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The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation (source code is available from http://homepages.uc.edu/~wang2x7/Research.htm ). From these assessments, we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61 to 93% of the time. When comparing across different instruments and quantitative technologies, using multiple replicates, differential genes were reproduced by other data sets from 67 to 99% of the time. Projecting gene differences to biological pathways and networks increased the degree of similarity. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation.

We assessed somatic alleles of six receptor tyrosine kinase genes mutated in lung adenocarcinoma for oncogenic activity. Five of these genes failed to score in transformation assays; however, novel recurring extracellular domain mutations of the receptor tyrosine kinase gene ERBB2 were potently oncogenic. These ERBB2 extracellular domain mutants were activated by two distinct mechanisms, characterized by elevated C-terminal tail phosphorylation or by covalent dimerization mediated by intermolecular disulfide bond formation. These distinct mechanisms of receptor activation converged upon tyrosine phosphorylation of cellular proteins, impacting cell motility. Survival of Ba/F3 cells transformed to IL-3 independence by the ERBB2 extracellular domain mutants was abrogated by treatment with small-molecule inhibitors of ERBB2, raising the possibility that patients harboring such mutations could benefit from ERBB2-directed therapy.

Introduction of antibodies specific for acetylated lysine has significantly improved the detection of endogenous acetylation sites by mass spectrometry. Here, we describe a new, commercially available mixture of anti-lysine acetylation (Kac) antibodies and show its utility for in-depth profiling of the acetylome. Specifically, seven complementary monoclones with high specificity for Kac were combined into a final anti-Kac reagent which results in at least a twofold increase in identification of Kac peptides over a commonly used Kac antibody. We outline optimal antibody usage conditions, effective offline basic reversed phase separation, and use of state-of-the-art LC-MS technology for achieving unprecedented coverage of the acetylome. The methods were applied to quantify acetylation sites in suberoylanilide hydroxamic acid-treated Jurkat cells. Over 10,000 Kac peptides from over 3000 Kac proteins were quantified from a single stable isotope labeling by amino acids in cell culture labeled sample using 7.5 mg of peptide input per state. This constitutes the deepest coverage of acetylation sites in quantitative experiments obtained to-date. The approach was also applied to breast tumor xenograft samples using isobaric mass tag labeling of peptides (iTRAQ4, TMT6 and TMT10-plex reagents) for quantification. Greater than 6700 Kac peptides from over 2300 Kac proteins were quantified using 1 mg of tumor protein per iTRAQ 4-plex channel. The novel reagents and methods we describe here enable quantitative, global acetylome analyses with depth and sensitivity approaching that obtained for other well-studied post-translational modifications such as phosphorylation and ubiquitylation, and should have widespread application in biological and clinical studies employing mass spectrometry-based proteomics.

There is a pressing need to identify therapeutic targets in tumors with low mutation rates such as the malignant pediatric brain tumor medulloblastoma. To address this challenge, we quantitatively profiled global proteomes and phospho-proteomes of 45 medulloblastoma samples. Integrated analyses revealed that tumors with similar RNA expression vary extensively at the post-transcriptional and post-translational levels. We identified distinct pathways associated with two subsets of SHH tumors, and found post-translational modifications of MYC that are associated with poor outcomes in group 3 tumors. We found kinases associated with subtypes and showed that inhibiting PRKDC sensitizes MYC-driven cells to radiation. Our study shows that proteomics enables a more comprehensive, functional readout, providing a foundation for future therapeutic strategies.

In the Supplementary Information originally published with this article, a lane was missing in the β-actin blot in Supplementary Fig. 2. The lane has been added. The error has been corrected in the Supplementary Information associated with this article.

Because of their antagonistic catalytic functions, protein-tyrosine phosphatases (PTPs) and protein-tyrosine kinases act together to control phosphotyrosine-mediated signaling processes in mammalian cells. However, unlike for protein-tyrosine kinases, little is known about the cellular substrate specificity of many PTPs because of the lack of appropriate methods for the systematic and detailed analysis of cellular PTP function. Even for the most intensely studied, prototypic family member PTP1B many of its physiological functions cannot be explained by its known substrates. To gain better insights into cellular PTP1B function, we used quantitative MS to monitor alterations in the global tyrosine phosphorylation of PTP1B-deficient mouse embryonic fibroblasts in comparison with their wild-type counterparts. In total, we quantified 124 proteins containing 301 phosphotyrosine sites under basal, epidermal growth factor-, or platelet-derived growth factor-stimulated conditions. A subset of 18 proteins was found to harbor hyperphosphorylated phosphotyrosine sites in knock-out cells and was functionally linked to PTP1B. Among these proteins, regulators of cell motility and adhesion are overrepresented, such as cortactin, lipoma-preferred partner, ZO-1, or p120ctn. In addition, regulators of proliferation like p62DOK or p120RasGAP also showed increased cellular tyrosine phosphorylation. Physical interactions of these proteins with PTP1B were further demonstrated by using phosphatase-inactive substrate-trapping mutants in a parallel MS-based analysis. Our results correlate well with the described phenotype of PTP1B-deficient fibroblasts that is characterized by an increase in motility and reduced cell proliferation. The presented study provides a broad overview about phosphotyrosine signaling processes in mouse fibroblasts and, supported by the identification of various new potential substrate proteins, indicates a central role of PTP1B within cellular signaling networks. Importantly the MS-based strategies described here are entirely generic and can be used to address the poorly understood aspects of cellular PTP function.

