Ciphergen Biosystems

Fremont, CA, United States

Ciphergen Biosystems

Fremont, CA, United States
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Constantinescu R.,Gothenburg University | Andreasson U.,Gothenburg University | Li S.,Gothenburg University | Podust V.N.,Ciphergen Biosystems | And 9 more authors.
Parkinsonism and Related Disorders | Year: 2010

Parkinson's disease (PD) and atypical parkinsonian disorders (APD), including multiple system atrophy (MSA), progressive supranuclear palsy (PSP), and corticobasal degeneration (CBD), are a group of neurodegenerative diseases sharing many similar signs and symptoms but distinguished by their particular clinical features, treatment response, prognosis and mortality. The differential diagnosis may be challenging, especially in early disease stages. Considering the importance of an accurate diagnosis both for clinical management and for research, new diagnostic tools are needed. In this study, we investigated 56 PD, 42 MSA, 39 PSP, 9 CBD patients, and 24 healthy controls. After screening the cerebrospinal fluid (CSF) proteome using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), we identified 4 proteins (ubiquitin [mass-to-charge ratio (m/z) 8590], β2-microglobulin [m/ z 11730], and 2 secretogranin 1 [chromogranin B] fragments [m/z 7260 and m/ z 6250]) that differentiated healthy controls and PD patients from patients with APD. However, they could not differentiate PD patients from controls. As none of these changes were APD subgroup-specific, they most likely reflect the intensity and/or extent of the neurodegenerative process in general. © 2010 Elsevier Ltd.


Jayanthi S.,U.S. National Institutes of Health | Buie S.,U.S. National Institutes of Health | Moore S.,Ciphergen Biosystems | Herning R.I.,U.S. National Institutes of Health | And 4 more authors.
Molecular Psychiatry | Year: 2010

Marijuana (MJ) is the most commonly used illicit drug in the United States. Its abuse is associated with cognitive dysfunctions and increased resistance to blood flow in the cerebral vasculature. In addition, MJ abuse is associated with increased risks of potentially serious cardiovascular disorders. In the present study, we used the protein chip platform based on surface-enhanced laser desorption/ionization time-of-flight mass spectroscopy (SELDI-TOF-MS) to test the possibility that MJ abuse might be associated with changes in serum protein levels. Indeed, MJ users showed significant increases in three protein peaks, which were identified as three isoforms of apolipoprotein (apo) C-III. Immunoprecipitation using an apoC-III antibody also validated the identification of the proteins. Marijuana-induced increases in apoC-III levels might occur through chronic stimulation of hepatic cannabinoid receptors (CB1 and/or CB2) by its active ingredient, Δ 9 tetrahydrocannibol (THC). Thus, chronic MJ abuse might cause increased transcription and/or translation of apoC-III in the liver with corresponding changes reflected in the plasma of these patients. In any case, because apoC-III is a cardiovascular risk factor, the increased levels observed in MJ users might explain, in part, the cardiac and cerebral abnormalities reported in these patients. © 2010 Nature Publishing Group All rights reserved.


Majewski T.,University of Houston | Spiess P.E.,University of Houston | Spiess P.E.,H. Lee Moffitt Cancer Center and Research Institute | Bondaruk J.,University of Houston | And 9 more authors.
PLoS ONE | Year: 2012

We used protein expression profiles to develop a classification rule for the detection and prognostic assessment of bladder cancer in voided urine samples. Using the Ciphergen PBS II ProteinChip Reader, we analyzed the protein profiles of 18 pairs of samples of bladder tumor and adjacent urothelium tissue, a training set of 85 voided urine samples (32 controls and 53 bladder cancer), and a blinded testing set of 68 voided urine samples (33 controls and 35 bladder cancer). Using t-tests, we identified 473 peaks showing significant differential expression across different categories of paired bladder tumor and adjacent urothelial samples compared to normal urothelium. Then the intensities of those 473 peaks were examined in a training set of voided urine samples. Using this approach, we identified 41 protein peaks that were differentially expressed in both sets of samples. The expression pattern of the 41 protein peaks was used to classify the voided urine samples as malignant or benign. This approach yielded a sensitivity and specificity of 59% and 90%, respectively, on the training set and 80% and 100%, respectively, on the testing set. The proteomic classification rule performed with similar accuracy in low- and high-grade bladder carcinomas. In addition, we used hierarchical clustering with all 473 protein peaks on 65 benign voided urine samples, 88 samples from patients with clinically evident bladder cancer, and 127 samples from patients with a history of bladder cancer to classify the samples into Cluster A or B. The tumors in Cluster B were characterized by clinically aggressive behavior with significantly shorter metastasis-free and disease-specific survival. © 2012 Majewski et al.


