Protein Profiling of Breast Carcinomas Reveals Expression of Immune-Suppressive Factors and Signatures Relevant for Patient Outcome

In cancer, the complex interplay between tumor cells and the tumor microenvironment results in the modulation of signaling processes. By assessing the expression of a multitude of proteins and protein variants in cancer tissue, wide-ranging information on signaling pathway activation and the status of the immunological landscape is obtainable and may provide viable information on the treatment response. Archived breast cancer tissues from a cohort of 84 patients (no adjuvant therapy) were analyzed by high-throughput Western blotting, and the expression of 150 proteins covering central cancer pathways and immune cell markers was examined. By assessing CD8α, CD11c, CD16 and CD68 expression, immune cell infiltration was determined and revealed a strong correlation between event-free patient survival and the infiltration of immune cells. The presence of tumor-infiltrating lymphocytes was linked to the pronounced activation of the Jak/Stat signaling pathway and apoptotic processes. The elevated phosphorylation of PPARγ (pS112) in non-immune-infiltrated tumors suggests a novel immune evasion mechanism in breast cancer characterized by increased PPARγ phosphorylation. Multiplexed immune cell marker assessment and the protein profiling of tumor tissue provide functional signaling data facilitating breast cancer patient stratification.

Glycosphingolipids are mediators of cancer plasticity through independent signaling pathways

The molecular repertoire promoting cancer cell plasticity is not fully elucidated. Here, we propose that glycosphingolipids (GSLs), specifically the globo and ganglio series, correlate and promote the transition between epithelial and mesenchymal cells. The epithelial character of ovarian cancer remains stable throughout disease progression, and spatial glycosphingolipidomics reveals elevated globosides in the tumor compartment compared with the ganglioside-rich stroma. CRISPR-Cas9 knockin mediated truncation of endogenous E-cadherin induces epithelial-to-mesenchymal transition (EMT) and decreases globosides. The transcriptomics analysis identifies the ganglioside-synthesizing enzyme ST8SIA1 to be consistently elevated in mesenchymal-like samples, predicting poor outcome. Subsequent deletion of ST8SIA1 induces epithelial cell features through mTOR^S2448 phosphorylation, whereas loss of globosides in ΔA4GALT cells, resulting in EMT, is accompanied by increased ERK^Y202/T204 and AKT^S124. The GSL composition dynamics corroborate cancer cell plasticity, and further evidence suggests that mesenchymal cells are maintained through ganglioside-dependent, calcium-mediated mechanisms.

Cell Type-Specific Anti-Adhesion Properties of Peritoneal Cell Treatment with Plasma-Activated Media (PAM)

Postoperative abdominal adhesions are responsible for serious clinical disorders. Administration of plasma-activated media (PAM) to cell type-specific modulated proliferation and protein biosynthesis is a promising therapeutic strategy to prevent pathological cell responses in the context of wound healing disorders. We analyzed PAM as a therapeutic option based on cell type-specific anti-adhesive responses. Primary human peritoneal fibroblasts and mesothelial cells were isolated, characterized and exposed to different PAM dosages. Cell type-specific PAM effects on different cell components were identified by contact- and marker-independent Raman imaging, followed by thorough validation by specific molecular biological methods. The investigation revealed cell type-specific molecular responses after PAM treatment, including significant cell growth retardation in peritoneal fibroblasts due to transient DNA damage, cell cycle arrest and apoptosis. We identified a therapeutic dose window wherein specifically pro-adhesive peritoneal fibroblasts were targeted, whereas peritoneal mesothelial cells retained their anti-adhesive potential of epithelial wound closure. Finally, we demonstrate that PAM treatment of peritoneal fibroblasts reduced the expression and secretion of pro-adhesive cytokines and extracellular matrix proteins. Altogether, we provide insights into biochemical PAM mechanisms which lead to cell type-specific pro-therapeutic cell responses. This may open the door for the prevention of pro-adhesive clinical disorders.

Multiplexed Serum Antibody Screening Platform Using Virus Extracts from Endemic Coronaviridae and SARS-CoV-2

The presence of antibodies against endemic coronaviruses has been linked to disease severity after SARS-CoV-2 infection. Assays capable of concomitantly detecting antibodies against endemic coronaviridae such as OC43, 229E, NL63, and SARS-CoV-2 may help to elucidate this question. We developed a serum screening platform using a bead-based Western blot system called DigiWest, capable of running hundreds of assays using microgram amounts of protein prepared directly from different viruses. Characterization of the immunoassay for detection of SARS-CoV-2 specific antibodies revealed a sensitivity of 90.3% and a diagnostic specificity of 98.1%. Concordance analysis with the SARS-CoV-2 immunoassays available by Roche, Siemens, and Euroimmun indicates comparable assay performances (Cohen's κ ranging from 0.8874 to 0.9508). Analogous assays for OC43, 229E, and NL63 were established and combined into one multiplex with the SARS-CoV-2 assay. Seroreactivity for different coronaviruses was detected with high incidence, and the multiplex assay was adapted for serum screening.