Finding the components of cellular circuits and determining their functions systematically remains a major challenge in mammalian cells. Here, we introduced genome-wide pooled CRISPR-Cas9 libraries into dendritic cells (DCs) to identify genes that control the induction of tumor necrosis factor (Tnf) by bacterial lipopolysaccharide (LPS), a key process in the host response to pathogens, mediated by the Tlr4 pathway. We found many of the known regulators of Tlr4 signaling, as well as dozens of previously unknown candidates that we validated. By measuring protein markers and mRNA profiles in DCs that are deficient in known or candidate genes, we classified the genes into three functional modules with distinct effects on the canonical responses to LPS and highlighted functions for the PAF complex and oligosaccharyltransferase (OST) complex. Our findings uncover new facets of innate immune circuits in primary cells and provide a genetic approach for dissection of mammalian cell circuits., Broad Institute, National Institutes of Health (U.S.) (NIMH: 5DP1-MH100706), National Institutes of Health (U.S.) (NIDDK: 5R01-DK097768), National Science Foundation (U.S.) (Waterman Award), W. M. Keck Foundation, New York Stem Cell Foundation, Damon Runyon Cancer Research Foundation, Searle Scholars Program, Vallee Foundation, Robert Metcalfe, Massachusetts Institute of Technology. Simons Center for the Social Brain, National Human Genome Research Institute (U.S.) (K99- HG008171), National Science Foundation (U.S.). Graduate Research Fellowship Program (grant number 1122374), Human Frontier Science Program (Strasbourg, France)

A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding sequences (CDSs), e.g., they are conserved, do not overlap, and exceed a minimum length. However, an increasing number of newly discovered proteins violate these rules. Here we present an experimental and analytical framework, based on ribosome profiling and linear regression, for systematic identification and quantification of translation. Application of this approach to lipopolysaccharide-stimulated mouse dendritic cells and HCMV-infected human fibroblasts identifies thousands of novel CDSs, including micropeptides and variants of known proteins, that bear the hallmarks of canonical translation and exhibit translation levels and dynamics comparable to that of annotated CDSs. Remarkably, many translation events are identified in both mouse and human cells even when the peptide sequence is not conserved. Our work thus reveals an unexpected complexity to mammalian translation suited to provide both conserved regulatory or protein-based functions., Klarman Cell Observatory

How the immune system readies for battle Although gene expression is tightly controlled at both the RNA and protein levels, the quantitative contribution of each step, especially during dynamic responses, remains largely unknown. Indeed, there has been much debate whether changes in RNA level contribute substantially to protein-level regulation. Jovanovic et al. built a genome-scale model of the temporal dynamics of differential protein expression during the stimulation of immunological dendritic cells (see the Perspective by Li and Biggin). Newly stimulated functions involved the up-regulation of specific RNAs and concomitant increases in the levels of the proteins they encode, whereas housekeeping functions were regulated posttranscriptionally at the protein level. Science , this issue 10.1126/science.1259038 ; see also p. 1066

Several receptor protein tyrosine phosphatases (RPTPs) are cell adhesion molecules involved in homophilic interactions, suggesting that RPTP outside-in signaling is coupled to cell contact formation. However, little is known about the mechanisms by which cell density regulates RPTP function. We show that the MAM family prototype RPTP is cleaved by three proteases: furin, ADAM 10, and -secretase. Cell density promotes ADAM 10-mediated cleavage and shedding of RPTP. This is followed by -secretase-dependent intramembrane proteolysis of the remaining transmembrane part to release the phosphatase intracellular portion (PIC) from the membrane, thereby allowing its translocation to the nucleus. When cells were treated with leptomycin B, a nuclear export inhibitor, PIC accumulated in nuclear bodies. PIC is an active protein tyrosine phosphatase that binds to and dephosphorylates -catenin, an RPTP substrate. The expression of RPTP suppresses -catenin’s transcriptional activity, whereas the expression of PIC increases it. Notably, this increase required the phosphatase activity of PIC. Thus, both isoforms have acquired opposing roles in the regulation of -catenin signaling. We also found that RPTP, another MAM family member, undergoes -secretasedependent processing. Our results identify intramembrane proteolysis as a regulatory switch in RPTP signaling and implicate PIC in the activation of -catenin-mediated transcription. The phosphorylation of cellular proteins on tyrosine residues is reversible and regulated by the coordinated and competing actions of two enzyme families: protein tyrosine kinases and protein tyrosine phosphatases (PTPs). The PTP family is structurally diverse and includes both receptor-like and cytoplasmic enzymes. The majority of the receptor PTPs (RPTPs) contain two catalytic domains: a membrane-proximal domain (D1), which is responsible for mainly catalysis, and a membrane-distal domain (D2), which contains little or no phosphatase activity (45). The extracellular (E) portion exhibits broad structural variation. The MAM (meprin/A5 glycoprotein/PTPmu) family of RPTPs, including RPTP ,- ,- ,- , and PCP-2, are characterized by the presence of the MAM domain at their N termini (3, 6, 18, 29, 46). Additional structural features of the extracellular portions involve one immu

CDK5 activates the tumor suppressor DLC1 by phosphorylating and diminishing the binding of an autoinhibitory region of DLC1 to its Rho-GAP domain and allows it to localize to focal adhesions., DLC1 is a tumor suppressor protein whose full activity depends on its presence at focal adhesions, its Rho–GTPase activating protein (Rho-GAP) function, and its ability to bind several ligands, including tensin and talin. However, the mechanisms that regulate and coordinate these activities remain poorly understood. Here we identify CDK5, a predominantly cytoplasmic serine/threonine kinase, as an important regulator of DLC1 functions. The CDK5 kinase phosphorylates four serines in DLC1 located N-terminal to the Rho-GAP domain. When not phosphorylated, this N-terminal region functions as an autoinhibitory domain that places DLC1 in a closed, inactive conformation by efficiently binding to the Rho-GAP domain. CDK5 phosphorylation reduces this binding and orchestrates the coordinate activation DLC1, including its localization to focal adhesions, its Rho-GAP activity, and its ability to bind tensin and talin. In cancer, these anti-oncogenic effects of CDK5 can provide selective pressure for the down-regulation of DLC1, which occurs frequently in tumors, and can contribute to the pro-oncogenic activity of CDK5 in lung adenocarcinoma.

