RNA aptamers targeting the carboxyl terminus of KRAS oncoprotein generated by an improved SELEX with isothermal RNA amplification

Mutations in the KRAS gene occur frequently in various human tumors and are known to lead to malignant transformation. We isolated RNA aptamers targeting activated mutant KRAS proteins using an improved SELEX method by isothermal RNA amplification. RNA aptamers were selected against mutant KRAS (G12V) proteins, as well as a biotinylated 15-amino-acid peptide from the carboxyl terminal of KRAS that contains a farnesylation site. All the selected RNA aptamers bound to the basic carboxy-terminal region of KRAS protein and the highest K(D) value was 2.3 microM. By an in vitro scintillation proximity assay, we demonstrated that KRAS aptamers inhibited farnesylation moderately. From these aptamers, we determined a consensus sequence (U)CCAAGCAC(AC) that, when concatamerized, exhibited higher binding affinity to the carboxy-terminal region of KRAS protein. Further improvement of binding affinity between aptamers and KRAS protein might provide a new therapeutic approach for activated mutant KRAS proteins.     

CDK1 Is a Synthetic Lethal Target for KRAS Mutant Tumours

Activating KRAS mutations are found in approximately 20% of human cancers but no RAS-directed therapies are currently available. Here we describe a novel, robust, KRAS synthetic lethal interaction with the cyclin dependent kinase, CDK1. This was discovered using parallel siRNA screens in KRAS mutant and wild type colorectal isogenic tumour cells and subsequently validated in a genetically diverse panel of 26 colorectal and pancreatic tumour cell models. This established that the KRAS/CDK1 synthetic lethality applies in tumour cells with either amino acid position 12 (p.G12V, pG12D, p.G12S) or amino acid position 13 (p.G13D) KRAS mutations and can also be replicated in vivo in a xenograft model using a small molecule CDK1 inhibitor. Mechanistically, CDK1 inhibition caused a reduction in the S-phase fraction of KRAS mutant cells, an effect also characterised by modulation of Rb, a master control of the G₁/S checkpoint. Taken together, these observations suggest that the KRAS/CDK1 interaction is a robust synthetic lethal effect worthy of further investigation.     

KRAS G12V mutation upregulates PD-L1 expression via TGF-β/EMT signaling pathway in human non-small-cell lung cancer

Although clinical data suggest remarkable promise for targeting programmed cell death protein-1 (PD-1) and ligand (PD-L1) signaling in non-small-cell lung cancer (NSCLC), it is still largely undetermined which subtype of patients will be responsive to checkpoint blockade. In the present study, we explored whether PD-L1 was regulated by mutant Kirsten rat sarcoma viral oncogene homolog (KRAS), which is frequently mutated in NSCLC and results in poor prognosis and low survival rates. We verified that PD-L1 levels were dramatically increased in KRAS mutant cell lines, particularly in NCI-H441 cells with KRAS G12V mutation. Overexpression of KRAS G12V remarkably elevated PD-L1 messenger RNA and protein levels, while suppression of KRAS G12V led to decreased PD-L1 levels in NCI-H441 cells. Consistently, higher levels of PD-L1 were observed in KRAS-mutated tissues as well as tumor tissues-derived CD4⁺ and CD8⁺ T cells using a tumor xenograft in B-NDG mice. Mechanically, both in vitro and in vivo assays found that KRAS G12V upregulated PD-L1 via regulating the progression of epithelial-to-mesenchymal transition (EMT). Moreover, pembrolizumab activated the antitumor activity and decreased tumor growth with KRAS G12V mutated NSCLC. This study demonstrates that KRAS G12V mutation could induce PD-L1 expression and promote immune escape via transforming growth factor-β/EMT signaling pathway in KRAS-mutant NSCLC, providing a potential therapeutic approach for NSCLC harboring KRAS mutations.     

