Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes

BACKGROUND

RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the composition of tissues and reveal cells that influence key functions in both healthy and disease tissues. However, the use of these technologies is operationally challenging because of high costs and stringent sample-collection requirements. Computational deconvolution methods that infer the composition of bulk-profiled samples using scnRNA-seq-characterized cell types can broaden scnRNA-seq applications, but their effectiveness remains controversial.

RESULTS

We produced the first systematic evaluation of deconvolution methods on datasets with either known or scnRNA-seq-estimated compositions. Our analyses revealed biases that are common to scnRNA-seq 10X Genomics assays and illustrated the importance of accurate and properly controlled data preprocessing and method selection and optimization. Moreover, our results suggested that concurrent RNA-seq and scnRNA-seq profiles can help improve the accuracy of both scnRNA-seq preprocessing and the deconvolution methods that employ them. Indeed, our proposed method, Single-cell RNA Quantity Informed Deconvolution (SQUID), which combines RNA-seq transformation and dampened weighted least-squares deconvolution approaches, consistently outperformed other methods in predicting the composition of cell mixtures and tissue samples.

CONCLUSIONS

We showed that analysis of concurrent RNA-seq and scnRNA-seq profiles with SQUID can produce accurate cell-type abundance estimates and that this accuracy improvement was necessary for identifying outcomes-predictive cancer cell subclones in pediatric acute myeloid leukemia and neuroblastoma datasets. These results suggest that deconvolution accuracy improvements are vital to enabling its applications in the life sciences.

Targeted AURKA degradation: Towards new therapeutic agents for neuroblastoma

Aurora kinase A (AURKA) is a well-established target in neuroblastoma (NB) due to both its catalytic functions during mitosis and its kinase-independent functions, including stabilization of the key oncoprotein MYCN. We present a structure-activity relationship (SAR) study of MK-5108-derived PROTACs against AURKA by exploring different linker lengths and exit vectors on the thalidomide moiety. PROTAC SK2188 induces the most potent AURKA degradation (DC_50,24h 3.9 nM, D_max,24h 89%) and shows an excellent binding and degradation selectivity profile. Treatment of NGP neuroblastoma cells with SK2188 induced concomitant MYCN degradation, high replication stress/DNA damage levels and apoptosis. Moreover, SK2188 significantly outperforms the parent inhibitor MK-5108 in a cell proliferation screen and patient-derived organoids. Furthermore, altering the attachment point of the PEG linker to the 5-position of thalidomide allowed us to identify a potent AURKA degrader with a linker as short as 2 PEG units. With this, our SAR-study provides interesting lead structures for further optimization and validation of AURKA degradation as a potential therapeutic strategy in neuroblastoma.

Learning from COVID-19: The inclusion of vulnerable groups in COVID-19 responses across Europe

Background

More than two years into the pandemic, many European countries have begun to evaluate their COVID-19 public health responses and draw lessons for future preparedness. As the COVID-19 crisis has exacerbated intersectional social and health inequalities, it is pertinent to evaluate the extent to which COVID-19 responses have successfully responded to the diverse needs of various vulnerable groups. We present a comparative analysis of how evaluations of European COVID-19 responses have assessed efforts to adapt or tailor COVID-19 responses to vulnerable groups, focusing on public testing and tracing strategies and vaccination campaigns.

Methods

We draw on data collected in the H2020 project COVINFORM. We combine insights from qualitative interviews conducted with public health policy- and decision makers in COVINFORM partner countries with a document review of available evaluations of COVID-19 responses published by both government and academic actors between March 2020 and June 2022.

Results

Across countries, evaluations of COVID-19 responses show that efforts to adapt or target public health responses to specific vulnerable groups became more common as the pandemic stretched on. Differences across countries were observed in relation to which groups were considered particularly vulnerable; the types of responses considered successful; as well as the organisational/governmental level at which responses were coordinated. Analyses reveal that the heavy emphasis on medical vulnerability distracted from efforts to address broader, structural inequalities, complicating the development of tailor-made policies.

Conclusions

The results inform ongoing policies that deal with the long-term consequences of the COVID-19 pandemic and aim to reduce disproportionate impacts faced by vulnerable groups. Our findings also add to a better understanding of how future preparedness structures should take into account how pandemic measures have unequal impacts.

