Epigenetic reprogramming of pancreatic cancer cells as a new therapeutic option

Large-scale gene expression analyses have demonstrated that pancreatic ductal adenocarcinoma can be classified into different molecular subtypes with clinical significance (Collisson et al., 2011, Moffitt et al., 2016, Bailey et al., 2016). So far, great effort has been put into unveiling the factors responsible for tumor heterogeneity in pancreatic cancer. Since epigenetic modifiers are, besides the four driver gene mutations KRAS, p16, p53, and SMAD4, among the most frequently mutated genes in PDAC, this study aimed at investigating the role of epigenetic changes in the two molecular PDAC cancer subtypes, represented by a classical and basal phenotype, as well as their therapeutic potential in pancreatic cancer cell lines (Bailey et al., 2016). The data showed that subtype-specific gene expression of cellular differentiation marker genes, such as EpCAM and GATA6, is epigenetically regulated. Chromatin-immunoprecipitation results demonstrated that the expression of these epithelial differentiation marker genes is activated through histone acetylation marks in the classical subtype. In contrast, their expression is repressed in the basal or quasimesenchymal subtype through increased levels of histone ubiquitination as well as a loss of histone acetylation marks. DNA methylation seemed to only play a minor part in regulating subtype-specific gene expression profiles of EpCAM and GATA6. Despite subtype-specific histone acetylation levels, single-drug treatment with chemical inhibitors targeting histone acetylation and deacetylation marks only showed limited effects in vitro. Classical and basal PDAC cell lines were almost completely resistant to HAT inhibitor treatment with A485. Only one of the basal cell lines, MIAPaca-2, reached a 50 % survival rate at the maximum dosage of 10 µM A485 (see Figure 12A, left panel). High doses of the HDAC inhibitor Vorinostat were able to inhibit cell survival to a greater extent, but the response was independent of the transcriptomic subtypes. It is possible that a compensatory upregulation of other epigenetic modifications limits the therapeutic effects. Hence, a multiplex CRISPR/Cas9 knockout plasmid targeting a combination of epigenetic modifiers (HDAC2, DNMT3A, RING1B) was constructed to induce simultaneous genetic knockout of all three target genes. However, transfection of a basal pancreatic cancer cell line with this plasmid did not yield a successful knockout cell line. Most likely, the combinatory knockout impaired critical cellular functions to such an extent that cell death occurred. To overcome the limitations of a multiplex CRISPR/Cas9 knockout strategy, a successive knockout of one target gene after the other might be a more successful strategy to analyze the effect of a combinatory loss of different epigenetic modifiers. Furthermore, a selection marker should be included in the plasmids to ensure successful transfection. The generated knockout cell line can then be used for transcriptome analysis by RNA sequencing as well as for basic cell assays and drug sensitivity tests. In order to translate preclinical data with epigenetic inhibitors into successful clinical trials, further studies are needed to determine subtype-specific changes after epigenetic targeting. For instance, unpublished data within the working group showed that HAT inhibitor treatment of cell lines with a classical PDAC subtype strongly downregulated the expression of GATA6 and decreased Gemcitabine drug sensitivity indicating a poorer outcome. These results emphasize the importance of establishing patient stratification systems in order to maximize the success of current treatment strategies. Overall, this thesis showed that the transcriptomic profiles defining molecular PDAC subtypes are in part regulated through epigenetic modifications. Although the targeting of single epigenetic modifiers showed some success in tumor cell reprogramming, the therapeutic targeting with epigenetic drugs remains limited. Thus, the precise effects of combination therapies with multiple epigenetic inhibitors need further investigation

Evaluation of parameterized quantum circuits: on the relation between classification accuracy, expressibility, and entangling capability

An active area of investigation in the search for quantum advantage is quantum machine learning. Quantum machine learning, and parameterized quantum circuits in a hybrid quantum-classical setup in particular, could bring advancements in accuracy by utilizing the high dimensionality of the Hilbert space as feature space. But is the ability of a quantum circuit to uniformly address the Hilbert space a good indicator of classification accuracy? In our work, we use methods and quantifications from prior art to perform a numerical study in order to evaluate the level of correlation. We find a moderate to strong correlation between the ability of the circuit to uniformly address the Hilbert space and the achieved classification accuracy for circuits that entail a single embedding layer followed by 1 or 2 circuit designs. This is based on our study encompassing 19 circuits in both 1- and 2-layer configurations, evaluated on 9 datasets of increasing difficulty. We also evaluate the correlation between entangling capability and classification accuracy in a similar setup, and find a weak correlation. Future work will focus on evaluating if this holds for different circuit designs

Implementation of neuro-oncology service reconfiguration in accordance with NICE guidance provides enhanced clinical care for patients with glioblastoma multiforme.

