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Aberrations in epidermal growth factor receptor (EGFR/ErbB1) are the most common oncogenic alterations in glioblastoma multiforme (GBM), the most common primary brain tumor. Interactions between wild-type (wt) and mutant EGFRs and their subsequent activation are of biologic and potential therapeutic importance in GBMs. We recently showed that in situ proximity ligation assay (PLA) allows for quantitative evaluation of EGFR dimerization and activation in intact cells. Using this in situ platform, we show the aberrant homo-/heterodimeric properties of EGFRvIII and EGFRc958 mutants, the two most common EGFR mutants in GBMs. In addition, dimer phosphoactivation status could be detected by PLA with superior signal–noise ratio (>17-fold) and sensitivity (>16-fold) than immunofluorescence-based phospho-EGFR measurements. Dimer activation analysis indicated quantitative activation differences of mutant dimers. These aberrant features were not overexpression dependent but appeared independent of cellular expression levels, suggesting inherent properties of the mutant receptors. Moreover, we observed in situ detection of EGFRwt-EGFRvIII heterodimerization in GBM specimens, supporting our cell line observations. Notably, currently used anti-EGFR therapeutics, such as cetuximab, matuzumab, and panitumumab, could effectively block EGFRwt dimerization and activation but did not equally impair EGFRvIII homodimers, EGFRwt-EGFRvIII, or EGFRvIII-EGFRc958 heterodimers. EGFRvIII appears to have intrinsic phosphoactivation independent of dimerization as matuzumab blockade of homodimerization had no effect on receptor phosphorylation levels. These data suggest differences in the dimerization-blocking efficacy of EGFR monoclonal antibodies as mutant EGFR dimer configurations prevalent in GBMs can evade blockade by anti-EGFR treatments. Further studies are warranted to evaluate whether this evasion contributes to poor therapeutic response or resistance. Mol Cancer Res; 10(3); 428–40. ©2012 AACR.

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Custom pathway and substrate-kinase libraries for tumor-specific pathway enrichment analyses.

Tyrosine phosphorylation (pTyr) plays a pivotal role in signal transduction and is commonly dysregulated in cancer. As a result, profiling tumor pTyr levels may reveal therapeutic insights critical to combating disease. Existing discovery and targeted mass spectrometry–based methods used to monitor pTyr networks involve a tradeoff between broad coverage of the pTyr network, reproducibility in target identification across analyses, and accurate quantification. To address these limitations, we developed a targeted approach, termed “SureQuant pTyr,” coupling low input pTyr enrichment with a panel of isotopically labeled internal standard peptides to guide data acquisition of low-abundance tyrosine phosphopeptides. SureQuant pTyr allowed for reliable quantification of several hundred commonly dysregulated pTyr targets with high quantitative accuracy, improving the robustness and usability of targeted mass spectrometry assays. We established the clinical applicability of SureQuant pTyr by profiling pTyr signaling levels in human colorectal tumors using minimal sample input, characterizing patient-specific oncogenic-driving mechanisms. While in some cases pTyr profiles aligned with previously reported proteomic, genomic, and transcriptomic molecular characterizations, we highlighted instances of new insights gained using pTyr characterization and emphasized the complementary nature of pTyr measurements with traditional biomarkers for improving patient stratification and identifying therapeutic targets. The turn-key nature of this approach opens the door to rapid and reproducible pTyr profiling in research and clinical settings alike and enables pTyr-based measurements for applications in precision medicine.Significance:SureQuant pTyr is a mass spectrometry–based targeted method that enables sensitive and selective targeted quantitation of several hundred low-abundance tyrosine phosphorylated peptides commonly dysregulated in cancer, including oncogenic signaling networks.

Supplementary figures, table legends, and methods.

Supplementary Table 2. Basal state of ovarian tumor samples

Methods and Supplementary Figures 1-9. Supplementary Figure 1: Histopathology images of tumors used in ischemia time-course and spatial heterogeneity experiments. Supplementary Figure 2: Schematic overview of ovarian tumor ischemia time-course experiment. Supplementary Figure 3: Distinct inter-patient ischemia regulated temporal dynamics are observed. Supplementary Figure 4: Similar ischemia response temporal patterns are observed across ovarian tumors. Supplementary Figure 5: Schematic overview of the colon tumor spatial heterogeneity and ischemia time-course experiment. Supplementary Figure 6: Spatial phosphorylation heterogeneity in colons tumors cannot be attributed solely to technical measurement error. Supplementary Figure 7: Weak correlations and minimal shared covariance between spatially proximal colon tumor samples. Supplementary Figure 8: Schematic overview of the colon tumor protein expression profiling experiment. Supplementary Figure 9: Delayed freezing of tumors affects pTyr sites involved in numerous pathways and processes.