Key messages

• As the COVID-19 crisis has exacerbated intersectional social and health inequalities, it is important to learn from efforts to adapt or tailor COVID-19 responses to vulnerable groups.

• The findings demonstrate how across Europe, the combination of particular sets of country-specific COVID-19 responses, tailor-made or not, yield specific consequences for vulnerable groups.

RRM2 enhances MYCN-driven neuroblastoma formation and acts as a synergistic target with CHK1 inhibition

High-risk neuroblastoma, a pediatric tumor originating from the sympathetic nervous system, has a low mutation load but highly recurrent somatic DNA copy number variants. Previously, segmental gains and/or amplifications allowed identification of drivers for neuroblastoma development. Using this approach, combined with gene dosage impact on expression and survival, we identified ribonucleotide reductase subunit M2 (RRM2) as a candidate dependency factor further supported by growth inhibition upon in vitro knockdown and accelerated tumor formation in a neuroblastoma zebrafish model coexpressing human RRM2 with MYCN. Forced RRM2 induction alleviates excessive replicative stress induced by CHK1 inhibition, while high RRM2 expression in human neuroblastomas correlates with high CHK1 activity. MYCN-driven zebrafish tumors with RRM2 co-overexpression exhibit differentially expressed DNA repair genes in keeping with enhanced ATR-CHK1 signaling activity. In vitro, RRM2 inhibition enhances intrinsic replication stress checkpoint addiction. Last, combinatorial RRM2-CHK1 inhibition acts synergistic in high-risk neuroblastoma cell lines and patient-derived xenograft models, illustrating the therapeutic potential.

Orally bioavailable CDK9/2 inhibitor shows mechanism-based therapeutic potential in MYCN-driven neuroblastoma

The undruggable nature of oncogenic Myc transcription factors poses a therapeutic challenge in neuroblastoma, a pediatric cancer in which MYCN amplification is strongly associated with unfavorable outcome. Here, we show that CYC065 (fadraciclib), a clinical inhibitor of CDK9 and CDK2, selectively targeted MYCN-amplified neuroblastoma via multiple mechanisms. CDK9 - a component of the transcription elongation complex P-TEFb - bound to the MYCN-amplicon superenhancer, and its inhibition resulted in selective loss of nascent MYCN transcription. MYCN loss led to growth arrest, sensitizing cells for apoptosis following CDK2 inhibition. In MYCN-amplified neuroblastoma, MYCN invaded active enhancers, driving a transcriptionally encoded adrenergic gene expression program that was selectively reversed by CYC065. MYCN overexpression in mesenchymal neuroblastoma was sufficient to induce adrenergic identity and sensitize cells to CYC065. CYC065, used together with temozolomide, a reference therapy for relapsed neuroblastoma, caused long-term suppression of neuroblastoma growth in vivo, highlighting the clinical potential of CDK9/2 inhibition in the treatment of MYCN-amplified neuroblastoma.

Phenotypic profiling with a living biobank of primary rhabdomyosarcoma unravels disease heterogeneity and AKT sensitivity

Cancer therapy is currently shifting from broadly used cytotoxic drugs to patient-specific precision therapies. Druggable driver oncogenes, identified by molecular analyses, are present in only a subset of patients. Functional profiling of primary tumor cells could circumvent these limitations, but suitable platforms are unavailable for most cancer entities. Here, we describe an in vitro drug profiling platform for rhabdomyosarcoma (RMS), using a living biobank composed of twenty RMS patient-derived xenografts (PDX) for high-throughput drug testing. Optimized in vitro conditions preserve phenotypic and molecular characteristics of primary PDX cells and are compatible with propagation of cells directly isolated from patient tumors. Besides a heterogeneous spectrum of responses of largely patient-specific vulnerabilities, profiling with a large drug library reveals a strong sensitivity towards AKT inhibitors in a subgroup of RMS. Overall, our study highlights the feasibility of in vitro drug profiling of primary RMS for patient-specific treatment selection in a co-clinical setting.