Nature Communications 8: Article number: 14864 (2017)); Published: 28 March 2017; Updated: 25 April 2017 The original version of this Article contained a typographical error in the spelling of the author Beifang Niu, which was incorrectly given as Beifung Niu. This has now been corrected in both thePDF and HTML versions of the Article.

Protein abundance and phosphorylation convey important information about pathway activity and molecular pathophysiology in diseases including cancer, providing biological insight, informing drug and diagnostic development, and guiding therapeutic intervention. Analyzed tissues are usually collected without tight regulation or documentation of ischemic time. To evaluate the impact of ischemia, we collected human ovarian tumor and breast cancer xenograft tissue without vascular interruption and performed quantitative proteomics and phosphoproteomics after defined ischemic intervals. Although the global expressed proteome and most of the >25,000 quantified phosphosites were unchanged after 60 min, rapid phosphorylation changes were observed in up to 24% of the phosphoproteome, representing activation of critical cancer pathways related to stress response, transcriptional regulation, and cell death. Both pan-tumor and tissue-specific changes were observed. The demonstrated impact of pre-analytical tissue ischemia on tumor biology mandates caution in interpreting stress-pathway activation in such samples and motivates reexamination of collection protocols for phosphoprotein analysis.

One of the adverse consequences of chemotherapy exposure is the development of therapy-related myeloid neoplasms (t-MNs). However, the cause and origin of most t-MNs are unknown, and the prognosis remains dismal. Novel work has shown that in addition to TP53, PPM1D is selectively mutated in 15% of therapy related MDS (Lindsley et al., ASH Abstract). Truncating mutations of PPM1D are also found to commonly occur in clonal hematopoiesis (Jaiswal et al., NEJM 2014; Genovese et al., NEJM 2014; Xie et al., Nat Med 2014), as well as in the blood of cancer patients, particularly after exposure to chemotherapy (Ruark et al., Nature 2013; Swisher et al., JAMA Oncol 2016). We hypothesized that PPM1D truncating mutations confer chemotherapy resistance, causing selective outgrowth of PPM1D mutant hematopoietic stem cells in states of genotoxic stress. In addition, since PPM1D mutations lead to a gain of function, we examined the potential of targeting PPM1D-mutant cells pharmacologically. The protein phosphatase PPM1Dis a direct regulator of TP53 activity and the DNA damage response pathway (Fiscella et al., PNAS 1997). Consequently, gain-of-function PPM1D mutations lead to decreased TP53 activity. To examine whether PPM1D mutations drive chemotherapy resistance through an abrogation of the TP53 dependent DNA damage response, we engineered PPM1D-mutant subclones using the CRISPR-Cas9 system in the TP53 wild-type AML cell line MOLM-13. PPM1D exon 6 truncation led to increased expression of PPM1D and resistance to DNA damaging agents, including cytarabine, cyclophosphamide and cisplatin. In addition, PPM1D-mutant cells exhibited a selective advantage over wild-type cells in the presence of chemotherapy, expanding 100-fold over a 24-day period (Fig. 1). While treatment with chemotherapy induced phosphorylation of Chk1 and p53, cell cycle arrest and apoptosis in wild-type cells, this response was abrogated in PPM1D-mutant cells due to gain of function of PPM1D. Using phosphoproteomic analysis, we further demonstrate decreased phosphorylation of known and novel targets in PPM1D-mutant compared to wild-type cells. We next investigated the effect of PPM1D mutation on normal marrow progenitors in response to chemotherapy treatment in vivo. We performed a competition experiment in which mouse bone marrow c-Kit+ cells expressing Cas9 were transduced with guide RNAs targeting exon 6 of PPM1D or a control guide, and then transplanted into mice in a 1:5 ratio. We observed a selective outgrowth of PPM1D-mutant myeloid cells in the peripheral blood of mice after exposure to chemotherapy. In addition, we found expansion of PPM1D-mutant cells in the lineage negative, c-Kit+ Sca-1+ population, which is enriched for hematopoietic stem cells and multipotent progenitors, indicating that PPM1D-mutant stem and progenitor cells have a competitive advantage over wild-type cells after exposure to genotoxic stress. The generation of a selective, allosteric inhibitor of PPM1D (Gilmartin et al., Nat Chem Biol 2014) allowed us to examine whether pharmacologic inhibition of PPM1D decreases the chemotherapy resistance or survival of PPM1D-mutant cells. We found that PPM1D-mutant cells have a significantly increased sensitivity to PPM1D inhibition when compared to wild-type controls. In addition, PPM1D inhibitor treatment was able to re-sensitize mutant cells to chemotherapy and abrogate the selective outgrowth of PPM1D-mutant cells during chemotherapy exposure. Lastly, we demonstrate that the proteome-wide phosphorylation profile characteristic of PPM1D-mutant cells can be reversed through treatment with the PPM1D inhibitor. In sum, these results demonstrate that PPM1D mutations confer a competitive advantage to hematopoietic stem cells undergoing genotoxic stress by abrogating the DNA damage response, and are likely to be the initiating mutation in a large proportion of t-MNs. Due to the gain-of-function nature of this mutation, PPM1D-mutant cells are differentially sensitive to treatment with a PPM1D inhibitor. PPM1D inhibition may therefore provide an opportunity for the prevention and targeted treatment of hematologic malignancies that harbor PPM1D mutations. Figure 1 PPM1D mutant cells have a competitive advantage under the selective pressure of chemotherapy (cytarabine) treatment. Figure 1. PPM1D mutant cells have a competitive advantage under the selective pressure of chemotherapy (cytarabine) treatment. Disclosures No relevant conflicts of interest to declare.