Timms J.F.,University College London | Arslan-Low E.,University College London | Kabir M.,University College London | Worthington J.,University College London | And 12 more authors.
Proteomics - Clinical Applications | Year: 2014

Purpose: Ovarian cancer is a devastating disease and biomarkers for its early diagnosis are urgently required. Serum may be a valuable source of biomarkers that may be revealed by proteomic profiling. Herein, complementary serum protein profiling strategies were employed for discovery of biomarkers that could discriminate cases of malignant and benign ovarian cancer. Experimental design: Identically collected and processed serum samples from 22 cases of invasive epithelial ovarian cancer, 45 benign ovarian neoplasms, and 64 healthy volunteers were subjected to immunodepletion and protein equalization coupled to 2D-DIGE/MS and multidimensional fractionation coupled to SELDI-TOF profiling with MS/MS for protein identification. Selected candidates were verified by ELISA in samples from malignant (n = 70) and benign (n = 89) cases and combined marker panels tested against serum CA125. Results: Both profiling platforms were complementary in identifying biomarker candidates, four of which (A1AT, SLPI, APOA4, VDBP) significantly discriminated malignant from benign cases. However, no combination of markers was as good as CA125 for diagnostic accuracy. SLPI was further tested as an early marker using prediagnosis serum samples. While it rose in cases toward diagnosis, it did not discriminate prediagnosis cases from controls. Conclusions and clinical relevance: The candidate biomarkers warrant further validation in independent sample sets. © 2014 The Authors PROTEOMICS - Clinical Applications Published by Wiley-VCH Verlag GmbH & Co. KGaA.


Cho W.C.S.,Queen Elizabeth Hospital | Yip T.T.,Ciphergen Biosystems | Cheng W.W.,Queen Elizabeth Hospital | Au J.S.K.,Queen Elizabeth Hospital
British Journal of Cancer | Year: 2010

Background:Lung cancer is known as the top cancer killer in most developed countries. However, there is currently no promising diagnostic or prognostic biomarker for lung cancer. This study aims to discover non-invasive differential markers in the serum of lung cancer patients, to determine the protein identity of the candidate biomarker(s), and to investigate any clinical implication of the biomarker(s) concerned.Methods:Blood specimens were collected from 154 pre-operative patients with lung cancer and 35 healthy blood donors with no evidence of lung cancer. Fractionated serum samples were processed by surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (MS). Candidate biomarker was identified using sodium dodecyl sulphate polyacrylamide gel electrophoresis and tryptic digestion followed by tandem MS fragmentation analysis, which was subsequently validated with immunoassay.Results:A differential protein with m/z 11.6 kDa was detected and identified as an isoform of human serum amyloid A (SAA). It was significantly increased by 1822% in lung cancer patients when compared with the healthy controls, which gave an area under the receiver operator characteristic curve of 0.88. In addition, the protein was also significantly elevated by 77% in lung cancer patients with survival <5 years when compared with patients with survival ≥5 years.Conclusion:There are several functions of the SAA protein, described in the context of inflammation, that are compatible with the mechanism of tumour invasion and metastasis. Our study not only detected increased SAA level in the serum of lung cancer patients but also identified that elevated SAA level may be a non-invasive biomarker useful for the prediction of lung cancer prognosis. © 2010 Cancer Research UK All rights reserved.


Patent
Ciphergen Biosystems | Date: 2011-09-28

The present invention provides protein-based biomarkers and biomarker combinations that are useful in qualifying Alzheimers disease status in a patient. In particular, the biomarkers of this invention are useful to classify a subject sample as Alzheimers or non-Alzheimers dementia or normal. The biomarkers can be detected by SELDI mass spectrometry. In addition, the invention provides appropriate treatment interventions and methods for measuring response to treatment. Certain biomarkers of the invention may also be suitable for employment as radio-labeled ligands in non-invasive imaging techniques such as Positron Emission Tomography (PET).


Patent
Ciphergen Biosystems | Date: 2011-09-28

The present invention provides protein-based biomarkers and biomarker combinations that are useful in qualifying Alzheimers disease status in a patient. In particular, the biomarkers of this invention are useful to classify a subject sample as Alzheimers or non-Alzheimers dementia or normal. The biomarkers can be detected by SELDI mass spectrometry. In addition, the invention provides appropriate treatment interventions and methods for measuring response to treatment. Certain biomarkers of the invention may also be suitable for employment as radio-labeled ligands in non-invasive imaging techniques such as Positron Emission Tomography (PET).

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