Patient-specific precision medicine approaches are important for future cancer therapies. Here, the authors show that functional drug profiling with Rhabdomyosarcoma cells isolated from PDX and primary patient tumors uncovers patient-specific vulnerabilities.

Accelerating drug development for neuroblastoma: Summary of the Second Neuroblastoma Drug Development Strategy forum from Innovative Therapies for Children with Cancer and International Society of Paediatric Oncology Europe Neuroblastoma

Only one class of targeted agents (anti-GD2 antibodies) has been incorporated into front-line therapy for neuroblastoma since the 1980s. The Neuroblastoma New Drug Development Strategy (NDDS) initiative commenced in 2012 to accelerate the development of new drugs for neuroblastoma. Advances have occurred, with eight of nine high-priority targets being evaluated in paediatric trials including anaplastic lymphoma kinase inhibitors being investigated in front-line, but significant challenges remain. This article reports the conclusions of the second NDDS forum, which expanded across the Atlantic to further develop the initiative. Pre-clinical and clinical data for 40 genetic targets and mechanisms of action were prioritised and drugs were identified for early-phase trials. Strategies to develop drugs targeting TERT, telomere maintenance, ATRX, alternative lengthening of telomeres (ALT), BRIP1 and RRM2 as well as direct targeting of MYCN are high priority and should be championed for drug discovery. Promising pre-clinical data suggest that targeting of ALT by ATM or PARP inhibition may be potential strategies. Drugs targeting CDK2/9, CDK7, ATR and telomere maintenance should enter paediatric clinical development rapidly. Optimising the response to anti-GD2 by combinations with chemotherapy, targeted agents and other immunological targets are crucial. Delivering this strategy in the face of small patient cohorts, genomically defined subpopulations and a large number of permutations of combination trials, demands even greater international collaboration. In conclusion, the NDDS provides an internationally agreed, biologically driven selection of prioritised genetic targets and drugs. Improvements in the strategy for conducting trials in neuroblastoma will accelerate bringing these new drugs more rapidly to front-line therapy.

Abstract A49: Combined targeting of the p53 and pRb pathway in neuroblastoma

Neuroblastomas account for approximately 15% of all childhood cancer deaths. Clinical complete remission is achieved in many stage 4 neuroblastoma patients, but the high risk of relapse and the accompanying treatment-resistant nature of these tumors is still a challenge. We have previously identified higher frequencies of mutations that affect both the p53 and the pRb pathway, such as the homozygous loss of CDKN2A or co-amplification of MDM2 and CDK4. In addition, both cyclin D1 and MDM2 overexpression is a common characteristic of primary neuroblastoma. These genes act upstream of pRb and p53 and hence play a major role in cell cycle regulation. To study whether these G1 checkpoint aberrations render cells more sensitive to CDK4 or MDM2 inhibition, we exposed a series of 11 cell lines to the most promising CDK4 (ribociclib, palbociclib, and abemaciclib) and MDM2 (SAR405838, HDM-201, and idasanutlin) inhibitors. These cell lines have well-defined mutational properties: homozygous CDKN2A deletion, co-amplification of CDK4 and MDM2, TP53 mutation, and MYCN amplification. Whereas sensitivity for the MDM2 inhibitors inversely correlated with TP53 mutation status, it did not correlate to other G1 checkpoint aberrations. Similarly, there was no clear correlation seen for the CDK4 inhibitors. To further explore this, we generated cell lines with inducible overexpression of CDK4, MDM2, or both. The overexpression did indeed not increase sensitivity to CDK4 or MDM2 inhibitors. Next, we were interested whether combined treatment with the most potent CDK4 and MDM2 inhibitors, abemaciclib and idasanutlin respectively, would be of added value. Cells were exposed to 10 different concentrations of both compounds and Bliss Independence values were calculated as a measure of synergy. Interestingly, combined treatment resulted in slight antagonism in the range of clinically relevant doses in most cell lines. This adverse effect was supported by cell cycle analyses, which showed a lower apoptotic fraction, as well as PARP and caspase 3 cleavage, after combined treatment, as opposed to MDM2 inhibition alone. As was previously suggested in the first clinical trials with CDK4 inhibitors, neither CDK4 nor CDKN2A status is a clear biomarker for CDK4 inhibitor sensitivity. Our results suggest that MDM2 and CDKN2A status also fail as biomarkers for MDM2 inhibitor sensitivity. Further testing is necessary to identify (other) biomarkers for these inhibitors. Moreover, the logical rationale to combine CDK4 and MDM2 inhibitors in neuroblastoma patients with both pRb and p53 pathway disturbances should be taken with precaution, as first results do not show a beneficial response. In vivo experiments to confirm this finding are currently ongoing.

