Beyond the genome to tissue proteomics

Laser capture microdissection: Big data from small samples

Any tissue is made up of a heterogeneous mix of spatially distributed cell types. In response to any (patho) physiological cue, responses of each cell type in any given tissue may be unique and cannot be homogenized across cell-types and spatial co-ordinates. For example, in response to myocardial infarction, on one hand myocytes and fibroblasts of the heart tissue respond differently. On the other hand, myocytes in the infarct core respond differently compared to those in the peri-infarct zone. Therefore, isolation of pure targeted cells is an important and essential step for the molecular analysis of cells involved in the progression of disease. Laser capture microdissection (LCM) is powerful to obtain a pure targeted cell subgroup, or even a single cell, quickly and precisely under the microscope, successfully tackling the problem of tissue heterogeneity in molecular analysis. This review presents an overview of LCM technology, the principles, advantages and limitations and its down-stream applications in the fields of proteomics, genomics and transcriptomics. With powerful technologies and appropriate applications, this technique provides unprecedented insights into cell biology from cells grown in their natural tissue habitat as opposed to those cultured in artificial petri dish conditions.

Quantitative proteomics in laser capture microdissected sleep nuclei from rat brain

The combination of stable isotope labeling of amino acids in mammals (SILAM) and laser capture microdissection (LCM) for selective proteomic analysis of the targeted tissues holds tremendous potential for refined characterization of proteome changes within complex tissues such as the brain. The authors have applied this approach to measure changes in relative protein abundance in ventral tegmental area (VTA) of the rat brain that correlate to pharmacological perturbations. Enriched ¹³C₆¹⁵N₂-lysine was introduced in vivo via diet. These animals were sacrificed during the middle of the 12-hour light period to extract isotopically “heavy” proteins, which were then used as a reference for extracts from dosed, unlabeled rats. Animals were administered an orexin peptide (Ox-B), an orexin receptor antagonist (ORA), or a mixture of both (Ox-B + ORA). All samples were obtained at same phase of the sleep cycle. Labeled-pair identification and differential quantitation provided protein identification and expression ratio data. Five proteins were found to exhibit decreased relative abundance after administration of an ORA, including α-synuclein and rat myelin basic protein. Conversely, six proteins showed increased relative abundance upon antagonist treatment, including 2’,3’-cyclic nucleotide 3’-phosphodiesterase.

Protein biomarkers in patients with subarachnoid hemorrhage, vasospasm, and delayed ischemic neurological deficits

Aneurysmal subarachnoid hemorrhage (aSAH) is a devastating neurological disease. It has many sequelae, including vasospasm and delayed ischemic neurological deficits (DINDs). We explored the blood proteome in patients with aSAH using transcranial Doppler (TCD) velocity as a guide to patients who are at risk for symptomatic vasospasm and DIND. Blood was drawn on all days that patients were observed in the neurocritical care unit (NCCU) after aSAH. A team of neurologists and neurosurgeons identified patients with clinical evidence of vasospasm and DIND. Serum was fractionated using protein chips and surface-enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF MS). We detected a pattern of protein expression associated with those at risk for elevated TCD velocities by day 8, compared with blood collected in the presymptomatic stage (days 1-3). We further analyzed serum using pooled samples from study entry to the time of elevated TCD velocities using a protein microarray that analyzed 500 human proteins thematically oriented toward inflammation. After identifying several candidates with elevated concentrations in the pooled samples, we then used reverse protein arrays to quantitate the concentration of potential candidate proteins in the individual samples. Proteins with significantly elevated concentrations included apolipoprotein-E, apolipoprotein-A, serum amyloid protein-4, and serum amyloid protein-P. Future studies in larger sample populations are needed to evaluate these biomarkers further as representative of biosystems involved in vasospasm and DIND or as potential biomarkers predictive of risk associated with disease.

Proteomic profiling of H-Ras-G12V induced hypertrophic cardiomyopathy in transgenic mice using comparative LC-MS analysis of thin fresh-frozen tissue sections

Determination of disease-relevant proteomic profiles from limited tissue specimens, such as pathological biopsies and tissues from small model organisms, remains an analytical challenge and a much needed clinical goal. In this study, a transgenic mouse disease model of cardiac-specific H-Ras-G12V induced hypertrophic cardiomyopathy provided a system to explore the potential of using mass spectrometry (MS)-based proteomics to obtain a disease-relevant molecular profile from amount-limited specimens that are routinely used in pathological diagnosis. Our method employs a two-stage methanol-assisted solubilization to digest lysates prepared from 8-μm-thick fresh-frozen histological tissue sections of diseased/experimental and normal/control hearts. Coupling this approach with a nanoflow reversed-phase liquid chromatography (LC) and a hybrid linear ion trap/Fourier transform-ion cyclotron resonance MS resulted in the identification of 704 and 752 proteins in hypertrophic and wild-type (control) myocardium, respectively. The disease driving H-Ras protein along with vimentin were unambiguously identified by LC-MS in hypertrophic myocardium and cross-validated by immunohistochemistry and western blotting. The pathway analysis involving proteins identified by MS showed strong association of proteomic data with cardiovascular disease. More importantly, the MS identification and subsequent cross-validation of Wnt3a and β-catenin, in conjunction with IHC identification of phosphorylated GSK-3β and nuclear localization of β-catenin, provided evidence of Wnt/β-catenin canonical pathway activation secondary to Ras activation in the course of pathogenic myocardial hypertrophic transformation. Our method yields results indicating that the described proteomic approach permits molecular discovery and assessment of differentially expressed proteins regulating H-Ras induced hypertrophic cardiomyopathy. Selected proteins and pathways can be further investigated using immunohistochemical techniques applied to serial tissue sections of similar or different origin.