N[superscript 6]-methyladenosine (m[superscript 6]A) is the most ubiquitous mRNA base modification, but little is known about its precise location, temporal dynamics, and regulation. Here, we generated genomic maps of m[superscript 6]A sites in meiotic yeast transcripts at nearly single-nucleotide resolution, identifying 1,308 putatively methylated sites within 1,183 transcripts. We validated eight out of eight methylation sites in different genes with direct genetic analysis, demonstrated that methylated sites are significantly conserved in a related species, and built a model that predicts methylated sites directly from sequence. Sites vary in their methylation profiles along a dense meiotic time course and are regulated both locally, via predictable methylatability of each site, and globally, through the core meiotic circuitry. The methyltransferase complex components localize to the yeast nucleolus, and this localization is essential for mRNA methylation. Our data illuminate a conserved, dynamically regulated methylation program in yeast meiosis and provide an important resource for studying the function of this epitranscriptomic modification., American Cancer Society (Professor of Genetics), National Institutes of Health (U.S.) (NIH Grant GM035010), National Institutes of Health (U.S.) (NIH Grant U54 HG003067), Broad Institute of MIT and Harvard (Funds), National Human Genome Research Institute (U.S.) (NHGRI Pioneer Award), Howard Hughes Medical Institute, Human Frontier Science Program (Strasbourg, France) (Fellowship)

Background Tumor-associated macrophages (TAM) promote malignant progression, yet the repertoire of oncogenic factors secreted by TAM has not been clearly defined. We sought to analyze which EGFR- and STAT3-activating factors are secreted by monocytes/macrophages exposed to tumor cell-secreted factors. Methods Following exposure of primary human monocytes and macrophages to supernatants of a variety of tumor cell lines, we have analyzed transcript and secreted protein levels of EGFR family ligands and of STAT3 activators. To validate our findings, we have analyzed TAM infiltration levels, systemic and local protein levels as well as clinical data of primary breast cancer patients. Results Primary human monocytes and macrophages respond to tumor cell-derived factors by secreting EGFR- and STAT3-activating ligands, thus inducing two important oncogenic pathways in carcinoma cells. Tumor cell-secreted factors trigger two stereotype secretory profiles in peripheral blood monocytes and differentiated macrophages: monocytes secrete epiregulin (EREG) and oncostatin-M (OSM), while macrophages secrete heparin-binding EGF-like growth factor (HB-EGF) and OSM. HB-EGF and OSM cooperatively induce tumor cell chemotaxis. HB-EGF and OSM are co-expressed by TAM in breast carcinoma patients, and plasma levels of both ligands correlate strongly. Elevated HB-EGF levels accompany TAM infiltration, tumor growth and dissemination in patients with invasive disease. Conclusions Our work identifies systemic markers for TAM involvement in cancer progression, with the potential to be developed into molecular targets in cancer therapy.

Detection of endogenous ubiquitination sites by mass spectrometry has dramatically improved with the commercialization of anti-di-glycine remnant (K-e-GG) antibodies. Here, we describe a number of improvements to the K-e-GG enrichment workflow, including optimized antibody and peptide input requirements, antibody cross-linking, and improved off-line fractionation prior to enrichment. This refined and practical workflow enables routine identification and quantification of ∼20,000 distinct endogenous ubiquitination sites in a single SILAC experiment using moderate amounts of protein input.

Many human cancers have high AKT activity and constitutive up-regulation of Rho-GTP, which is a major factor in the neoplastic process, but AKT is not known to regulate Rho-GTP. In this study, we show that AKT positively regulates Rho-GTP by directly phosphorylating tumor suppressor DLC1 and attenuating the Rho-GAP activity of DLC1, which catalyzes the conversion of active Rho-GTP to inactive Rho-GDP. Interestingly, AKT was found to increase Rho-GTP and its downstream activities in DLC1-positive cancer lines whether the DLC1 was endogenous or transfected, but not in DLC1-negative lines. Similarly, when epithelial cell lines were stimulated with EGF, they activated AKT, which increased Rho-GTP in a DLC1-dependent manner. Three Serines (S298, S329, S567) in DLC1 have AKT consensus motifs and were phosphorylated by AKT in vitro and in vivo. Their phosphorylation attenuated the Rho-GAP and tumor suppressor activities of DLC1 - including decreased cell migration, focal adhesion turnover, anchorage-independent growth, and tumor growth in mice - as did the combined phosphomimetic mutant DLC1-3D. By contrast, the combined Serine to Alanine mutant DLC1-3A was even more active than wild type DLC1 (DLC1-WT). Remarkably, an AKT inhibitor stimulated the tumor suppressor and Rho-GAP activities of DLC1-WT, but did not influence DLC1-3A or DLC1-3D. The N-terminal half of DLC1 (amino acids 1-600) bound the DLC1 Rho-GAP domain (amino acids 609-878), as determined by in vivo complex formation and by microscale thermophoresis, which measures protein interactions in close-to-native conditions. There was increased binding and decreased Rho-GAP activity when the three Serines in the N-terminus were phosphorylated or carried the 3D mutations. Conversely, there was decreased binding and increased Rho-GAP activity when the Serines were not phosphorylated or carried the 3A mutations. In a xenograft mouse model, AKT inhibitor treatment of DLC1-positive palpable tumors reduced their size, their Rho-GTP level, and their Rho-dependent signaling, but did not affect these three parameters in isogenic DLC1-negative tumors. Similarly, in the MMTV-PyMT breast cancer model, which had high AKT activity, high Rho-GTP, and expressed DLC1, an AKT inhibitor reduced the size of palpable tumors, and reduced Rho-GTP and its downstream signaling. AKT inhibition reduced DLC1 phosphorylation in both tumor models. We conclude: AKT can increase Rho-GTP by phosphorylating three N-terminal Serines in DLC1, which attenuates its Rho-GAP and tumor suppressor functions; the N-terminus of DLC1 is an auto-inhibitory domain that reversibly binds the Rho-GAP domain; AKT attenuates DLC1 functions by phosphorylating the Serines in the N-terminus, which increases its binding the Rho-GAP domain; and AKT inhibition has greater anti-tumor activity in DLC1-positive tumors than in DLC1-negative tumors. Citation Format: Brajendra K. Tripathi, Tiera Grant, Philipp Mertins, Xiaolan Qian, Dunrui Wang, Alex G. Papageorge, Steven A. Carr, Douglas R. Lowy. AKT positively regulates Rho-GTP by attenuating the GAP activity of the DLC1 tumor suppressor: a mechanistic study with translational implications. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4377.