Proteomic Analysis of Exosomes from Mutant KRAS Colon Cancer Cells Identifies Intercellular Transfer of Mutant KRAS

Activating mutations in KRAS occur in 30% to 40% of colorectal cancers. How mutant KRAS alters cancer cell behavior has been studied intensively, but non-cell autonomous effects of mutant KRAS are less understood. We recently reported that exosomes isolated from mutant KRAS-expressing colon cancer cells enhanced the invasiveness of recipient cells relative to exosomes purified from wild-type KRAS-expressing cells, leading us to hypothesize mutant KRAS might affect neighboring and distant cells by regulating exosome composition and behavior. Herein, we show the results of a comprehensive proteomic analysis of exosomes from parental DLD-1 cells that contain both wild-type and G13D mutant KRAS alleles and isogenically matched derivative cell lines, DKO-1 (mutant KRAS allele only) and DKs-8 (wild-type KRAS allele only). Mutant KRAS status dramatically affects the composition of the exosome proteome. Exosomes from mutant KRAS cells contain many tumor-promoting proteins, including KRAS, EGFR, SRC family kinases, and integrins. DKs-8 cells internalize DKO-1 exosomes, and, notably, DKO-1 exosomes transfer mutant KRAS to DKs-8 cells, leading to enhanced three-dimensional growth of these wild-type KRAS-expressing non-transformed cells. These results have important implications for non-cell autonomous effects of mutant KRAS, such as field effect and tumor progression.K-RAS (KRAS) is a small, monomeric GTPase whose biological activity is specified by its nucleotide binding state. Multiple lines of evidence highlight the importance of KRAS in colorectal cancer (CRC).¹ For example, activating missense mutations in KRAS, which lock the protein into the GTP-bound state, occur in 30% to 40% of CRCs and are strongly associated with poor prognosis (1, 2). Also, mutant KRAS negatively predicts responsiveness to anti-EGF receptor (EGFR) therapy (3).Early attempts to decipher the neoplastic consequences of mutant KRAS relied on overexpression studies. A drawback of these studies is their failure to simulate the genetic conditions present in human tumors, where there is often one wild-type (WT) and one mutant KRAS allele (1). More recently, KRAS mutant CRC cell lines have been engineered to selectively contain either the wild-type or the mutant KRAS allele (4), and a single mutant Kras allele has been activated in the intestine using genetically engineered mice (5). Detailed studies using these complementary approaches demonstrate a wide range of tumor-promoting effects of mutant KRAS (reviewed in Ref. 6). Much of what is known about mutant KRAS pertains to its ability to alter the behavior of a transformed cell in a cell autonomous manner. With the exception of increased tumor vascularity via increased tumor-derived VEGF expression (7, 8), non-cell autonomous effects of mutant KRAS have been much less studied.Exosomes are 30- to 100-nm secreted vesicles that have emerged as a novel mode of intercellular communication (9). We recently reported that exosomes purified from conditioned medium of mutant KRAS CRC cells contained higher levels of the EGFR ligand amphiregulin (AREG) and enhanced invasiveness of recipient cancer cells relative to exosomes from isogenically matched wild-type KRAS cells (10). These results prompted us to perform a comprehensive analysis of exosomes purified from these cells. Herein, we show that mutant KRAS induces many changes in exosomal protein composition. Notably, we show that (i) KRAS is contained within exosomes, (ii) exosomes can transfer mutant KRAS to cells expressing only wild-type KRAS, and (iii) mutant KRAS-containing exosomes enhance wild-type KRAS cell growth in collagen matrix and soft agar. These results have important implications for the progression of CRC tumors by providing a mechanism by which the tumor microenvironment may be influenced by non-cell autonomous signals released by mutant KRAS-expressing tumor cells.     