Citation Format: Nil Schubert, Linda Schild, Stijn van Oirschot, Kaylee Keller, Lindy Alles, Lindy Vernooij, Marloes Nulle, Emmy Dolman, Marlinde van den Boogaard, Jan Molenaar. Combined targeting of the p53 and pRb pathway in neuroblastoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A49.

Abstract A40: Integration of high-throughput drug screening on patient-derived organdies into pediatric precision medicine programs: The future is now!

Background/Objectives: The most promising option to improve outcomes for pediatric cancer patients with relapsed or refractory disease is through mutation-based targeted therapeutic strategies. However, only 50% of these tumors harbor actionable events. Therefore, compound screening on organoids grown from tumor tissue might reveal additional treatment options.

Design/Methods: The Dutch Childhood Oncology Group-individualized Therapies (DCOG-iTHER) clinical trial in collaboration with INFORM consists of whole-exome sequencing (WES), low-coverage whole-genome sequencing (WGS), RNA profiling using RNAseq and Affymetrix microarrays, and a methylation array. Data are analyzed using the Dutch R2 bioinformatic platform. In addition, tumor-derived organoids are cultured profiled through the same pipeline. Semi-high-throughput screening of a 170-compound library is performed, and effect on cell viability using the CellTiter-Glo® 3D cell viability assay is assessed.

Results: To date, 133 patients with relapsed/refractory pediatric malignancies have been enrolled and analysis has been completed in 80 study subjects. In 47 patients, a total of 128 molecular targets were identified and 29 patients harbored an actionable event with priority score ≥ moderate (46%). In 14% a matched targeted therapy was initiated, and one-third of these patients achieved complete remission. In addition, tumor organoids have been cultured of neuroblastoma tumors and molecular profiling was performed to confirm they reflect the patient’s tumor biology. High-throughput drug screen confirmed existing molecular targets such as ALK and c-kit and in addition revealed increased compound sensitivity to drugs not previously found through sequencing.

Conclusions: Our proof of concept of patient-specific drug testing on tumor organoids within our pediatric precision medicine program might reveal additional treatment options for children who currently have none. Clinical benefit will be evaluated in our upcoming clinical trial iTHER 2.0.

Citation Format: Karin Langenberg, Emmy Dolman, Jan Molenaar. Integration of high-throughput drug screening on patient-derived organdies into pediatric precision medicine programs: The future is now! [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A40.

Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA polymerase

MYC is an oncogenic transcription factor that binds globally to active promoters and promotes transcriptional elongation by RNA polymerase II (RNAPII)^1,2. Deregulated expression of the paralogous protein MYCN drives the development of neuronal and neuroendocrine tumours and is often associated with a particularly poor prognosis³. Here we show that, similar to MYC, activation of MYCN in human neuroblastoma cells induces escape of RNAPII from promoters. If the release of RNAPII from transcriptional pause sites (pause release) fails, MYCN recruits BRCA1 to promoter-proximal regions. Recruitment of BRCA1 prevents MYCN-dependent accumulation of stalled RNAPII and enhances transcriptional activation by MYCN. Mechanistically, BRCA1 stabilizes mRNA decapping complexes and enables MYCN to suppress R-loop formation in promoter-proximal regions. Recruitment of BRCA1 requires the ubiquitin-specific protease USP11, which binds specifically to MYCN when MYCN is dephosphorylated at Thr58. USP11, BRCA1 and MYCN stabilize each other on chromatin, preventing proteasomal turnover of MYCN. Because BRCA1 is highly expressed in neuronal progenitor cells during early development⁴ and MYC is less efficient than MYCN in recruiting BRCA1, our findings indicate that a cell-lineage-specific stress response enables MYCN-driven tumours to cope with deregulated RNAPII function.

