Tumour kinome re-wiring governs resistance to palbociclib in oestrogen receptor positive breast cancers, highlighting new therapeutic modalities.

Combination of CDK4/6 inhibitors and endocrine therapy improves clinical outcome in advanced oestrogen receptor (ER)-positive breast cancer, however relapse is inevitable. Here, we show in model systems that other than loss of RB1 few gene-copy number (CN) alterations are associated with irreversible-resistance to endocrine therapy and subsequent secondary resistance to palbociclib. Resistance to palbociclib occurred as a result of tumour cell re-wiring leading to increased expression of EGFR, MAPK, CDK4, CDK2, CDK7, CCNE1 and CCNE2. Resistance altered the ER genome wide-binding pattern, leading to decreased expression of 'classical' oestrogen-regulated genes and was accompanied by reduced sensitivity to fulvestrant and tamoxifen. Persistent CDK4 blockade decreased phosphorylation of tuberous sclerosis complex 2 (TSC2) enhancing EGFR signalling, leading to the re-wiring of ER. Kinome-knockdown confirmed dependency on ERBB-signalling and G2/M-checkpoint proteins such as WEE1, together with the cell cycle master regulator, CDK7. Noteworthy, sensitivity to CDK7 inhibition was associated with loss of ER and RB1 CN. Overall, we show that resistance to CDK4/6 inhibitors is dependent on kinase re-wiring and the redeployment of signalling cascades previously associated with endocrine resistance and highlights new therapeutic networks that can be exploited upon relapse after CDK4/6 inhibition

Investigating molecular factors regulating cancer biology : from proteomics to multi-omics

Recent technological advances in studying proteins using mass spectrometry (MS-based proteomics) have empowered in-depth profiling of the human proteome, such that MS-based proteomics can nowadays identify disease-specific proteins indicative of a particular cancer, and highlight molecular pathways associated with both sensitivity and resistance to drugs. However, in order to obtain a clearer picture of cancer biology, integrating information from multiple “-omic” data types such as genomics, transcriptomics, proteomics, metabolomics as well as different imaging techniques is considered vital. This thesis explores the application of multi-omics to study molecular mechanisms involved in the onset of cancer and drug resistance in several cancer models. From studying colorectal cancer, breast cancer and liposarcoma, the author demonstrates the benefits and challenges of integrating omics datatypes, which can assist in reaching the ultimate goal of improved therapeutic response in patients. To facilitate their data integration approaches, the author also developed a Python library named PaDuA for (phospho)proteomics analysis which provides a collection of tools that enable semi-automated data processing, filtering and statistical analysis. The ease with which PaDuA simplifies reproducibility and sharing of omics data strongly supports the standardization of analysis methods which is a recommended necessity for subsequent multi-omics data integration

PaDuA : a Python library for high-throughput (phospho)proteomic data analysis

The increased speed and sensitivity in mass spectrometry-based proteomics has encouraged its use in biomedical research in recent years. Large-scale detection of proteins in cells, tissues and whole organisms yields highly-complex quantitative data, the analysis of which poses significant challenges. Standardized proteomic workflows are necessary to ensure automated, sharable and reproducible proteomics analysis. Likewise, standardized data processing workflows are also essential for the overall reproducibility of results. To this purpose, we developed PaDuA, a Python package optimized for the processing and analysis of (phospho)proteomics data. PaDuA provides a collection of tools which can be used to build scripted workflows within Jupyter Notebooks, to facilitate bioinformatics analysis by both end-users and developers

Innovative strategies for measuring kinase activity to accelerate the next wave of novel kinase inhibitors

The development of protein kinase inhibitors (PKIs) has gained significance owing to their therapeutic potential for diseases like cancer. In addition, there has been a rise in refining kinase activity assays, each possessing unique biological and analytical characteristics crucial for PKI development. However, the PKI development pipeline experiences high attrition rates and approved PKIs exhibit unexploited potential because of variable patient responses. Enhancing PKI development efficiency involves addressing challenges related to understanding the PKI mechanism of action and employing biomarkers for precision medicine. Selecting appropriate kinase activity assays for these challenges can overcome these attrition rate issues. This review delves into the current obstacles in kinase inhibitor development and elucidates kinase activity assays that can provide solutions

Novel kinome profiling technology reveals drug treatment is patient and 2D/3D model dependent in glioblastoma