The genetic landscape of human breast cancer has been well defined in The Cancer Genome Atlas (TCGA) project. Mass spectrometry (MS)-based global proteome and phosphoproteome analyses provide a complementary, orthogonal approach to genomic studies to further improve the molecular taxonomy and biological understanding of breast cancer. We analyzed human breast cancer samples that had previously undergone comprehensive genomic and reversed phase protein array (RPPA) characterization by TCGA. Tumor samples were analyzed by global shotgun proteomics and phosphoproteomics at an unprecedented coverage of >11,000 quantified proteins and >27,000 phosphorylation sites for each tumor. We verified the translation of hundreds of genomically characterized single nucleotide and splice junction variants at the protein level. The correlation of mRNA to protein abundance was significant for 6,135 out of 9,302 protein/mRNA pairs, but differed amongst protein classes. Genes that did not correlate on the protein/mRNA level included components of basic cellular machineries such as the ribosome, RNA polymerase and spliceosome, as well as those involved in processes regulated by proteolysis. Hierarchical clustering yielded three major clusters in both the proteome and the phosphoproteome data: basal-enriched, luminal-enriched and stroma-enriched groups, the last also enriched for what have been previously designated “reactive-type” tumors by RPPA. Our deep proteome analysis promoted new insights including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. The 5q trans effects were interrogated using the Library of Integrated Network-based Cellular Signatures. Theses analyses connected the 5q genes CETN3 and SKP1 to elevated expression of EGFR, and SKP1 also to SRC. Differential phosphopeptide analyses, integrated with activity maps derived from knock-in mutated cell lines, identified multiple novel downstream effects of PIK3CA and TP53 mutation. Besides ERBB2, other amplicon-associated, highly phosphorylated kinases were identified, including CDK12, PAK1, PTK2, RIPK2 and TLK2. These and other examples demonstrate that proteogenomic analysis of breast cancer elucidates functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies potential therapeutic targets. Citation Format: Philipp Mertins, DR Mani, Kelly Ruggles, Michael Gillette, Karl Clauser, Pei Wang, Xianlong Wang, Jana Qiao, Song Cao, Francesca Petralia, Filip Mundt, Zhidong Tu, Jonathan Lei, Michael Gatza, Matthew Wilkerson, Charles Perou, Venkata Yellapantula, Kuan-lin Huang, Chenwei Lin, Michael McLellan, Ping Yan, Sherri Davies, Reid Townsend, Steven Skates, Jing Wang, Bing Zhang, Christopher Kinsinger, Mehdi Mesri, Henry Rodriguez, Li Ding, Amanda Paulovich, David Fenyo, Matthew Ellis, Steven Carr, NCI CPTAC. Proteogenomic and phosphoproteomic analysis of breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr IA29.

The innate immune system senses viral DNA that enters mammalian cells, or in aberrant situations self-DNA, and triggers type I interferon production. Here we present an integrative approach that combines quantitative proteomics, genomics and small molecule perturbations to identify genes involved in this pathway. We silenced 809 candidate genes, measured the response to dsDNA and connected resulting hits with the known signaling network. We identified ABCF1 as a critical protein that associates with dsDNA and the DNA-sensing components HMGB2 and IFI204. We also found that CDC37 regulates the stability of the signaling molecule TBK1 and that chemical inhibition of the CDC37-HSP90 interaction and several other pathway regulators potently modulates the innate immune response to DNA and retroviral infection.

Labeling of primary amines on peptides with reagents containing stable isotopes is a commonly used technique in quantitative mass spectrometry. Isobaric labeling techniques such as iTRAQ™ or TMT™ allow for relative quantification of peptides based on ratios of reporter ions in the low m/z region of spectra produced by precursor ion fragmentation. In contrast, nonisobaric labeling with mTRAQ™ yields precursors with different masses that can be directly quantified in MS1 spectra. In this study, we compare iTRAQ- and mTRAQ-based quantification of peptides and phosphopeptides derived from EGF-stimulated HeLa cells. Both labels have identical chemical structures, therefore precursor ion- and fragment ion-based quantification can be directly compared. Our results indicate that iTRAQ labeling has an additive effect on precursor intensities, whereas mTRAQ labeling leads to more redundant MS2 scanning events caused by triggering on the same peptide with different mTRAQ labels. We found that iTRAQ labeling quantified nearly threefold more phosphopeptides (12,129 versus 4,448) and nearly twofold more proteins (2,699 versus 1,597) than mTRAQ labeling. Although most key proteins in the EGFR signaling network were quantified with both techniques, iTRAQ labeling allowed quantification of twice as many kinases. Accuracy of reporter ion quantification by iTRAQ is adversely affected by peptides that are cofragmented in the same precursor isolation window, dampening observed ratios toward unity. However, because of tighter overall iTRAQ ratio distributions, the percentage of statistically significantly regulated phosphopeptides and proteins detected by iTRAQ and mTRAQ was similar. We observed a linear correlation of logarithmic iTRAQ to mTRAQ ratios over two orders of magnitude, indicating a possibility to correct iTRAQ ratios by an average compression factor. Spike-in experiments using peptides of defined ratios in a background of nonregulated peptides show that iTRAQ quantification is less accurate but not as variable as mTRAQ quantification.