Determining minimal output sets that ensure structural identifiability

The process of inferring parameter values from experimental data can be a cumbersome task. In addition, the collection of experimental data can be time consuming and costly. This paper covers both these issues by addressing the following question: “Which experimental outputs should be measured to ensure that unique model parameters can be calculated?”. Stated formally, we examine the topic of minimal output sets that guarantee a model’s structural identifiability. To that end, we introduce an algorithm that guides a researcher as to which model outputs to measure. Our algorithm consists of an iterative structural identifiability analysis and can determine multiple minimal output sets of a model. This choice in different output sets offers researchers flexibility during experimental design. Our method can determine minimal output sets of large differential equation models within short computational times.

Abstract 1925: High-throughput drug library screening identifies potent drugs and novel drug targets for high-risk acute leukemia in children

BACKGROUND: Acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) represent the most common types of cancer among children. Although the survival rates of pediatric ALL and AML have improved substantially over the last decades, the prognosis for some subgroups of pediatric leukemia remain poor. MLL-rearranged infant ALL, MLL-rearranged AML, and NUP98-rearranged AML, for instance, still have 5-year event-free survival rates of only ~40%. Evidently, these high-risk subtypes of childhood leukemia urgently require new treatment strategies in order to improve clinical outcome.

AIM: Identification of effective therapeutic drugs for high-risk leukemia subtypes harboring a translocation in the MLL or NUP98 gene, by using a drug repurposing strategy involving high-throughput screening of > 4000 compounds.

METHODS: Primary leukemic cells derived from six patients with either MLL-rearranged infant ALL, pediatric MLL-rearranged AML, or pediatric NUP98-rearranged AML at diagnosis, were screened using commercially available drug libraries comprising a total of 4165 compounds. Drug sensitivity was assessed after 4 days treatment with 10 nM, 100 nM and 1000 nM of the library compounds using MTT assays. Potential hits were subsequently validated using cytotoxicity assays with a more extensive range of drug concentrations.

RESULTS: The results of our drug screens showed that the most effective drugs, by far, were found for MLL-rearranged infant ALL. For MLL-rearranged AML the number of identified potent drugs was considerably less; notably, all of these compounds identified overlapped with the effective agents also found for MLL-rearranged infant ALL. Remarkably, for NUP98-translocated AML, only a few potential drug hits were identified, suggesting that this type of leukemia might be extremely chemo-resistant.

In addition to novel candidate compounds, we also found several agents either recently described to have strong anti-leukemic effects against MLL-rearranged leukemia, such as the BCL2 inhibitors Venetoclax (ABT199) and Navitoclax (ABT263), or the MDM2 inhibitor Idasanutlin (RG7388), as well as finding drugs currently being used in the treatment of MLL-rearranged acute leukemias. Taken together, these observations indicate that high-throughput drug screening on primary patient samples is indeed able to identify effective compounds, validating our experimental approach.

Interestingly, while validating newly identified drug hits, we observed a remarkable pattern for compounds effective against MLL-rearranged acute leukemia: the top hits seem to either directly or indirectly associate with p53 activity, albeit from various angles.

CONCLUSION: Our data suggests a potential role for p53 in MLL-rearranged acute leukemia, and indicates that targeting p53 may well become an important therapeutic strategy for these types of childhood leukemia.

Citation Format: Priscilla Wander, Sandra S. Pinhanços, Bianca Koopmans, M. Emmy M. Dolman, Pauline Schneider, Patricia Garrido Castro, Luke Jones, Susan T.C.J.M. Arentsen-Peters, Mark Kerstjens, Jan Molenaar, Huib N. Caron, Rob Pieters, Michel C. Zwaan, Ronald W. Stam. High-throughput drug library screening identifies potent drugs and novel drug targets for high-risk acute leukemia in children [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1925.