Supplementary Table 1. Ovarian pTyr ischemia response

Tumor protein phosphorylation analysis may provide insight into intracellular signaling networks underlying tumor behavior, revealing diagnostic, prognostic or therapeutic information. Human tumors collected by The Cancer Genome Atlas program potentially offer the opportunity to characterize activated networks driving tumor progression, in parallel with the genetic and transcriptional landscape already documented for these tumors. However, a critical question is whether cellular signaling networks can be reliably analyzed in surgical specimens, where freezing delays and spatial sampling disparities may potentially obscure physiologic signaling. To quantify the extent of these effects, we analyzed the stability of phosphotyrosine (pTyr) sites in ovarian and colon tumors collected under conditions of controlled ischemia and in the context of defined intratumoral sampling. Cold-ischemia produced a rapid, unpredictable, and widespread impact on tumor pTyr networks within 5 minutes of resection, altering up to 50% of pTyr sites by more than 2-fold. Effects on adhesion and migration, inflammatory response, proliferation, and stress response pathways were recapitulated in both ovarian and colon tumors. In addition, sampling of spatially distinct colon tumor biopsies revealed pTyr differences as dramatic as those associated with ischemic times, despite uniform protein expression profiles. Moreover, intratumoral spatial heterogeneity and pTyr dynamic response to ischemia varied dramatically between tumors collected from different patients. Overall, these findings reveal unforeseen phosphorylation complexity, thereby increasing the difficulty of extracting physiologically relevant pTyr signaling networks from archived tissue specimens. In light of this data, prospective tumor pTyr analysis will require appropriate sampling and collection protocols to preserve in vivo signaling features. Cancer Res; 75(7); 1495–503. ©2015 AACR.

Supplementary Table 4. Summary of colon tumor iTRAQ LC-MS/MS pTyr analysis

Supplementary Table 5. Summary of colon tumor iTRAQ LC-MS/MS protein expession analysis

Supplementary Table 6. Colon tumor pTyr and protein expression groups

Supplementary Table 3. Summary of similar ischemia response temporal patterns observed across multiple ovarian tumors, as shown in Supplementary Figure 4.

The rapidly increasing adoption of high-resolution accurate-mass methods in analytical laboratories has fueled demand for instruments that combine high performance and reliability with small size and greater ease-of-use. This paper presents the major design principles that are driving the evolution of the hybrid quadrupole-Orbitrap instrument architecture to enable a greater range of applications and users. These principles may be summarized as follows: better usage of physical space and better access for service by means of size reduction of pumping and ion optics; expanded use of technologies from electronics in ion-optical design; flexibility in performance via modularity of design of the hardware and software components; and, harmonization of interfaces with other instruments to facilitate sharing and transferability of analytical workflows. The design of a novel family of hybrid mass spectrometers is described in detail, and performance evaluation is carried out on a wide variety of samples for its three representatives: the Orbitrap Exploris 120, Orbitrap Exploris 240 and Orbitrap Exploris 480 mass spectrometers. The new instrument family is shown to offer compelling potential not only for high-end proteomics and biopharmaceutical applications, but also for screening, trace, targeted and clinical analysis by liquid chromatography/mass spectrometry methods.

Absolute quantification measurements (copies per cell) of peptide major histocompatibility complex (pMHC) antigens are necessary to inform targeted immunotherapy drug design; however, existing methods for absolute quantification have critical limitations. Here, we present a platform termed SureQuant-IsoMHC, utilizing a series of pMHC isotopologues and internal standard-triggered targeted mass spectrometry to generate an embedded multipoint calibration curve to determine endogenous pMHC concentrations for a panel of 18 tumor antigens. We apply SureQuant-IsoMHC to measure changes in expression of our target panel in a melanoma cell line treated with a MEK inhibitor and translate this approach to estimate antigen concentrations in melanoma tumor biopsies.

