischemic stressors also produce BL remodeling and impact cellular adhesion. Results Differential protein expression of collagen IV, laminin α2, and nidogen-1 indicated BL remodeling develops in F versus NF hearts Periodic disruption of cardiac myocyte BL accompanied this process in F, but not NF heart. The rat PO myocardium also developed BL remodeling and compromised myocyte adhesion compared to sham controls. Conclusions and clinical relevance Differential protein expression and evidence of structural and functional BL alterations develop during heart failure. The compromised adhesion associated with this remodeling indicates a high potential for dysfunctional cellular integrity and tethering in failing myocytes. Therapeutically targeting BL remodeling could slow or prevent the progression of heart disease.

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Quantitative pattern analysis of the N‐terminally processed isoforms of platelet factor‐4 in serum

Abstract: This study is the first report on the levels of N-terminally processed PF4 isoforms in serum. Also, this study shows the usefulness of SRM in determining concentrations of protein isoform variants, which can be often overlooked in immunoassay analysis.

Cited by 10 publications

References 33 publications

Plasma Peptide Biomarker Discovery for Amyotrophic Lateral Sclerosis by MALDI –TOF Mass Spectrometry Profiling

Plasma Peptide Biomarker Discovery for Amyotrophic Lateral Sclerosis by MALDI –TOF Mass Spectrometry Profiling

Comprehensive Analysis of Low-Molecular-Weight Human Plasma Proteome Using Top-Down Mass Spectrometry

Differential protein expression and basal lamina remodeling in human heart failure

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