Abstract 4266: Proteomics for precision oncology: Profiling the proteome of matching tumor and adjacent normal tissue using data-independent acquisition

Precision oncology requires a deep understanding of the molecular mechanism in cancer biology. The predominant approach today focuses on genome structure and gene expression data, which have become available with the rise of next-gen sequencing technology. On a phenotypic level, however, protein expression and activation are arguably more directly related to cellular function. The availability of combined genome and proteome level data from the same tumor is therefore expected to provide a much more complete picture of a tumor in a particular state. Until recently, proteomics technology could not match the scale of next-gen sequencing and consequently, precision medicine research has almost exclusively been based on gene-level data. Here we show the first truly large-scale data set for protein expression and protein phosphorylation for a large collection of biospecimens derived from the IndivuType cohort of Indivumed, Germany. Matching fresh-frozen tumor and adjacent normal tissue samples from thousands of patients including various cancer entities were obtained from Indivumed's network of partner hospitals Enabled by the novel data-independent acquisition (DIA) workflow, a mass spectrometric method that obtains peptide fragmentation data in a highly parallelized way with high reproducibility and sensitivity, more than 7,000 proteins in the whole proteome (WP) and 20,000 phospho-peptides in the phospho-proteome (PP) workflow were analyzed. Sample processing from 5 mg of tissue per sample was performed on 96-well plates with the help of a liquid handling robot. Phospho-peptide enrichment was carried out using a Kingfisher Flex device and MagReSyn Ti-IMAC magnetic beads (ReSyn Biosciences). Data-independent acquisition (DIA) LC-MS/MS was performed on multiple platforms consisting of a Thermo Scientific Q Exactive HF-X mass spectrometer coupled to a Waters M-Class LC. Chromatography was operating at 5 µL/min, and separation was achieved using 45 min (WP) and 60 min (PP) gradients. With a throughput of 850 WP and 650 PP samples per month, thousands of samples were analyzed to date. The resulting proteome data is integrated into Indivumed's IndivuType multi-omics database, supporting the identification and validation of new molecular cancer drug targets and biomarkers.

Citation Format: Jakob Vowinckel, Karel Novy, Thomas Corwin, Tobias Treiber, Roland Bruderer, Lukas Reiter, Eike von Leitner, Oliver Rinner, Claudia Escher. Proteomics for precision oncology: Profiling the proteome of matching tumor and adjacent normal tissue using data-independent acquisition [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4266.

Multi-omic based molecular profiling of advanced cancer identifies treatable targets and improves survival in individual patients

A proof-of-concept study was conducted to assess whether patients with advanced stage IV cancer for whom predominantly no standard therapy was available could benefit from comprehensive molecular profiling of their tumor tissue to provide targeted therapy. Tumor samples of 83 patients were collected under highly standardized conditions and analyzed using immunohistochemistry, next-generation sequencing and phosphoprotein profiling. Expression and phosphorylation of key oncogenic pathways were measured to identify targets at the (phospho-) proteomic level. At genomic level, 50 oncogenes and tumor suppressor genes were analyzed. Based on molecular profiling, targeted therapies were decided by the attending oncologist. Accordingly, 28 patients who met the defined criteria fell in two equal-sized groups. One group received targeted therapies while the other did not. Following six months of treatment, disease control was achieved by 49% of patients receiving targeted therapy (complete remission, 14%; partial remission, 21%; stable disease, 14%; disease progression, 36%; death, 14%) and 21% of patients receiving non-targeted therapy (stable disease, 21%; disease progression, 64%; death, 14%). Individual patients experienced dramatic responses to a therapy which otherwise would not have been applied. This approach clarifies the value of multi-omic molecular profiling for cancer diagnostics.

Follow-up after coronary arterial reperfusion with intravenous streptokinase in relation to residual myocardial infarct artery narrowings

Short- and long-term changes in residual stenosis of the myocardial infarct-related coronary arteries in patients with successful reperfusion by intravenous streptokinase have not been determined until now. In 15 patients the residual diameter stenosis decreased significantly from 62 +/- 9% after 24 hours to 55 +/- 13% in the fourth week (p less than 0.005). Quantitative angiographic analyses in 61 patients with patent infarct-related coronary arteries in the fourth week revealed a mean diameter stenosis of 61 +/- 13%. The patients were followed up 34 +/- 10 months. Sixteen had elective coronary artery bypass surgery or percutaneous transluminal coronary angioplasty (PTCA). Eighteen without coronary artery bypass surgery or PTCA had undergone repeat angiography after 26 +/- 9 months. Twenty-five (41%) have had a residual diameter stenosis greater than 65% in the fourth week. A stenosis greater than 65% was found in: 4 of 5 patients with late reinfarction; 3 of 7 with 1-vessel coronary artery disease and persistent angina, compared with none of 11 with a stenosis less than 65%; 6 of 7, whose silent reocclusion had been found at long-term follow-up compared with 1 of 9 with a residual stenosis less than 65%. In 8 patients with persistent patency of the infarct artery, the stenosis had decreased significantly from 55 +/- 6% to 36 +/- 12% (p less than 0.005). Correspondingly, there was a significant improvement in the infarct-related left ventricular wall motion disorders.(ABSTRACT TRUNCATED AT 250 WORDS)