Proteomic Technologies

 

Laser Capture Microdissection

Laser Capture Microdissection (LCM), a technology developed and patented by Dr. Liotta and colleagues at the National Institutes of Health in 1996, is utilized to isolate a pure population of cells under direct microscopic visualization. LCM can be used to collect specific cells from a heterogeneous tissue section or cell culture. The cells may be used for downstream analysis of DNA, RNA or proteins.

Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA. Laser capture microdissection. Science 1996 Nov;274(5289):998-1001.

Reverse Phase Protein Microarrays

The Reverse Phase Protein Microarrays (RPMA) technology, originated and developed by Drs. Liotta and Petricoin and their team, quantitatively measures post-translationally modified proteins (e.g. phosphorylated or cleaved), or total (phosphorylated and non-phosphorylated) proteins from a limited amount of sample.  This platform can be used to evaluate tissue samples, cells, serum and body fluids.

RPMA offer a revolutionary method to map the drug target activation state of each patient’s disease: creating a personalized “wiring diagram”.  Understanding protein networks is important because most drugs on the market today and in development are designed to target proteins, not genes.  A small amount of patient material from biopsies or body fluids is required, which makes this technology an essential component of individualized medicine. This technology along with related biomarker discoveries has been licensed to Theranostics Health, Inc.

Paweletz CP, Charboneau L, Bichsel VE, Simone NL, Chen T, Gillespie JW, Emmert-Buck MR, Roth MJ, Petricoin III EF, Liotta LA. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 2001 Apr;20(16):1981-1989.

Preservation Chemistry

A preservation solution which preserves cell morphology and stabilizes tissue biomolecules in one step has been developed by CAPMM scientists Dr. Virginia Espina and Dr. Claudius Mueller.  The preservation technology obviates the requirement for freezing of tissue for shipping, biobanking and molecular analysis, and overcomes the drawbacks of formalin fixation. This technology has been exclusively licensed to Theranostics Health, Inc.

Mueller C, Edmiston KH, Carpenter C, Gaffney E, Ryan C, Ward R, White S, Memeo L, Colarossi C, Petricoin EF 3rd, Liotta LA, Espina V. One-step preservation of phosphoproteins and tissue morphology at room temperature for diagnostic and research specimens. PLoS ONE 2011;6(8):e23780.

Mass Spectrometry

CAPMM scientists utilize high resolution mass spectrometry to discover, identify, and measure proteins and peptides in biological samples. The protein content of diseased/normal samples can be compared to discover potential biomarkers. Mass spectrometric analysis is often paired with CAPMM originated upfront enrichment and isolation technologies such as a novel nanoparticle technology, phosphoprotein isolation, or other sample preparation techniques to analyze low abundance and/or low molecular weight proteins that cannot be measured with other technologies. Once candidate markers are identified, the CAPMM is involved in a number of cutting-edge initiatives to develop antibody-free based mass spectrometry techniques such as multiple reaction monitoring (MRM) for routine clinical high-throughput measurement.

Nanoparticle Capture Mass Spectrometry
Fredolini C, Meani F, Luchini A, Zhou W, Russo P, Ross M, Patanarut A, Tamburro D, Gambara G, Ornstein D, Odicino F, Ragnoli M, Ravaggi A, Novelli F, Collura D, D'Urso L, Muto G, Belluco C, Pecorelli S, Liotta L, Petricoin EF 3rd. Investigation of the Ovarian and Prostate Cancer Peptidome for Candidate Early Detection Markers Using a Novel Nanoparticle Biomarker Capture Technology. AAPS J. 2010 Dec;12(4):504-18.

Phosphoprotein Mass Spectrometry
Zhou W, Ross MM, Tessitore A, Ornstein D, Vanmeter A, Liotta LA, Petricoin EF 3rd. An initial characterization of the serum phosphoproteome. J. Proteome Res 2009 Dec;8(12):5523-5531.

MRM Assay Analysis
Prakash A, Rezai T, Krastins B, Sarracino D, Athanas M, Russo P, Ross MM, Zhang H, Tian Y, Kulasingam V, Drabovich AP, Smith C, Batruch I, Liotta L, Petricoin E, Diamandis EP, Chan DW, Lopez MF. Platform for establishing interlaboratory reproducibility of selected reaction monitoring-based mass spectrometry peptide assays. J. Proteome Res 2010 Dec;9(12):6678-6688.

Smart Nanoparticles

CAPMM scientists developed a novel nanoparticle-based technology to trap, concentrate and protect potential rare disease biomarkers directly from blood, urine and saliva samples, in one step.  The nanoparticles capture small proteins and biomarkers that are currently hidden by larger, more abundant molecules and are difficult to detect in the laboratory due to their low concentration.  The hydrogel nanoparticles concentrate the biomarker of interest, which can be eluted from the nanoparticle and measured using standard platforms such as mass spectrometry, ELISA, Reverse Phase Protein Microarrays and Western Blotting. This technology has been exclusively licensed to Ceres Nanosciences, Inc.

Luchini A, Geho DH, Bishop B, Tran D, Xia C, Dufour RL, Jones CD, Espina V, Patanarut A, Zhou W, Ross MM, Tessitore A, Petricoin EF, Liotta LA. Smart hydrogel particles: biomarker harvesting: one-step affinity purification, size exclusion, and protection against degradation. Nano Lett 2008 Jan;8(1):350-361.

Protein Network Modeling
CAPMM scientists are developing theoretical and computational methods to interpret the complex data-sets that result from high-throughput profiling of cellular protein networks, and to understand how these signaling networks are affected and controlled by targeted inhibitors. Our laboratory has originated novel mathematical formulations of signaling networks and innovative approaches to the treatment of human disease, such as network-targeted combination therapies and control-oriented targeted therapies that emphasize network motifs, feedback loops and other regulatory and control mechanisms; as well as data-driven network reconstruction and control algorithms that take advantage of the sparse structure of signaling networks.
R.P. Araujo, L.A. Liotta and E.F. Petricoin, 2007.  Proteins, Drug Targets and the Mechanisms They Control:  The Simple Truth about Complex Networks.  Nature Reviews Drug Discovery, 6(11): 871-880.

D. Napoletani, T. Sauer, D. Struppa, E. Petricoin, L. Liotta. Augmented Sparse Reconstruction of Protein Signaling Networks. Journal of Theoretical Biology, vol. 255, Issue 1, 40-52 (2008).