Proteomics of rat prostate lobes treated with 2-N-hydroxylamino-1-methyl-6-phenylimidazo[4,5-b]pyridine, 5alpha-dihydrotestosterone, individually and in combination

Epidemiological and preclinical studies suggest that environmental factors, hormonal responses and lifestyle, including diet and physical inactivity, are likely contributors to the initiation and progression of prostate cancer in humans. Although the effects of the food derived carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) and/or testosterone (T) in the development of prostate cancer in the rat have been reported, the extent to which such compounds impact cancer related proteins is not clear. Knowledge of cancer-related proteins impacted by PhIP and/or T is prerequisite to developing novel strategies to early-detect prostate cancer. Male F344 rats were sacrificed, the prostate tissue isolated and separated into dorsolateral, ventral, and anterior lobes. The lobes were cultured and treated with 10(-3) M NHPhIP and/or 10(-7) M DT for 24 h. NHPhIP is the genotoxic form of PhIP and DT is the more proliferative form of T. We used 2D-DIGE and LC/MS/MS technologies to study the proteome of the prostate lobes to determine if the compounds will trigger detectable changes in expression of cancer-related proteins. Analysis of the signals from 2D-DIGE revealed that about 10% of proteins were differentially expressed in the NHPhIP and/or DT treatments compared to controls. Eight candidate protein spots detected by 2D-DIGE in at least two out of three lobes showed > or =2-fold difference between treated and control samples. Five out of the eight spots contained single proteins; including, phospholipase Calpha (PLP-Calpha), Rab7, SAR1a, ribosomal protein S7 (RPS7), and nucleoside diphosphate kinase (NDPK). A survey of the literature shows that NDPK expression is altered in human cancers, including prostate cancer. Thus, we validated the altered expression of NDPK by Western blot analysis. The concordance between 2D-DIGE and Western blot analysis was 80%. The results of this study demonstrate, for the first time, that the combination of 2D-DIGE and LC/MS/MS is a powerful tool for identification of proteins in the prostate tissue that are altered by environmental carcinogens and/or hormones.

Alterations in Barrett's-related adenocarcinomas: a proteomic approach

In this study, we applied high-resolution, two-dimensional, gel electrophoresis and matrix-assisted laser desorption/ionization, time-of-flight and tandem mass spectrometry analysis (MALDI TOF MS) to identify novel proteins that are involved in Barrett's tumorigenesis. We analyzed 12 primary tissue samples that included 8 Barrett's-related adenocarcinomas (BA) and 4 normal mucosae samples. Twenty-three spots were consistently altered (>or=2-fold) in at least half of the tumors when compared with all normal samples and thus subjected to further analysis. The MALDI TOF MS analysis demonstrated biologically interesting upregulated proteins such as ErbB3, Dr5 and Cyclin D1 as well as several members of the zinc finger proteins (Znf146, Znf212 and Znf363). Examples of downregulated proteins included Lgi1 and Klf6. We selected four proteins (ErbB3, Dr5, Znf146 and Lgi1) that are novel for BAs for validation using quantitative real-time reverse-transcription PCR on 39 BA tissue samples when compared with normal samples. We demonstrated mRNA upregulation of ERBB3 (51.3%), DR5 (41%) and ZNF146 (30.7%) and downregulation of LGI1 (100%) in BA. We have further validated the protein overexpression of ErbB3, Dr5 and Znf146, using immunohistochemical (IHC) analysis on a tissue microarray that contained 75 BAs and normal gastric and esophageal mucosae samples. BA tissue samples demonstrated overexpression of ErbB3 (42%), Dr5 (90%) and Znf146 (30%) when compared with normal tissues. In conclusion, we have identified and validated several novel proteins that are involved in Barrett's carcinogenesis.

Proteomic technologies for cancer target validation

Genomic and proteomic technologies have produced an abundance of drug targets, which is creating a bottleneck in drug development process. There is an increasing need for better target validation for cancer drug development and proteomic technologies are contributing to it. These technologies are compared to enable the selection of the one by matching the needs of a particular project. There are prospects for further improvement, and proteomics technologies will form an important addition to the existing genomic and chemical technologies for target validation.

Nuclear matrix proteins as biomarkers for breast cancer

Breast cancer remains a leading cause of cancer death in women despite widespread screening, in part because screening mammography has high rates of false-negative results and because many women decline to have routine mammograms. The development of sensitive and specific assays for breast tumor markers would improve detection and facilitate screening, diagnosis, therapeutic monitoring and surveillance for recurrence. Nuclear matrix proteins (NMPs) are promising candidates for tumor markers because they are involved in malignant transformation. Therefore, they may be useful for screening and early diagnosis of small tumors. Proteomic analysis was used to demonstrate that a 28.3 kD serum protein, designated NMP66, can distinguish malignant disease from benign conditions and normal controls. NMP66 is now being evaluated as a potential biomarker for early breast cancer detection in large-scale clinical trials.