AIM: The aim of this study was to identify markers that have the potential to predict BKM120 (a pan-class I PI3K inhibitor) effectiveness in triple negative breast cancer. INTRODUCTION: Triple negative breast cancer is an aggressive subtype that constitutes circa 20% of all breast cancers. This subtype of breast cancer is defined by its lack of estrogen-, progesterone- and HER2/neu expression. Since these are the operative receptors for targeted breast cancer therapies, current standard treatment instead centers on conventional cytotoxic chemotherapy. Unfortunately, the majority of triple negative breast cancer patients does not have meaningful response, and new therapeutic agents are needed. The PI3K/Akt/mTOR axis is often dysregulated in breast cancer, and clinical trials are ongoing for several inhibitors targeting this pathway. Differential analysis of the global proteome and phosphoproteome of BKM120-treated responsive and resistant tumors may identify markers, patterns and pathways associated with clinical response to support precision therapy. MATERIALS AND METHODS: We collected tumor material from triple negative breast cancer xenografts propagated in the mammary fat pads of NOD SCID mice after BKM120 treatment. Long term (∼30 days) treatment was performed to assess growth rates and sensitivity to the drug. For mass spectrometry analyses, tumor material from 6 different mouse models across 5 treatment conditions was lysed and digested into peptides. Samples were labeled with TMT6-plex reagents, and analyzed together with one reference sample in a total of 6 TMT6-plex experiments. To increase proteome coverage, sample complexity was reduced using high-pH reversed-phase separation, and phospho-peptides were enriched using immobilized metal affinity chromatography. All samples were analyzed on a Q Exactive mass spectrometer. RESULTS AND DATA ANALYSES: Cumulatively, >19,000 proteins were identified, with an average of >10,000 proteins and >21,000 phosphosites per sample. The 6 mice showed a continuum of response to the drug from highly sensitive to highly resistant. Pearson correlation analysis was used to identify proteins and phosphosites that correlate to this response gradient, while moderate t-tests were used to identify commonly regulated markers. Preliminary analyses indicate several interesting proteins and phospho-sites, some pertaining to the PI3K/Akt pathway. Further canonical pathways were detected using Gene Set Enrichment Analysis on a sample-by sample basis and additional network and pathway analyses were performed using the network analysis program GeNets, as well as Ingenuity Pathway Analysis. Citation Format: Filip O. Mundt*, Cynthia Ma*, Philipp Mertins, Zhanfang Guo, Matthew Meyer, Jana Qiao, DR Mani, Karl Clauser, Shunqiang Li, Kuan Huang, Jason Held, Sherri Davies, Kelly Ruggles, Li Ding, Michael Gillette, David Fenyo, Reid Townsend, Matthew Ellis, Steven A. Carr. Effects of PI3K/Akt pathway inhibition on global proteome levels and phosphorylation signaling in patient-derived xenograft models of triple negative breast cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C200.

SUMMARY Deciphering the signaling networks that underlie normal and disease processes remains a major challenge. Here, we report the discovery of signaling components involved in the Toll-like receptor (TLR) response of immune dendritic cells (DCs), including a previously unkown pathway shared across mammalian antiviral responses. By combining transcriptional profiling, genetic and small-molecule perturbations, and phosphoproteomics, we uncover 35 signaling regulators, including 16 known regulators, involved in TLR signaling. In particular, we find that Polo-like kinases (Plk) 2 and 4 are essential components of antiviral pathways in vitro and in vivo and activate a signaling branch involving a dozen proteins, among which is Tnfaip2, a gene associated with autoimmune diseases but whose role was unknown. Our study illustrates the power of combining systematic measurements and perturbations to elucidate complex signaling circuits and discover potential therapeutic targets.

Using the cloned Saccharomyces cerevisiae YPT1 gene as hybridization probe, a gene, designated ypt2, was isolated from the fission yeast Schizosaccharomyces pombe and found to encode a 200 amino acid long protein most closely related to the ypt branch of the ras superfamily. Disruption of the ypt2 gene is lethal. The bacterially produced ypt2 gene product is shown to bind GTP. A region of the ypt2 protein corresponding to but different from the 'effector region' of ras proteins is also different from that of ypt1 proteins of different species but identical to the 'effector loop' of the S.cerevisiae SEC4 gene product, a protein known to be required for vesicular protein transport. The S.pombe ypt2 gene under control of the S.cerevisiae GAL10 promoter is able to suppress the temperature-sensitive phenotype of a S. cerevisiae sec4 mutant, indicating a functional similarity of these GTP-binding proteins from the two very distantly related yeasts.

The genetic landscape of human breast cancer has been well defined in The Cancer Genome Atlas (TCGA) project. Mass spectrometry (MS)-based global proteome and phosphoproteome analyses may provide an orthogonal approach to genomic studies to further improve the molecular taxonomy and our understanding of breast cancer. Central questions in breast cancer biology that will be addressed in this study are: (1) Which genomic characteristics are executed at the protein level? (2) How is the molecular taxonomy of breast cancer reinforced and revised by protein and phosphorylation data? and (3) What phosphorylation-driven signaling networks emerge from genetic alterations? We analyzed human breast cancer samples that have been previously genetically characterized by the TCGA project. Tumor samples were analyzed by global shotgun-proteomics and phosphoproteomics using iTRAQ4-plex peptide labeling. All mass spectrometry data was acquired using nearly 5,000 h of measurement time on a Q Exactive instrument and the data was analyzed in Spectrum Mill using patient-specific RNA-sequencing derived protein databases. In total we quantified >16,000 proteins and >70,000 phosphorylation sites, with an average of >12,000 quantified proteins and >20,000 phosphorylation-sites for each tumor. Only 1-2% of all 9,600 genetically encoded somatic single amino acid variants and 1-2% of 36,000 alternative splice junctions were detected at the protein level despite the very comprehensive proteome coverage obtained. While the global mRNA protein abundance correlation was rather low (Spearman's correlation of 0.4), we found very good correlation for most protein kinase gene amplifications for mRNA, protein and phosphoprotein abundance. Hierarchical clustering analysis of both the proteome and the phosphoproteome data yielded an overlapping set of three major clusters: a basal-enriched, a luminal-enriched and a normal-inclusive group. The two most recurrently mutated genes in human breast cancer are PIK3CA and TP53 at frequencies of 30-40%. Comparison of PIK3CA or TP53 mutated vs non-mutated tumors highlights specific phosphorylation signaling events downstream of mutated PI3-kinase and increased phosphorylation of cell cycle check point kinases in p53-mutated tumors. Network and pathway analysis is being performed to comprehensively integrate genetic and phospho-/proteomic alterations in one model. The effects observed in human tumors will be compared to a set of 24 patient-derived xenograft tumors that will allow drug efficacy studies in fully genetically characterized tumors in the future. Citation Format: Philipp Mertins, DR Mani, Karl Clauser, Michael Gillette, Pei Wang, Jana Qiao, David Fenyo, Kelly Ruggles, Sherri Davies, Bing Zhang, Michael Gatza, Sean Wang, Ping Yan, Chenwei Lin, Michael McLellan, Reid Townsend, Li Ding, Song Cao, Henry Rodriguez, Amanda Paulovich, Matthew Ellis, Steven A. Carr, Clinical Proteomics Tumor Analysis Consortium: CPTAC. Proteogenomic and phosphoproteomic analysis of breast cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr SY44-02. doi:10.1158/1538-7445.AM2015-SY44-02