Abstract PS17-42: A fast and effective 3D preclinical assay system comprised of patient derived breast cancer microtumors combined with DigiWest protein signaling pathway analyses for therapeutic response prediction (Project PRIMO)

In the era of personalized medicine, the ability of pre-selecting individualized therapeutic options and pre-defining their suitability in advance of clinical treatment might facilitate decision making in breast cancer treatment and hence, improve patient outcome. In order to preclinically validate anti-cancer drug efficacy, it is crucial to design a model system that reveals the influence of cellular interactions of the tumor microenvironment and cellular heterogeneity on drug response. Within the PRIMO (Personalized Medicine for tailored cancer therapies) project, such a 3D preclinical model system comprised of patient-derived microtumors (PDM) and autologous tumor-infiltrating lymphocytes (TILs) isolated from fresh primary breast cancer tissue using limited digestion and subsequent culture in defined media in the absence of serum is established. Herein, the heterogeneous cellular composition of isolated PDM is analyzed by FFPE immunohistochemistry and compared to corresponding primary tumor tissue. The composition of autologous TILs influencing individual treatment responses is characterized by multi-color flow cytometry detecting different cell populations, such as tumor-specific CD8+ or regulatory CD4+ T-cells. By using the DigiWest technology, a proprietary high throughput immune assay screening tool, in-depth protein profiling of up to 200 analytes from low amounts of PDM material is performed. The generated protein profiles of PDM are compared to their corresponding primary tumor tissue as well as the pathological receptor grading. Furthermore, differences in activation of key signal transduction pathways are detected and related to treatment responses to small molecules, chemotherapeutics as well as immunotherapeutic agents within PDM and PDM-TIL co-cultures assessed by a functional viability assay in a microplate format. To expand this preclinical model system, we established PDM-co-cultures adding further immune cell types including natural killer (NK) cells or dendritic cells (DC).

In summary, immunohistochemical analyses combined with protein profiling of breast cancer PDM enables drug-mode-of-action analyses, biomarker identification together with personalized therapeutic sensitivity prediction. The platform presented here expands the preclinical repertoire of relevant test systems for efficacy testing of drugs and investigational compounds, pre-identified by protein pathways as well as genetic profiling in personalized medicine of breast cancer.

Citation Format: Nicole Anderle, Felix Ruoff, Simge Yuez, André Koch, Andreas Hartkopf, Sara Brucker, Michael Pawlak, Markus Templin, Christian Schmees. A fast and effective 3D preclinical assay system comprised of patient derived breast cancer microtumors combined with DigiWest protein signaling pathway analyses for therapeutic response prediction (Project PRIMO) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS17-42.

Abstract 1915: Intrinsic and acquired trastuzumab resistance pathways in breast cancer cell lines using DigiWest® phospho-protein profiling

Introduction

The widespread clinical use of monoclonal antibodies such as trastuzumab in personalized medicine, targeting upstream proteins such as receptors with cascading effects on downstream signaling, elicits the importance of studying the phosphoproteome in the investigation of resistance to targeted therapy. This study sought to differentiate between the complex mechanisms of intrinsic and acquired trastuzumab resistance, by quantifying changes in expression and activity of proteins in key signal transduction pathways, in cellular models of resistance.

Method

DigiWest®, a Luminex® xMAP® bead-based high-throughput protein profiling method, was utilized to measure 194 proteins and phospho-proteins from 12µg of total protein, obtained from HER2-positive cell lines which were trastuzumab-sensitive (SKBR3), intrinsically resistant (JIMT-1, UACC-893) and with acquired resistance (T15, obtained by long-term culture of SKBR3 in 15µg/mL trastuzumab). The resulting median fluorescence intensities (MFI) were normalized to total protein content. Relative quantification was done against SKBR3 and a log2 fold-change of ±1 was considered to be significant. For each of the three trastuzumab-resistant cell lines, targets which were differentially expressed were organized into established signal transduction pathways, and specific phosphosite expression values were used to determine whether each protein was under- or over-activated.

Results

A total of 115 proteins were expressed in at least one of the HER2-positive cell lines at a normalized MFI above the set threshold. JIMT-1 showed the most concurrent resistance mechanisms, including PI3K/Akt and RAS/RAF/MEK/ERK activation, β-catenin stabilization, cell cycle progression by Rb suppression, and CREB-mediated cell survival. MAPK (ERK) pathway activation was common to both intrinsic and acquired resistance – it was over-activated in all the three trastuzumab-resistant cell lines. The overexpression of upstream RAS, however, was confined to the intrinsically resistant cell lines JIMT-1 and UACC-893; meanwhile, in T15, entry into the ERK pathway was mostly mediated by pan-PKC overexpression. PKCs, especially PKCα, were also highly activated in UACC-893. β-catenin stabilization was another mechanism observed only in the intrinsically trastuzumab-resistant cell lines.

Conclusion

Both distinct and overlapping mechanisms are involved in intrinsic and acquired trastuzumab resistance. Multiple pathways can also co-exist to promote cell survival, as was mostly exemplified by JIMT-1, derived from an aggressive, basal-like tumor. Furthermore, different models of intrinsic resistance (JIMT-1 vs UACC-893) showed significant differences in differentially activated signal transduction pathways. DigiWest® provided a simple and robust multiplexing solution for this phospho-proteomic study.

Citation Format: Jeanesse Scerri, Felix Ruoff, Markus Templin, Godfrey Grech, Christian Scerri. Intrinsic and acquired trastuzumab resistance pathways in breast cancer cell lines using DigiWest® phospho-protein profiling [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 1915.