R0: Host Longevity Matters

The basic reproduction ratio, R₀, is a fundamental concept in epidemiology. It is defined as the total number of secondary infections brought on by a single primary infection, in a totally susceptible population. The value of R₀ indicates whether a starting epidemic reaches a considerable part of the population and causes a lot of damage, or whether it remains restricted to a relatively small number of individuals. To calculate R₀ one has to evaluate an integral that ranges over the duration of the infection of the host. This duration is, of course, limited by remaining host longevity. So, R₀ depends on remaining host longevity and in this paper we show that for long-lived hosts this aspect may not be ignored for long-lasting infections. We investigate in particular how this epidemiological measure of pathogen fitness depends on host longevity. For our analyses we adopt and combine a generic within- and between-host model from the literature. To find the optimal strategy for a pathogen from an evolutionary point of view, we focus on the indicator \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R_0^{{opt}}$$\end{document}R0opt, i.e., the optimum of R₀ as a function of its replication and mutation rates. These are the within-host parameters that the pathogen has at its disposal to optimize its strategy. We show that \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R_0^{{opt}}$$\end{document}R0opt is highly influenced by remaining host longevity in combination with the contact rate between hosts in a susceptible population. In addition, these two parameters determine whether a killer-like or a milker-like strategy is optimal for a given pathogen. In the killer-like strategy the pathogen has a high rate of reproduction within the host in a short time span causing a relatively short disease, whereas in the milker-like strategy the pathogen multiplies relatively slowly, producing a continuous small amount of offspring over time with a small effect on host health. The present research allows for the determination of a bifurcation line in the plane of host longevity versus contact rate that forms the boundary between the milker-like and killer-like regions. This plot shows that for short remaining host longevities the killer-like strategy is optimal, whereas for very long remaining host longevities the milker-like strategy is advantageous. For in-between values of host longevity, the contact rate determines which of both strategies is optimal.

Observability of Complex Systems: Finding the Gap

For a reconstruction of state and parameter values in a dynamic system model, first the question whether these values can be uniquely determined from the data must be answered. This structural model property is known as observability or, in case of parameter calibration only, identifiability. Testing a given model for observability is a well studied problem in the systems and control sciences. However, it is increasingly difficult, if not impossible, to address this property for large size models that, nowadays, are frequently used. We demonstrate the application of a recently developed algorithm that overcomes this problem and is remarkably efficient. As an illustration we show how an observability analysis for a Chinese Hamster Ovary Cell model (34 states, 117 parameters), a JAKSTAT signalling model (31 states, 51 parameters), and a MAP Kinase model (100 states, 88 parameters) can be established in a very short time.

Accelerating drug development for neuroblastoma - New Drug Development Strategy: an Innovative Therapies for Children with Cancer, European Network for Cancer Research in Children and Adolescents and International Society of Paediatric Oncology Europe Neuroblastoma project

INTRODUCTION

Neuroblastoma, the commonest paediatric extra-cranial tumour, remains a leading cause of death from cancer in children. There is an urgent need to develop new drugs to improve cure rates and reduce long-term toxicity and to incorporate molecularly targeted therapies into treatment. Many potential drugs are becoming available, but have to be prioritised for clinical trials due to the relatively small numbers of patients. Areas covered: The current drug development model has been slow, associated with significant attrition, and few new drugs have been developed for neuroblastoma. The Neuroblastoma New Drug Development Strategy (NDDS) has: 1) established a group with expertise in drug development; 2) prioritised targets and drugs according to tumour biology (target expression, dependency, pre-clinical data; potential combinations; biomarkers), identifying as priority targets ALK, MEK, CDK4/6, MDM2, MYCN (druggable by BET bromodomain, aurora kinase, mTORC1/2) BIRC5 and checkpoint kinase 1; 3) promoted clinical trials with target-prioritised drugs. Drugs showing activity can be rapidly transitioned via parallel randomised trials into front-line studies. Expert opinion: The Neuroblastoma NDDS is based on the premise that optimal drug development is reliant on knowledge of tumour biology and prioritisation. This approach will accelerate neuroblastoma drug development and other poor prognosis childhood malignancies.

