The Protein Chip® System from Ciphergen Biosystems uses patented SELDI (Surface-Enhanced Laser Desorption/ Ionization) ProteinChip technology to rapidly perform the separation, detection and analysis of proteins at the femtomole level directly from biological samples. The ProteinChip System can replace and complement a wide range of traditional analytical methods, which are not only more time consuming but require specialized scientific expertise.

Ongoing project:

• Serum proteomics profiling for the detection of prostate cancer (PCa).
  Serum protein expression patterns were determined in 148 patients that were subsequently evaluated by biopsy of the prostate. Serum biomarkers were selected by metal affinity chromatography on copper-activated IMAC 30 chips and displayed by SELDI -TOF-MS using the Ciphergen PBS II analyzer. Detected peaks with m/z ratios in the range of 1000 to 40,000, S/N ratios > 1.2, and intensities > 0.1 were grouped by m/z ratio so as to define 573 parameters of the serum biomarker profile. Parameters that discriminated the Ca from the non-Ca group were identified by binary logistic regression. Logistic regression models were evaluated in a randomly chosen set of 98 training cases (28 Ca, 70 Non-Ca), and tested in an independent set of 50 test cases (21 Ca, 29 Non-Ca). A 10-parameter model was derived that had a sensitivity (Se) of 0.79 and a specificity (Sp) of 0.89, for predicting the presence of PCa in a subsequent biopsy for the cases in the training set. However, Se and Sp for this model decreased to 0.50 and 0.76 respectively, in the test set. As the number of parameters in the models was reduced from 10 to 2, there was a progressive decrease in Se, but Sp remained at 0.70 or above in models that included the parameter corresponding to a protein peak with an m/z ratio of 14,900. Mass spectrometric analysis of serum is a promising approach to biomarker discovery and PCa diagnosis.

Recent projects:

• Plant antiviral compound MEP is a possible topical microbicide.
  MEP was prepared from the dried aerial parts of the plant Echinacea purpurea by a multi-step process that included: a 20 hr. aqueous extraction; organic solvent precipitations; dialysis; and hydrolyses in strong acid and strong base. The final product was analyzed by HPLC-GPC, FTIR, and MALDI-TOF mass spectrometry. MEP is composed of oligomers with molecular weights in the range of 4-7 kDa. Its UV, FTIR, and MALDI mass spectra were similar to those previously published for natural and synthetic melanins. The in vitro anti-HSV activity of MEP was tested by NIAID, NIH using standard plaque reduction assays. MEP inhibits HSV-1 and HSV-2 infection in vitro with EC50's of 4.5 and 1.7 ug/mL, respectively. The in vitro anti-HIV activity was tested in CD4-dependent and CD4-independent HIV transmission inhibition assays developed by the Targeted Interventions Branch of the Division of AIDS, NIAID, NIH. MEP inhibits HIV infection in CD4 independent and CD4 dependent transmission assays with IC50’s of 23.6 and 2.1 ug/mL, respectively. The IC50's for MEP inhibition in HIV attachment and HIV fusion assays were 0.63 and 17.7 ug/mL, respectively. The effectiveness of MEP as a topical microbicide was tested in mouse and guinea pig models of HSV infection. MEP was effective in preventing HSV infection and HSV disease in mouse and guinea pig models of genital HSV infection. MEP is nontoxic to cultured human cells and to lactobacilli. As the prevalence of HSV and HIV continue to increase, so does the need to develop new agents for the prevention of sexually transmitted infections. MEP and phytomelanins with similar structures appear to be promising candidates for further development as topical microbicides.
• Proteomic profiling of human and non-human plasma using a proteinchip array method.
  The plasma protein composition of human and animals appears to have similar protein profiles when electrophoretic methods are used. In order to demonstrate species dependent variation in protein/peptide distribution profile in the range of 150-150,000 Da, plasma samples from human and non-human (primate, pig, dog, rabbit, rat and mouse) were analyzed using anionic biomarker chips. Although the overall protein distribution patterns were similar, there were several specific biomarkers that were unique to a given species. Characteristic differences in the pre-albumin region were noted. Of major interest were the differences in the region below 20 kDa. Marked differences in the biomarker distribution profile were noted among all species. Each species exhibited a characteristic biomarker profile in the 5 – 10 kDa range. It is likely that in a pathophysiologic condition, the distribution of the biomarkers may further change. Because of this molecular heterogeneity of the biomarker peak in the resting state, the proteomic profiling of disease in animal models should be carefully evaluated. Furthermore, the data obtained from one species may not reflect similar changes in another species. These studies clearly point out that different species may exhibit wide variations that can further amplify disease states.