Comprehensive assessment of the flow of genetic information through multi-omic data integration can reveal the molecular consequences of genetic variation underlying human disease. Next generation sequencing (NGS) is used to identify genetic variants and characterize gene function (e.g. transcriptome and epigenome), while mass spectrometry is used to assess the proteome through characterization of protein abundances, modifications, and interactions. A new plasma profiling platform, the Proteograph࣪ Product Suite, leverages multiple nanoparticles with distinct physiochemical properties to enable deep plasma proteome analyses at scale. Here, we present a cloud-based, data analysis software platform called Proteograph Analysis Suite (PAS) for proteogenomic data analyses through the integration of proteomics data derived from the Proteograph with genomic variant information derived from NGS experiments. PAS features include an experiment data management system, analysis protocols, an analysis setup wizard, and tools for reviewing and visualizing results. PAS can support both Data Independent Analysis (DIA) and Data Dependent Analysis (DDA) proteomics workflows and is compatible with variant call format (vcf) files from NGS workflows to enable personalized database searches. To assess quality of the resulting data PAS includes various metrics like peptide/protein group intensity, protein sequence coverage, relative protein abundance distribution, peptide and protein group counts. Visualizations including principal component analysis, hierarchical clustering, and heatmaps allow intuitive identification of experimental trends. To enable biological insights, differential expression analyses results are reported with interactive visualizations such as volcano plots, protein interaction maps, and protein-set enrichment. From data to insight, PAS provides an easy-to-use and efficient suite of functionality to enable proteogenomic data analysis. Integration of proteomics and genomics data require a variety of tools, many of which require command-line interfaces and operating system-specific requirements that can act as a barrier for researchers to adapt new data analysis tools. Here, we demonstrate the utility of PAS by analyzing samples from the Proteograph NSCLC plasma dataset1. PAS can analyze VCF files generated from NGS pipelines in combination with mass spec data to identify peptide variants using personalized libraries. Using the cloud-based architecture computational tasks are distributed for rapid analysis. The integrated proteogenomics viewers allow variant IDs to be interpreted in the context of genomic coordinates, protein sequence, functional domains and features. Together, these results show the utility of PAS for seamless and fast proteomic data analysis. Reference: 1 Blume, J. E. et al. Nature Communications, 2020 Citation Format: Aaron S. Gajadhar, Margaret K. Donovan, Harsharn Auluck, Yan Berk, Yuandan Lou, Theo Platt, Serafim Batzoglou. A cloud-scalable software suite for large-cohort proteogenomics data analysis and visualization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6348.

Tyrosine phosphorylation (pTyr) plays a pivotal role in signal transduction and is commonly dysregulated in cancer. As a result, profiling tumor pTyr levels may reveal therapeutic insights critical to combating disease. Existing discovery and targeted mass spectrometry-based methods used to monitor pTyr networks involve a tradeoff between broad coverage of the pTyr network, reproducibility in target identification across analyses, and accurate quantification. To address these limitations, we developed a targeted approach, termed “SureQuant pTyr,” coupling low input pTyr enrichment with a panel of isotopically labeled, tyrosine phosphorylated internal standard (IS) peptides. Using internal standard guided acquisition, the real-time detection of IS peptides during the analysis initiates the sensitive and selective quantitation of endogenous pTyr targets. This framework allows for reliable quantification of several hundred commonly dysregulated pTyr targets with high quantitative accuracy, enhances target detection success rates, and improves the robustness and usability of targeted acquisition. We establish the clinical applicability of SureQuant pTyr by profiling pTyr signaling levels in human colorectal tumors using minimal sample input, characterizing patient specific oncogenic driving mechanisms. While in some cases pTyr profiles align with previously reported proteomic, genomic, and transcriptomic molecular characterizations, we highlight instances of new insights gained using pTyr characterization and emphasize the complementary nature of pTyr measurements with traditional biomarkers for improving patient stratification and identifying therapeutic targets. The turn-key nature of this approach opens the door to rapid and reproducible pTyr profiling in research and clinical settings alike and enable pTyr-based measurements for applications in precision medicine.SummaryA targeted, mass spectrometry-based method, termed “SureQuant pTyr,” enables highly sensitive and reproducible profiling of tyrosine phosphorylation levels in human colorectal tumors and reveals dysregulated signaling networks for enhanced tumor characterization and biomarker identification.