Polo-like Kinase Inhibitor Volasertib Exhibits Antitumor Activity and Synergy with Vincristine in Pediatric Malignancies

BACKGROUND

Polo-like kinase 1 (PLK1) controls the main cell-cycle checkpoints, suggesting utility of its inhibition for cancer treatment, including of highly proliferative pediatric cancer. This preclinical study explored the selective PLK1 inhibitor volasertib (BI 6727) alone and combined with chemotherapy in pediatric malignancies.

MATERIALS AND METHODS

Inhibition of proliferation was explored in vitro using dimethylthiazol carboxymethoxyphenyl sulfophenyl tetrazolium (MTS) assay. Mice bearing human xenografts were treated with weekly intravenous injections of volasertib.

RESULTS

Volasertib inhibited proliferation in all 40 cell lines tested, with a mean half-maximal growth inhibitory concentration of 313 nmol/l (range: 4-5000 nmol/l). Volasertib was highly active against RMS-1 alveolar rhabdomyosarcoma xenografts, resulting in 100% tumor regression. Activity was associated with complete and prolonged G2/M arrest and subsequent apoptotic cell death. Volasertib showed synergistic activity with vincristine but antagonistic effects with etoposide.

CONCLUSION

These findings support the further exploration of volasertib for pediatric malignancies, particularly alveolar rhabdomyosarcoma, and its combination with mitotic spindle poison.

Phase segregation through transient network formation in a binary particle suspension in simple shear: application to dough

In this paper we describe a viscoelastic type of phase separation in a simulated binary fluid with a sticky and an inert component, without any external gradients. Phase segregation under simple shear occurs due to transient network formation of the sticky component, expelling the inert particles from the network. When model parameters are adjusted to reduce network formation and rearrangement, the segregation effect is significantly smaller or absent. The behavior is independent of shear rate; segregation increases mainly with shear strain. The model is applied to wheat dough. Recent experiments have shown that prolonged shear flow of wheat dough can even give macroscopic segregation.

Modelling the impact of HIV on the populations of South Africa and Botswana

We develop and use mathematical models that describe changes in the South African population over the last decades, brought on by HIV and AIDS. We do not model all the phases in HIV progression but rather, we show that a relatively simple model is sufficient to represent the data and allows us to investigate important aspects of HIV infection: firstly, we are able to investigate the effect of awareness on the prevalence of HIV and secondly, it enables us to make a comparison between South Africa and Botswana. A comparison is made between two models: a model that does not reflect awareness of the devastating impact of HIV and AIDS, and a model with an added psychological awareness factor. Both models are fitted to data that reflects the incidence of HIV and AIDS within South Africa. This allows us to examine the impact of psychological awareness. We show that inclusion of the effect of awareness is absolutely necessary to arrive at a model description that satisfactorily fits the available HIV and AIDS data for South Africa. We also show that a relatively simple modelling of awareness (as opposed to more complex mathematical techniques that have been used in past studies) is sufficient to accurately describe the observed patterns in the data. Even though awareness alone is not sufficient to eradicate any disease and other control strategies should be explored and implemented concurrently with educational campaigns, we are able to conclude (through thorough model analyses procedures) that the current level of awareness in South Africa is far below the level that is effectively required to eradicate HIV from the South African population. The awareness model is also fitted to HIV-related data for Botswana and we compare the results with the South African case. Though the effect of awareness is currently estimated at a much higher level in Botswana, other factors such as poorer health care and cultural differences may play a role in limiting the ability of awareness to combat HIV in Botswana.

Work satisfaction at a multidisciplinary gastrointestinal oncology fast-track outpatient clinic