The tumor suppressor Deleted in Liver Cancer 1 (DLC1) is frequently down-regulated in various human cancers, including breast, prostate, liver, and non-small cell lung cancer (NSCLC). Although the tumor suppressor function of DLC1 depends on its Rho-GAP (GTPase activating protein) activity, which converts Rho from the active GTP-bound form to the inactive GDP-bound form, the mechanisms regulating this activity are poorly understood. Here we determined that CDK5, a predominantly cytoplasmic serine/threonine kinase, negatively regulates Rho-GTP in normal and transformed cells that express DLC1, and that this regulation is attributable to the ability of CDK5 to activate DLC1. We found that CDK5, phosphorylates four serine residues (S120, S205, S422, S509) in the N-terminal region of DLC1, which reduces the binding of the N-terminus to the Rho-GAP domain. The phosphorylation of these serine residues stimulate the tumor suppressor activity of DLC1 - as determined by anchorage-independent growth and tumor xenograft formation - by increasing its Rho-GAP activity and facilitating its binding of several ligands. Serine-to-alanine mutations of the 4 serines increased binding between the DLC1 N-terminus and its Rho-GAP domain, resulting in a mutant protein that lacked these activities. We infer that the N-terminus of DLC1 functions as an auto-inhibitory domain that binds the Rho-GAP domain, and that phosphorylation of the N-terminal 4 serines by CDK5 reduces this interaction, activateing the Rho-GAP and tumor suppressor activities of DLC1. Interestingly, in NSCLC, the expression of CDK5, which has numerous targets, can be associated with a poor prognosis, suggesting that its activity in NSCLC might select for down-regulation of DLC1. Consistent with this hypothesis, we found that siRNA knock-down of endogenous DLC1 in a NSCLC line greatly increased the ability of CDK5 to stimulate neoplastic growth of the line. We also found, in a publicly available tumor database, that poorly differentiated NSCLC is much more likely to express high levels of CDK5 mRNA together with low levels of DLC1 mRNA than is well differentiated NSCLC. Thus, we have identified negative Rho regulation as a new function for CDK5, found DLC1 is the key target for this regulation, elucidated a CDK5-dependent post-translational modification for activating DLC1, and demonstrated the relevance of these observations to NSCLC. Citation Format: Brajendra K. Tripathi, Xiaolan Qian, Philipp Mertins, Dunrui Wang, Alex Papageorge, Steven Carr, Douglas R. Lowy. CDK5 negatively regulates Rho by phosphorylating and activating the Rho-GAP and tumor suppressor functions of DLC1. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1574. doi:10.1158/1538-7445.AM2014-1574

Type-1 diabetes (T1D) is an autoimmune disease in which insulin-secreting pancreatic beta cells are destroyed by the immune system. An emerging strategy to regenerate beta-cell mass is through transdifferentiation of pancreatic alpha cells to beta cells. We previously reported two small molecules, BRD7389 and GW8510, that induce insulin expression in a mouse alpha cell line and provide a glimpse into potential intermediate cell states in beta-cell reprogramming from alpha cells. These small-molecule studies suggested that inhibition of kinases in particular may induce the expression of several beta-cell markers in alpha cells. To identify potential lineage reprogramming protein targets, we compared the transcriptome, proteome, and phosphoproteome of alpha cells, beta cells, and compound-treated alpha cells. Our phosphoproteomic analysis indicated that two kinases, BRSK1 and CAMKK2, exhibit decreased phosphorylation in beta cells compared to alpha cells, and in compound-treated alpha cells compared to DMSO-treated alpha cells. Knock-down of these kinases in alpha cells resulted in expression of key beta-cell markers. These results provide evidence that perturbation of the kinome may be important for lineage reprogramming of alpha cells to beta cells., Juvenile Diabetes Research Foundation International (JDRF 17-2008-1030), Juvenile Diabetes Research Foundation International (JDRF 17-2011-260), Harvard University. Society of Fellows

The ERBB2 receptor tyrosine kinase gene is frequently amplified and mutated in human cancer. However, mutations characterized to date have been located in the kinase domain of the receptor. Using publically-available sequencing datasets, we have found that extracellular domain mutations of ERBB2 located beneath the dimerization arm recur in lung, breast, and ovarian cancers. We expressed cDNAs harboring these mutations in NIH-3T3 cells and found that the mutants support anchorage-independent proliferation. We furthermore found that substitution of any one of a number of amino acids in this region of the protein is oncogenic. We sought to biochemically characterize the extracellular domain mutations of ERBB2 and found that they cause oncogenic transformation by one of two mechanisms: elevation of C-terminal tail phosphorylation, or reduction-sensitive covalent dimerization unaccompanied by increases in C-terminal phosphorylation. Analysis of tyrosine phosphorylated proteins in the cell by stable isotope labeling followed by mass spectrometry (SILAC) revealed that both classes of mutant receptor phosphorylated the same set of proteins to effect transformation. The most prominent targets were proteins involved in cytoskeletal and membrane dynamics, controlling cell motility. STAT3 was also phosphorylated to a limited extent in ERBB2-transformed cells. Interestingly, STAT3 phosphorylation was mediated solely by a JAK-dependent autocrine loop in cells transformed by the ERBB2 mutants activated by reduction-sensitive dimerization; whereas both ERBB2 and JAK family kinases contributed to STAT3 phosphorylation in cells transformed by ERBB2 mutants exhibiting increased C-terminal phosphorylation. In order to characterize inhibitor sensitivity, we transformed Ba/F3 cells to IL-3 independence with the ERBB2 extracellular domain mutants. All extracellular domain mutants tested were sensitive to irreversible inhibitors of ERBB2, suggesting that treatment with such inhibitors may benefit patients harboring mutations of the extracellular domain of ERBB2. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1. doi:1538-7445.AM2012-1