Ras Effector Mutant Expression Suggest a Negative Regulator Inhibits Lung Tumor Formation

Lung cancer is currently the most deadly malignancy in industrialized countries and accounts for 18% of all cancer-related deaths worldwide. Over 70% of patients with non-small cell lung cancer (NSCLC) are diagnosed at a late stage, with a 5-year survival below 10%. KRAS and the EGFR are frequently mutated in NSCLC and while targeted therapies for patients with EGFR mutations exist, oncogenic KRAS is thus far not druggable. KRAS activates multiple signalling pathways, including the PI3K/Akt pathway, the Raf-Mek-Erk pathway and the RalGDS/Ral pathway. Lung-specific expression of BrafV600E, the most prevalent BRAF mutation found in human tumors, results in Raf-Mek-Erk pathway activation and in the formation of benign adenomas that undergo widespread senescence in a Cre-activated Braf mouse model (Braf^CA). However, oncogenic KRAS expression in mice induces adenocarcinomas, suggesting additional KRAS-activated pathways cooperate with sustained RAF-MEK-ERK signalling to bypass the oncogene-induced senescence proliferation arrest.To determine which KRAS effectors were responsible for tumor progression, we created four effector domain mutants (S35, G37, E38 and C40) in G12V-activated KRAS and expressed these alone or with BrafV600E in mouse lungs… The S35 and E38 mutants bind to Raf proteins but not PI3K or RalGDS; the G37 mutant binds to RalGDS and not Raf or PI3K and the C40 mutant is specific to PI3K. We designed lentiviral vectors to code for Cre recombinase along with KRAS mutants (V12, V12/S35, V12/G37, V12/E38 or V12/C40) or EGFP as a negative control.. These lentiviruses were used to infect Braf^CA and wild-type mice. Surprisingly there was a significant decrease in tumor number and penetrance with each KRAS effector domain mutant relative to controls, suggesting that KRAS directly activates effectors with tumor suppressive functions.     

KRASG12D- and BRAFV600E-Induced Transformation of Murine Pancreatic Epithelial Cells Requires MEK/ERK-Stimulated IGF1R Signaling

Mutation of KRAS is a common initiating event in pancreatic ductal adenocarcinoma (PDAC). Yet, the specific roles of KRAS-stimulated signaling pathways in the transformation of pancreatic ductal epithelial cells (PDEC), putative cells of origin for PDAC, remain unclear. Here, we show that KRAS(G12D) and BRAF(V600E) enhance PDEC proliferation and increase survival after exposure to apoptotic stimuli in a manner dependent on MEK/ERK and PI3K/AKT signaling. Interestingly, we find that activation of PI3K/AKT signaling occurs downstream of MAP-ERK kinase (MEK), and is dependent on the autocrine activation of the insulin-like growth factor (IGF) receptor (IGF1R) by IGF2. Importantly, IGF1R inhibition impairs KRAS(G12D)- and BRAF(V600E)-induced survival, whereas ectopic IGF2 expression rescues KRAS(G12D)- and BRAF(V600E)-mediated survival downstream of MEK inhibition. Moreover, we show that KRAS(G12D)- and BRAF(V600E)-induced tumor formation in an orthotopic model requires IGF1R. Interestingly, we show that while individual inhibition of MEK or IGF1R does not sensitize PDAC cells to apoptosis, their concomitant inhibition reduces survival. Our findings identify a novel mechanism of PI3K/AKT activation downstream of activated KRAS, illustrate the importance of MEK/ERK, PI3K/AKT, and IGF1R signaling in pancreatic tumor initiation, and suggest potential therapeutic strategies for this malignancy. Mol Cancer Res; 10(9); 1228-39. ?2012 AACR.     

A multiplexed quantitative strategy for membrane proteomics: opportunities for mining therapeutic targets for autosomal dominant polycystic kidney disease

