Eyk, Jennifer E. Van

e12601 Background: Mammography remains the standard modality for breast cancer (BC) screening but has several limitations. There is a critical need for minimally invasive markers that can aid in distinguishing benign, non-invasive lesions from those likely to progress to invasive BC. Platelets are nature’s transport mechanism for delivery of growth factors and inhibitors. Assaying the platelet proteome, Hessian Labs developed HeLP (Hessian Labs Personalized) test designed to identify early malignancy, as well as its grade, and invasiveness. The test is based on a discovery that platelets sequester oncogenic regulators against a concentration gradient in plasma early in tumor development. Hence, it has the potential to differentiate benign from invasive BC at various stages, stratifying the need for intervention. Methods: Platelet samples from 120 women with BC were analyzed using a discovery data-independent acquisition mass spectrometry (DIA-MS). The identified differentially expressed platelet-associated proteins, were prioritized using ClariaIQ , a proprietary computational platform that ranks proteins based on their relevance to stage-specific oncogenic pathways and established Cancer Hallmarks, to identify stage- and grade-associated proteomic signatures and create the HeLP panel. Results: DIA-MS identified multiple platelet sequestered proteins that were differentially expressed between indolent disease and invasive BC. ClariaIQ prioritization resulted in the selection of 13 proteins for inclusion in the HeLP breast cancer assay. We present two examples: SAA1 and SERPIN proteins demonstrated differential expression between healthy, benign breast lesions and malignant invasive disease (Table 1). SAA1 peaks in early BC and SERPIN in advanced stages. With SAA1, in HER negative BC the levels rise to an average of 285,000 RE units when compared to HER2 positive BC. Conclusions: Platelet sequestered protein signatures provide clinically relevant information regarding breast cancer status, grade, and invasiveness. The findings support the robustness of the signal, and a more patient-specific signature than traditional plasma or serum biomarkers. It suggests a role for HeLP as a minimally invasive adjunct to mammography to improve diagnostic stratification and therapeutic decision-making. Disease Group SAA1 Mean (RE) SAA1 SD (RE) SERPIN A3 Mean (RE) SERPIN A3 SD (RE) Healthy Controls 119,592 206,349 490,231 279,017 Benign Breast Lesions 622,187 50,855 341,102 153,144 Stage I Breast Cancer 1,223,865 1,878,654 742,409 466,468 Stage II Breast Cancer 663,369 1,970,265 922,381 844,512 Stage III Breast Cancer 437,853 662,211 705,994 597,399 Stage IV Breast Cancer 225,265 384,826 1,068,874 1,415,934 RE=Relative Expression units. N=20 subjects included in each group.

Abstract Primary liver cancers, including hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), arise from the neoplastic transformation of hepatocytes and cholangiocytes, respectively. Loss or downregulation of PTEN, a tumor suppressor negatively regulating the PI3K/AKT pathway, is frequently observed in CCA and HCC. Notably, PTEN mutations are observed at nearly twice the frequency in combined CCA-HCC tumors than either HCC or CCA alone. Using lineage-specific liver-targeted PTEN-deficient mouse models, we demonstrate that PTEN loss drives cellular dedifferentiation and tumorigenesis, a process that is critically dependent on AKT2. Mechanistically, PTEN deficiency induces activation of NOTCH and upregulation of transcriptional factor SOX9, which plays a central role in tumor cell transformation. In parallel, PTEN loss increases SMAD4 expression and sensitizes the tumor cells to TGFβ signaling, with TGFβ treatment repressing SOX9 expression in tumor cells lacking PTEN. Together, our study defined a critical role for PTEN-AKT2 signaling in maintaining liver epithelial lineage fidelity and revealed how its disruption promotes the conversion of mature hepatocytes or cholangiocytes into liver cancer stem-like cells (LCSCs). Furthermore, we identify a PTEN-dependent crosstalk between NOTCH and TGFβ pathways that governs liver tumor development. Together, this work provides mechanistic insight into lineage plasticity in liver cancer with implications for pathway-directed therapy.

AbstractBACKGROUNDFor many years, basic and clinical researchers have taken advantage of the analytical sensitivity and specificity afforded by mass spectrometry in the measurement of proteins. Clinical laboratories are now beginning to deploy these work flows as well. For assays that use proteolysis to generate peptides for protein quantification and characterization, synthetic stable isotope–labeled internal standard peptides are of central importance. No general recommendations are currently available surrounding the use of peptides in protein mass spectrometric assays.CONTENTThe Clinical Proteomic Tumor Analysis Consortium of the National Cancer Institute has collaborated with clinical laboratorians, peptide manufacturers, metrologists, representatives of the pharmaceutical industry, and other professionals to develop a consensus set of recommendations for peptide procurement, characterization, storage, and handling, as well as approaches to the interpretation of the data generated by mass spectrometric protein assays. Additionally, the importance of carefully characterized reference materials—in particular, peptide standards for the improved concordance of amino acid analysis methods across the industry—is highlighted. The alignment of practices around the use of peptides and the transparency of sample preparation protocols should allow for the harmonization of peptide and protein quantification in research and clinical care.

Ischemic preconditioning is characterized by resistance to ischemia reperfusion injury in response to previous short ischemic episodes, a protective effect that can be mimicked pharmacologically. The underlying mechanism of protection remains controversial and requires greater understanding before it can be fully exploited therapeutically. To investigate the overall effect of preconditioning on the myocardial proteome, isolated rabbit ventricular myocytes were treated with drugs known to induce preconditioning, adenosine or diazoxide (each at 100 μmol/L for 60 minutes). Their protein profiles were then compared with vehicle-treated controls (n=4 animals per treatment) using a multitiered 2D gel electrophoresis approach. Of 28 significantly altered protein spots, 19 nonredundant proteins were identified (5 spots remained unidentified). The majority of these proteins are involved in mitochondrial energetics, including subunits of tricarboxylic acid cycle enzymes and oxidative phosphorylation complexes. These changes were not indiscriminate, with only a small number of enzymes or complex subunits altered, indicating a very specific and targeted affect of these 2 preconditioning mimetics. Among the changes were shifts in the extent of posttranslational modification of 4 proteins. One of these, the adenosine-induced phosphorylation of the ATP synthase β subunit, was fully characterized with the identification of 5 novel phosphorylation sites. This proteomics approach provides an overall assessment of the cellular response to pharmacological treatment with adenosine and diazoxide and identifies a distinct subset of enzymes and protein complex subunit that may underlie the preconditioned phenotype.