Glioblastoma is the deadliest brain cancer. One of the main reasons for poor outcome resides in therapy resistance, which adds additional challenges in finding an effective treatment. Small protein kinase inhibitors are molecules that have become widely studied for cancer treatments, including glioblastoma. However, none of these drugs have demonstrated a therapeutic activity or brought more benefit compared to the current standard procedure in clinical trials. Hence, understanding the reasons of the limited efficacy and drug resistance is valuable to develop more effective strategies toward the future. To gain novel insights into the method of action and drug resistance in glioblastoma, we established in parallel two patient-derived glioblastoma 2D and 3D organotypic multicellular spheroids models, and exposed them to a prolonged treatment of three weeks with temozolomide or either the two small protein kinase inhibitors enzastaurin and imatinib. We coupled the phenotypic evidence of cytotoxicity, proliferation, and migration to a novel kinase activity profiling platform (QuantaKinome™) that measured the activities of the intracellular network of kinases affected by the drug treatments. The results revealed a heterogeneous inter-patient phenotypic and molecular response to the different drugs. In general, small differences in kinase activation were observed, suggesting an intrinsic low influence of the drugs to the fundamental cellular processes like proliferation and migration. The pathway analysis indicated that many of the endogenously detected kinases were associated with the ErbB signaling pathway. We showed the intertumoral variability in drug responses, both in terms of efficacy and resistance, indicating the importance of pursuing a more personalized approach. In addition, we observed the influence derived from the application of 2D or 3D models in in vitro studies of kinases involved in the ErbB signaling pathway. We identified in one 3D sample a new resistance mechanism derived from imatinib treatment that results in a more invasive behavior. The present study applied a new approach to detect unique and specific drug effects associated with pathways in in vitro screening of compounds, to foster future drug development strategies for clinical research in glioblastoma

Bio-Engineering tissue and V.A.C. therapy: A new method for the treatment of extensive necrotizing infection in the diabetic foot

AIM: The aim of the study is to compare the standard care for progressive necrotizing infection in diabetic foot with a treatment protocol based on the association between autologous fibroblast grafts and vacuum-assisted closure therapy (V.A.C.). MATERIAL OF STUDY: A retrospective matched Case-Control study was carried out on 20 patients with diabetic foot infection, 10 treated with the standard care and 10 with our new protocol. Inclusion criteria were: acute diabetic foot necrosis (Wagner III and IV), ulcer size (30 to 80 cm2), tendon and bone exposure. Success in the treatment was evaluated as: percentage of healing at the 20th week, time of healing, deambulation, recurrence and major amputation rate. RESULTS: A 90% healing rate was observed after 20 weeks in the study group, compared to a 28.6% in the control group. The recurrence rate in the treated areas was 20% in the study group and 100% in the control group. None of the patients in either group required major amputations. DISCUSSION: We achieved very promising results by associating autologous fibroblasts grafts and V.A.C. therapy, in comparison with standard care. V.A.C. therapy seems to improve the growth rate of the fibroblasts, probably by sealing the wound and providing a moist environment following the fibroblast graft. The improved neoangiogenesis of the neo-dermis could explain the reduced recurrence rate of the study group. CONCLUSIONS: Despite the low number of patients involved and the retrospective nature of the analysis, this study showed a reliable, safe and cost-effective method of treating extensive infection in the diabetic foot

Predicting treatment outcome using kinome activity profiling in HER2+ breast cancer biopsies

Summary: In this study, we measured the kinase activity profiles of 32 pre-treatment tumor biopsies of HER2-positive breast cancer patients. The aim of this study was to assess the prognostic potential of kinase activity levels, to identify potential mechanisms of resistance and to predict treatment success of HER2-targeted therapy combined with chemotherapy. Indeed, our system-wide kinase activity analysis allowed us to link kinase activity to treatment response. Overall, high kinase activity in the HER2-pathway was associated with good treatment outcome. We found eleven kinases differentially regulated between treatment outcome groups, including well-known players in therapy resistance, such as p38a, ERK, and FAK, and an unreported one, namely MARK1. Lastly, we defined an optimal signature of four kinases in a multiple logistic regression diagnostic test for prediction of treatment outcome (AUC = 0.926). This kinase signature showed high sensitivity and specificity, indicating its potential as predictive biomarker for treatment success of HER2-targeted therapy

Anaplastic large-cell periprosthetic lymphoma of the breast: could fibrin be an early radiological indicator of the presence of disease?

The onset characteristics of the anaplastic large cell lymphoma (BI-ALCL) are non-specific and the diagnosis is often difficult and based on clinical suspicion and cytological sampling. The presence of non-pathognomonic radiological signs may delay the diagnosis of BI-ALCL, influencing patient prognosis. This could have an important social impact, considering that the incidence of BI-ALCL correlates with the number of prosthetic implants, which is in constant increase worldwide. The aim of this study was to verify if fibrin can represent a potential early radiological sign of the disease