Toward multiplexed, comprehensive, and robust quantitation of the membrane proteome, we report a strategy combining gel-assisted digestion, iTRAQ (isobaric tags for relative and absolute quantitation) labeling, and LC-MS/MS. Quantitation of four independently purified membrane fractions from HeLa cells gave high accuracy (<8% error) and precision (<12% relative S.D.), demonstrating a high degree of consistency and reproducibility of this quantitation platform. Under stringent identification criteria (false discovery rate = 0%), the strategy efficiently quantified membrane proteins; as many as 520 proteins (91%) were membrane proteins, each quantified based on an average of 14.1 peptides per integral membrane protein. In addition to significant improvements in signal intensity for most quantified proteins, most remarkably, topological analysis revealed that the biggest improvement was achieved in detection of transmembrane peptides from integral membrane proteins with up to 19 transmembrane helices. To the best of our knowledge, this level of coverage exceeds that achieved previously using MS and provides superior quantitation accuracy compared with other methods. We applied this approach to the first proteomics delineation of phenotypic expression in a mouse model of autosomal dominant polycystic kidney disease (ADPKD). By characterizing kidney cell plasma membrane from wild-type versus PKD1 knock-out mice, 791 proteins were quantified, and 67 and 37 proteins showed > or =2-fold up-regulation and down-regulation, respectively. Some of these differentially expressed membrane proteins are involved in the mechanisms underlying major abnormalities in ADPKD, including epithelial cell proliferation and apoptosis, cell-cell and cell-matrix interactions, ion and fluid secretion, and membrane protein polarity. Among these proteins, targeting therapeutics to certain transporters/receptors, such as epidermal growth factor receptor, has proven effective in preclinical studies of ADPKD; others are known drug targets in various diseases. Our method demonstrates how comparative membrane proteomics can provide insight into the molecular mechanisms underlying ADPKD and the identification of potential drug targets, which may lead to new therapeutic opportunities to prevent or retard the disease.     

Glycoprotein cytoplasmic domain sequences required for rescue of a vesicular stomatitis virus glycoprotein mutant.

We have used transient expression of the wild-type vesicular stomatitis virus (VSV) glycoprotein (G protein) from cloned cDNA to rescue a temperature-sensitive G protein mutant of VSV in cells at the nonpermissive temperature. Using cDNAs encoding G proteins with deletions in the normal 29-amino-acid cytoplasmic domain, we determined that the presence of either the membrane-proximal 9 amino acids or the membrane-distal 12 amino acids was sufficient for rescue of the temperature-sensitive mutant. G proteins with cytoplasmic domains derived from other cellular or viral G proteins did not rescue the mutant, nor did G proteins with one or three amino acids of the normal cytoplasmic domain. Rescue correlated directly with the ability of the G proteins to be incorporated into virus particles. This was shown by analysis of radiolabeled particles separated on sucrose gradients as well as by electron microscopy of rescued virus after immunogold labeling. Quantitation of surface expression showed that all of the mutated G proteins were expressed less efficiently on the cell surface than was wild-type G protein. However, we were able to correct for differences in rescue efficiency resulting from differences in the level of surface expression by reducing wild-type G protein expression to levels equivalent to those observed for the mutated G proteins. Our results provide evidence that at least a portion of the cytoplasmic domain is required for efficient assembly of the VSV G protein into virions during virus budding.     

Quantitation of soybean allergens using tandem mass spectrometry

Soybean (Glycine max) seed contain some proteins that are allergenic to humans and animals. However, the concentration of these allergens and their expression variability among germplasms is presently unknown. To address this problem, 10 allergens were quantified from 20 nongenetically modified commercial soybean varieties using parallel, label-free mass spectrometry approaches. Relative quantitation was performed by spectral counting and absolute quantitation was performed using multiple reaction monitoring (MRM) with synthetic, isotope-labeled peptides as internal standards. During relative quantitation analysis, 10 target allergens were identified, and five of these allergens showed expression levels higher than technical variation observed for bovine serum albumin (BSA) internal standard (～11%), suggesting expression differences among the varieties. To confirm this observation, absolute quantitation of these allergens from each variety was performed using MRM. Eight of the 10 allergens were quantified for their concentration in seed and ranged from approximately 0.5 to 5.7 μg/mg of soy protein. MRM analysis reduced technical variance of BSA internal standards to approximately 7%, and confirmed differential expression for four allergens across the 20 varieties. This is the first quantitative assessment of all major soybean allergens. The results show the total quantity of allergens measured among the 20 soy varieties was mostly similar.     