Chromatin regulators play important roles in the safeguarding of cell identities by opposing the induction of ectopic cell fates and, thereby, preventing forced conversion of cell identities by reprogramming approaches. Our knowledge of chromatin regulators acting as reprogramming barriers in living organisms needs improvement as most studies use tissue culture. We used Caenorhabditis elegans as an in vivo gene discovery model and automated solid-phase RNA interference screening, by which we identified 10 chromatin-regulating factors that protect cells against ectopic fate induction. Specifically, the chromodomain protein MRG-1 safeguards germ cells against conversion into neurons. MRG-1 is the ortholog of mammalian MRG15 (MORF-related gene on chromosome 15) and is required during germline development in C. elegans. However, MRG-1’s function as a barrier for germ cell reprogramming has not been revealed previously. Here, we further provide protein-protein and genome interactions of MRG-1 to characterize its molecular functions. Conserved chromatin regulators may have similar functions in higher organisms, and therefore, understanding cell fate protection in C. elegans may also help to facilitate reprogramming of human cells.

Despite advances in multi-modal treatment approaches, clinical outcomes of patients suffering from PAX3-FOXO1 fusion oncogene-expressing alveolar rhabdomyosarcoma (ARMS) remain dismal. Here we show that PAX3-FOXO1-expressing ARMS cells are sensitive to pharmacological ataxia telangiectasia and Rad3 related protein (ATR) inhibition. Expression of PAX3-FOXO1 in muscle progenitor cells is not only sufficient to increase sensitivity to ATR inhibition, but PAX3-FOXO1-expressing rhabdomyosarcoma cells also exhibit increased sensitivity to structurally diverse inhibitors of ATR. Mechanistically, ATR inhibition leads to replication stress exacerbation, decreased BRCA1 phosphorylation and reduced homologous recombination-mediated DNA repair pathway activity. Consequently, ATR inhibitor treatment increases sensitivity of ARMS cells to PARP1 inhibition in vitro, and combined treatment with ATR and PARP1 inhibitors induces complete regression of primary patient-derived ARMS xenografts in vivo. Lastly, a genome-wide CRISPR activation screen (CRISPRa) in combination with transcriptional analyses of ATR inhibitor resistant ARMS cells identifies the RAS-MAPK pathway and its targets, the FOS gene family, as inducers of resistance to ATR inhibition. Our findings provide a rationale for upcoming biomarker-driven clinical trials of ATR inhibitors in patients suffering from ARMS.

Neutrophils provide a critical line of defense in immune responses to various pathogens, inflicting self-damage upon transition to a hyperactivated, procoagulant state. Recent work has highlighted proinflammatory neutrophil phenotypes contributing to lung injury and acute respiratory distress syndrome (ARDS) in patients with coronavirus disease 2019 (COVID-19). Here, we use state-of-the art mass spectrometry-based proteomics and transcriptomic and correlative analyses as well as functional in vitro and in vivo studies to dissect how neutrophils contribute to the progression to severe COVID-19. We identify a reinforcing loop of both systemic and neutrophil intrinsic IL-8 (CXCL8/IL-8) dysregulation, which initiates and perpetuates neutrophil-driven immunopathology. This positive feedback loop of systemic and neutrophil autocrine IL-8 production leads to an activated, prothrombotic neutrophil phenotype characterized by degranulation and neutrophil extracellular trap (NET) formation. In severe COVID-19, neutrophils directly initiate the coagulation and complement cascade, highlighting a link to the immunothrombotic state observed in these patients. Targeting the IL-8-CXCR-1/-2 axis interferes with this vicious cycle and attenuates neutrophil activation, degranulation, NETosis, and IL-8 release. Finally, we show that blocking IL-8-like signaling reduces severe acute respiratory distress syndrome of coronavirus 2 (SARS-CoV-2) spike protein-induced, human ACE2-dependent pulmonary microthrombosis in mice. In summary, our data provide comprehensive insights into the activation mechanisms of neutrophils in COVID-19 and uncover a self-sustaining neutrophil-IL-8 axis as a promising therapeutic target in severe SARS-CoV-2 infection.

Diffuse midline glioma is the leading cause of solid cancer-related deaths in children with very limited treatment options. A majority of the tumors carry a point mutation in the histone 3 variant (H3.3) creating a potential HLA-A*02:01 binding epitope (H3.3K27M26-35). Here, we isolated an H3.3K27M-specific T cell receptor (TCR) from transgenic mice expressing a diverse human TCR repertoire. Despite a high functional avidity of H3.3K27M-specific T cells, we were not able to achieve recognition of cells naturally expressing the H3.3K27M mutation, even when overexpressed as a transgene. Similar results were obtained with T cells expressing the published TCR 1H5 against the same epitope. CRISPR/Cas9 editing was used to exclude interference by endogenous TCRs in donor T cells. Overall, our data provide strong evidence that the H3.3K27M mutation is not a suitable target for cancer immunotherapy, most likely due to insufficient epitope processing and/or amount to be recognized by HLA-A*02:01 restricted CD8+T cells.