BACKGROUND: Brain tumours account for <2% of all primary neoplasms but are responsible for 7% of the years of life lost from cancer before age 70 years. The latest survival trends for patients with CNS malignancies have remained largely static. The objective of this study was to evaluate the change in practice as a result of implementing the Improving Outcomes Guidance from the UK National Institute for Health and Clinical Excellence (NICE). METHODS: Patients were identified from the local cancer registry and hospital databases. We compared time from diagnosis to treatment, proportion of patients discussed at multidisciplinary team (MDT) meetings, treatment received, length of inpatient stay and survival. Inpatient and imaging costs were also estimated. RESULTS: Service reconfiguration and implementation of NICE guidance resulted in significantly more patients being discussed by the MDT--increased from 66 to 87%, reduced emergency admission in favour of elective surgery, reduced median hospital stay from 8 to 4.5 days, increased use of post-operative MRI from 17 to 91% facilitating early discharge and treatment planning, and reduced cost of inpatient stay from £2096 in 2006 to £1316 in 2009. Patients treated with optimal surgery followed by radiotherapy with concomitant and adjuvant temozolomide achieved outcomes comparable to those reported in clinical trials: median overall survival 18 months (2-year survival 35%). CONCLUSIONS: Advancing the management of neuro-oncology patients by moving from an emergency-based system of patient referral and management to a more planned elective outpatient-based pattern of care improves patient experience and has the potential to deliver better outcomes and research opportunities

Topical Application of Activity-based Probes for Visualization of Brain Tumor Tissue

Several investigators have shown the utility of systemically delivered optical imaging probes to image tumors in small animal models of cancer. Here we demonstrate an innovative method for imaging tumors and tumor margins during surgery. Specifically, we show that optical imaging probes topically applied to tumors and surrounding normal tissue rapidly differentiate between tissues. In contrast to systemic delivery of optical imaging probes which label tumors uniformly over time, topical probe application results in rapid and robust probe activation that is detectable as early as 5 minutes following application. Importantly, labeling is primarily associated with peri-tumor spaces. This methodology provides a means for rapid visualization of tumor and potentially infiltrating tumor cells and has potential applications for directed surgical excision of tumor tissues. Furthermore, this technology could find use in surgical resections for any tumors having differential regulation of cysteine cathepsin activity

Tallness is associated with risk of testicular cancer: evidence for the nutrition hypothesis

The pathogenesis of testicular germ cell tumours (GCTs) is potentially influenced by high-energy nutrition during infancy. As adult height is a proxy for childhood nutrition, we investigated the role of nutrition in GCT pathogenesis by comparing stature of patients with healthy men. In a matched case–control study, 6415 patients with GCT were compared with healthy army conscripts (1:6 matching modus) with regard to height (cm) and body mass index (BMI; kg/m2). Statistical analysis involved tabulation of descriptive height measures and BMI. Conditional logistic regression models were used to quantify the association of GCT with height, with odds ratios (OR) adjusted for BMI. The literature was searched for studies on stature in GCT patients. Body size is significantly associated with risk of GCT, very tall men (>195 cm) having a GCT risk of OR=3.35 (95% confidence intervals (CI): 2.88–3.90; adjusted). Short stature is protective (OR=0.798; 95% CI: 0.68–0.93). Both histologic subgroups are associated with tallness. Of 16 previous reports, 7 were confirmative, 5 had null and 4 equivocal results. The association of stature with GCT risk accords with the nutrition hypothesis of GCT. This study expands the current view of GCT tumorigenesis by suggesting that high-calorie intake in childhood promotes GCT precursors originating in utero