Oxaliplatin-based Chemotherapy Might Provide Longer Progression-Free Survival in KRAS Mutant Metastatic Colorectal Cancer

The identification of better regimens in currently available chemotherapeutic agents is crucial for treating patients with KRAS mutant metastatic colorectal cancer (mCRC). Records of mCRC patients who received first-line oxaliplatin- based or irinotecan-based regimens were reviewed retrospectively. Clinicopathologic features and treatment outcome of patients with first-line progression-free survival (PFS) and overall survival (OS) in association with KRAS mutation status were analyzed using the Cox proportional hazard model. Between 2007 and 2010, a total of 118 mCRC patients were enrolled. Among them, 67 were males and 51 were females. In patients who received first-line oxaliplatin-based regimens, the PFS was significantly longer in KRAS mutant patients (N = 32) than that in KRAS wild-type patients (N = 51). The median PFS was 8.5 months in KRAS mutant versus 5.8 months in KRAS wild-type patients (P = .008). In contrast, in patients who received first-line irinotecan-based regimens, the PFS was shorter in KRAS mutant patients (N = 15) than that in KRAS wild-type patients (N = 20). Median PFS was 3.9 months in KRAS mutant versus 6.0 months in KRAS wild-type patients (P = .23). Median OS between KRAS mutant and wild-type patients was not significantly different in both oxaliplatin-based and irinotecan-based regimens. In multivariate analyses, KRAS mutation remains an independent predictive factor for longer PFS in first-line oxaliplatin-based regimens. In conclusion, oxaliplatin-based chemotherapy in KRAS mutant mCRC might result in longer PFS than in KRAS wild-type mCRC.     

高分辨率熔解曲线分析法检测结直肠癌KRAS基因突变

目的:采用高分辨率熔解曲线分析法检测结直肠癌中KRAS基因突变,探讨其用于临床检测的可行性。方法:首先用高分辨率熔解曲线分析法检测64例结直肠癌患者KRAS基因第2外显子的突变情况,再用直接测序法对结果进行验证。结果:通过高分辨率熔解曲线分析法检测,发现有23例KRAS基因突变(35.9%),经直接测序法验证,证实所有患者的突变情况与高分辨率熔解曲线法的结果完全一致;共检测出6种KRAS突变类型,G12D(GGT>GAT)的突变率最高(47.8%),G12D、G12V和G13D等3种常见突变型占总突变数的78.3%。结论:与直接测序法相比,应用高分辨率熔解曲线分析法检测KRAS基因突变具有操作简单快捷、结果准确、成本低的优点,适合应用于临床检测。     

A fusion-defective mutant of the vesicular stomatitis virus glycoprotein.

We have recently described an assay in which a temperature-sensitive mutant of vesicular stomatitis virus (VSV; mutant tsO45), encoding a glycoprotein that is not transported to the cell surface, can be rescued by expression of wild-type VSV glycoproteins from cDNA (M. Whitt, L. Chong, and J. Rose, J. Virol. 63:3569-3578, 1989). Here we examined the ability of mutant G proteins to rescue tsO45. We found that one mutant protein (QN-1) having an additional N-linked oligosaccharide at amino acid 117 in the extracellular domain was incorporated into VSV virions but that the virions containing this glycoprotein were not infectious. Further analysis showed that virus particles containing the mutant protein would bind to cells and were endocytosed with kinetics identical to those of virions rescued with wild-type G protein. We also found that QN-1 lacked the normal membrane fusion activity characteristic of wild-type G protein. The absence of fusion activity appears to explain lack of particle infectivity. The proximity of the new glycosylation site to a sequence of 19 uncharged amino acids (residues 118 to 136) that is conserved in the glycoproteins of the two VSV serotypes suggests that this region may be involved in membrane fusion. The mutant glycoprotein also interferes strongly with rescue of virus by wild-type G protein. The strong interference may result from formation of heterotrimers that lack fusion activity.     

The effect of Glu75 of staphylococcal nuclease on enzyme activity, protein stability and protein unfolding.

Staphylococcal nuclease mutants, E57G and E75G, were generated. A comparison of the kinetic parameters both for mutants and wild-type protein shows that the Michaelis constants (Km) were almost identical for the wild-type protein and E57G mutant. An approximately 30-fold decrease in Km compared with the wild-type protein was observed for the E75G mutant. The turnover numbers for the enzyme (kcat) were higher with both the wild-type protein and the E57G mutant (3.88 +/- 0.21 x 103 s-1 and 3.71 +/- 0.28 x 103 s-1) than with the E75G mutant (3.04 +/- 0.02 x 102 s-1). The results of thermal denaturation with differential scanning microcalorimetry indicate that the excess calorimetric enthalpy of denaturations, DeltaHcal, was almost identical for the wild-type protein and E57G mutant (84.1 +/- 6.2 kcal.mol-1 and 79.3 +/- 7.1 kcal.mol-1, respectively). An approximately twofold decrease in DeltaHcal compared with the wild-type protein was observed for the E75G mutant (42.7 +/- 5.5 kcal.mol-1). These outcomes imply that Glu at position 75 plays a significant role in maintaining enzyme activity and protein stability. Further study of the unfolding of the wild-type protein and E75G mutant was conducted by using time-resolved fluorescence with a picosecond laser pulse. Two fluorescent lifetimes were found in the subnanosecond time range. The faster lifetime (tau2) did not generally vary with either pH or the concentration of guanidinium hydrochloride (GdmHCl) in the wild-type protein and the E75G mutant. The slow lifetime (tau1), however, did vary with these parameters and was faster as the protein is unfolded by either pH or GdmHCl denaturation. The midpoints of the transition for tau1 are pH 3.5 and 5.8 for the wild-type protein and E75G mutant, respectively, and the GdmHCl concentrations are 1.1 m and 0.6 m for the wild-type protein and E75G mutant, respectively. Parallel steady-state fluorescence measurements have also been carried out and the results are in general agreement with the time-resolved fluorescence experiments, indicating that Glu at position 75 plays an important role in protein unfolding.     

Identification of a C3′-nitrile nucleoside analogue inhibitor of pancreatic cancer cell line growth

A synthetic strategy to access a novel family of nucleoside analogues bearing a C3′-nitrile substituted all-carbon quaternary center is presented herein. These purine bearing scaffolds were tested in two pancreatic cancer cell lines harboring either wild-type (BxPC3) or G12V KRAS (Capan2) mutations. A promising compound was shown to have significantly greater efficacy in the Capan2 cell line as compared to Gemcitabine, the clinical gold standard used to treat pancreatic cancer.     

Effect of KRAS mutation status on the efficiency of Avastin therapy of colorectal cancer

Anti-angiogenic therapy became a standard care of advanced colorectal cancer. Since the most frequent genetic alteration of colorectal cancer is KRAS mutation we have analyzed its effect on the efficacy of Avastin treatment. Since 2008 we have determined the KRAS status of 575 patients with colorectal carcinoma using a sensitive screening method and sequencing. In our database the frequency of KRAS mutation in colorectal cancer is 37% (codon 12: 31% followed by codon 13: 6%). We have examined the effect of KRAS status on the efficacy of Avastin treatment in 35 patients. Progression-free survival of KRAS mutant patients was highly similar to that of wild-type patients using log-rank test (9.2+/-5.5 months versus 8.7+/-5.7 months, respectively). Our data support those observations that KRAS status of colorectal cancer does not interfere with the efficacy of Avastin treatment.     

Multiple Reaction Monitoring-based, Multiplexed, Absolute Quantitation of 45 Proteins in Human Plasma

Mass spectrometry-based multiple reaction monitoring (MRM) quantitation of proteins can dramatically impact the discovery and quantitation of biomarkers via rapid, targeted, multiplexed protein expression profiling of clinical samples. A mixture of 45 peptide standards, easily adaptable to common plasma proteomics work flows, was created to permit absolute quantitation of 45 endogenous proteins in human plasma trypsin digests. All experiments were performed on simple tryptic digests of human EDTA-plasma without prior affinity depletion or enrichment. Stable isotope-labeled standard peptides were added immediately following tryptic digestion because addition of stable isotope-labeled standard peptides prior to trypsin digestion was found to generate elevated and unpredictable results. Proteotypic tryptic peptides containing isotopically coded amino acids ([¹³C₆]Arg or [¹³C₆]Lys) were synthesized for all 45 proteins. Peptide purity was assessed by capillary zone electrophoresis, and the peptide quantity was determined by amino acid analysis. For maximum sensitivity and specificity, instrumental parameters were empirically determined to generate the most abundant precursor ions and y ion fragments. Concentrations of individual peptide standards in the mixture were optimized to approximate endogenous concentrations of analytes and to ensure the maximum linear dynamic range of the MRM assays. Excellent linear responses (r > 0.99) were obtained for 43 of the 45 proteins with attomole level limits of quantitation (<20% coefficient of variation) for 27 of the 45 proteins. Analytical precision for 44 of the 45 assays varied by <10%. LC-MRM/MS analyses performed on 3 different days on different batches of plasma trypsin digests resulted in coefficients of variation of <20% for 42 of the 45 assays. Concentrations for 39 of the 45 proteins are within a factor of 2 of reported literature values. This mixture of internal standards has many uses and can be applied to the characterization of trypsin digestion kinetics and plasma protein expression profiling because 31 of the 45 proteins are putative biomarkers of cardiovascular disease.MS is capable of sensitive and accurate protein quantitation based on the quantitation of proteolytic peptides as surrogates for the corresponding intact proteins. Over the past 10 years, MS-based protein quantitation based on the analysis of peptides (in other words, based on “bottom-up” proteomics) has had a profound impact on how biological problems can be addressed (1, 2). Although advances in MS instrumentation have contributed to the improvement of MS-based protein quantitation, the use of stable isotopes in quantitative work flows has arguably had the greatest impact in improving the quality and reproducibility of MS-based protein quantitation (3–5).The ongoing development of untargeted MS-based quantitation work flows has focused on increasingly exhaustive sample prefractionation methods, at both the protein and peptide levels, with the goal of detecting and quantifying entire proteomes (6). Although untargeted MS-based quantitation work flows have their utility, they are costly in terms of lengthy MS data acquisition and analysis times, and as a result, they are often limited to quantifying differences between small sample sets (n < 10). To facilitate rapid quantitation of larger, clinically relevant sample sets (n > 100) there is a need to both simplify sample preparation and reduce MS analysis time.Multiple reaction monitoring (MRM)¹ is a tandem MS (MS/MS) scan mode unique to triple quadrupole MS instrumentation that is capable of rapid, sensitive, and specific quantitation of analytes in highly complex sample matrices (7). MRM is a targeted approach that requires knowledge of the molecular weight of an analyte and its fragmentation behavior under CID. MRM is capable of highly reproducible concentration determination when stable isotope-labeled internal standards are included in work flows and has been used for decades for the quantitation of low molecular mass analytes (<1000 Da) in pharmaceutical, clinical, and environmental applications (7, 8).The combination of triple quadrupole MS instrumentation with nanoliter flow rate high performance LC and nanoelectrospray ionization provides the necessary sensitivity for detection and quantitation of biological molecules such as peptides in complex samples such as plasma by MRM. When combined with the use of isotopically labeled synthetic peptide standards, MRM analysis is capable of sensitive (attomole level) and absolute determination of peptide concentrations across a wide concentration scale spanning a dynamic range of 10³–10⁴ (1, 9–13).Several recent studies involving MRM-based analysis of plasma proteins have focused on increasing MRM detection sensitivity by fractionating plasma using either multidimensional liquid chromatography, affinity depletion of high abundance proteins (11, 14, 15), or affinity enrichment of low abundance peptides (16, 17). Anderson and Hunter (14) have shown that LC-MRM/MS analysis is capable of detecting 47 moderate to high abundance proteins in plasma without depletion even though ∼90% of the total protein by weight in trypsin-digested plasma can be attributed to 10 high abundance proteins (18).Relative abundance of a protein does not preclude its involvement in disease. In fact, 32 of the 47 plasma proteins detected by Anderson and Hunter (14) have been implicated as putative markers for cardiovascular disease. The ability to rapidly quantify proteins in a highly multiplexed manner using MRM and internal standard peptides expands the potential application of MRM quantitation beyond biomarker validation and into the field of biomarker discovery. Targeted, simultaneous quantitation of hundreds of proteins in a single analysis will enable rapid protein expression profiling of large (n > 100) clinically relevant sample sets in a manner similar to DNA microarray expression profiling. By allowing researchers to look at patterns of expression levels of a large number of proteins in a large number of samples (as opposed to looking at the expression levels of only a single protein), multiplexed MRM-based quantitation will allow the correlation of expression patterns with particular diseases. Once these characteristic patterns have been established, physicians will be able to use these protein expression patterns to diagnose diseases in the same way they currently use blood chemistry panels or comprehensive metabolic panels.When considering the clinical utility of MS-based assays, direct comparisons are often made to ELISA, which is considered the “gold standard” for protein quantitation in clinical samples. Attributes of ELISAs, such as “time to first result” (1–2 h (19)) and the ability to quantify 96 or 384 samples in parallel because of their microtiter plate-based format, are currently difficult to match with MS-based protein assays. However, MRM protein assays may surpass ELISA in the rapid development of clinically useful, multiplexed protein assays. The impact of multiplexed assays in the field of genomics has increased interest in multiplexed quantitation of many proteins in individual clinical samples (19). Development and characterization of MRM-based protein assays using isotopically labeled peptides is rapid and inexpensive compared with the time and cost associated with the generation and characterization of antibodies for ELISA development.In this study, we describe the creation of a customizable mixture of concentration-balanced stable isotope-labeled standard (SIS) peptides representing an initial panel of 45 human plasma proteins. We used this mixture of SIS peptides to develop a suite of multiplexed, rapid, and reproducible MRM-based assays for expression profiling of these 45 proteins in simple tryptic digests of whole plasma. Additionally we characterized the analytical performance of these MRM peptide assays with respect to their reproducibility, and we demonstrated their utility for absolute protein concentration determination.Multiplexed MRM quantitation of peptides for protein quantitation has the potential to replace iTRAQ or other isotope label and label-free quantitative proteomics approaches because the approach is much faster than these other methods (30–60 min per analysis compared with 4 days for LC-MALDI-based iTRAQ), has greater reproducibility (CV <5% versus iTRAQ CV >20%), and enables absolute quantitation (concentration and copy number versus only x-fold up- or down-regulated). Additionally MRM-based quantitation with SIS peptides does not “miss” peptides because the SIS peptide must be detected in every sample: this means that if an endogenous peptide is not observed then it is below the limit of detection.     

Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring

In many studies, particularly in the field of systems biology, it is essential that identical protein sets are precisely quantified in multiple samples such as those representing differentially perturbed cell states. The high degree of reproducibility required for such experiments has not been achieved by classical mass spectrometry-based proteomics methods. In this study we describe the implementation of a targeted quantitative approach by which predetermined protein sets are first identified and subsequently quantified at high sensitivity reliably in multiple samples. This approach consists of three steps. First, the proteome is extensively mapped out by multidimensional fractionation and tandem mass spectrometry, and the data generated are assembled in the PeptideAtlas database. Second, based on this proteome map, peptides uniquely identifying the proteins of interest, proteotypic peptides, are selected, and multiple reaction monitoring (MRM) transitions are established and validated by MS2 spectrum acquisition. This process of peptide selection, transition selection, and validation is supported by a suite of software tools, TIQAM (Targeted Identification for Quantitative Analysis by MRM), described in this study. Third, the selected target protein set is quantified in multiple samples by MRM. Applying this approach we were able to reliably quantify low abundance virulence factors from cultures of the human pathogen Streptococcus pyogenes exposed to increasing amounts of plasma. The resulting quantitative protein patterns enabled us to clearly define the subset of virulence proteins that is regulated upon plasma exposure.