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Background: Physician and nurse satisfaction is positively correlated with patient satisfaction. In our university centre we have established the Gastrointestinal Oncology Clinic Amsterdam (GIOCA), a patient centred multidisciplinary one day diagnostics and fast track treatment planning outpatient clinic for gastrointestinal malignancies. The GIOCA team consists of dedicated surgeons, gastroenterologists, medical oncologists, radiation oncologists, radiologists, nuclear radiologists, pathologists, and specialized nurses. We have measured a high patient satisfaction. However to our knowledge there are no studies that focus on the satisfaction of physicians and nurses working within a multidisciplinary team. Our aim was to evaluate the experience and work satisfaction of the physicians and nurses at GIOCA. Methods: A qualitative observational study was performed to compose a questionnaire. This questionnaire was then sent to every physician (specialist, fellow, and resident) and nurse (n=77) working at the outpatient clinic. Answers were given on a 5-point Likert scale. Data were analysed using non-parametric tests. Results: The questionnaire was answered by 73 respondents, of whom 8.2% were nurses and 91.8% were physicians (95% overall response rate). Overall satisfaction with the fast track outpatient clinic was high for all groups (4; 3-5). The workload was experienced as average by physicians and high by nurses (p<0.001). The highest emotional strain was reported by nurses and residents. The emotional strain reported by residents was significantly higher compared to the level of emotional strain reported by specialists (p=0.034). The quality of the multidisciplinary meeting was rated high by both physicians and nurses. The importance of a multidisciplinary one day diagnostics outpatient clinic was invariably rated high to very high by all physicians and nurses. Conclusions: The overall work satisfaction at GIOCA is high. A patient centred one day diagnostics and fast track treatment outpatient clinic for gastrointestinal malignancies is indispensible according to the physicians and nurses. This may have contributed to a high patient satisfaction and a high overall work satisfaction.

Crop management impacts the efficiency of quantitative trait loci (QTL) detection and use: case study of fruit load×QTL interactions

Mapping studies using populations with introgressed marker-defined genomic regions are continuously increasing knowledge about quantitative trait loci (QTL) that correlate with variation in important crop traits. This knowledge is useful for plant breeding, although combining desired traits in one genotype might be complicated by the mode of inheritance and co-localization of QTL with antagonistic effects, and by physiological trade-offs, and feed-back or feed-forward mechanisms. Therefore, integrating advances at the genetic level with insight into influences of environment and crop management on crop performance remains difficult. Whereas mapping studies can pinpoint correlations between QTL and phenotypic traits for specific conditions, ignoring or overlooking the importance of environment or crop management can jeopardize the relevance of such assessments. Here, we focus on fruit load (a measure determining competition among fruits on one plant) and its strong modulation of QTL effects on fruit size and composition. Following an integral approach, we show which fruit traits are affected by fruit load, to which underlying processes these traits can be linked, and which processes at lower and higher integration levels are affected by fruit load (and subsequently influence fruit traits). This opinion paper (i) argues that a mechanistic framework to interpret interactions between fruit load and QTL effects is needed, (ii) pleads for consideration of the context of agronomic management when detecting QTL, (iii) makes a case for incorporating interacting factors in the experimental set-up of QTL mapping studies, and (iv) provides recommendations to improve efficiency in QTL detection and use, with particular focus on model-based marker-assisted breeding.

Abstract 4596: LIN28B drives neuroblastoma oncogenesis through let7-MYCN signaling

LIN28B regulates developmental processes by modulating miRNAs of the let-7 family. A role for LIN28B in cancer has been proposed, but has not been established in vivo. We report LIN28B amplification or overexpression in high risk neuroblastoma. LIN28B repressed let-7 family miRNAs and induced MYCN expression in neuroblastoma cells in vitro. LIN28B-let-7-MYCN signaling induced proliferation and blocked differentiation of normal neuroblasts and neuroblastoma cells. The effect of LIN28B knock-down was rescued by overexpression of let-7-resistant MYCN. To analyse the tumor-initiating capacity and oncogenicity of Lin28b in vivo, mice were generated by knock-in of the CAG-LSL-Lin28b-IRES-Luciferse vector (LSL-Lin28b) into the ROSA26 locus. Crossbreeding these mice with DBH-iCre mice targeted Lin28b expression to the neural crest. Abdominal tumors developed in 7 of 18 DBHiCre;LSL-Lin28b mice at 36-62 days of age. Autopsy revealed uni- or bilateral adrenal tumors in all mice, reflecting the most frequent localization of human NB. Tumors consisted of small round blue cells and expressed the NB markers, DBH, TH and Phox2b. The macroscopic tumor appearance, primary tumor sites, tumor histology and marker gene expression confirmed these tumors as NB. Successful serial transplantation supported that the primary tumors from this model system were fully transformed malignant tumors. Both the Lin28b and MYCN proteins were strongly expressed in all tumors and members of the let-7 miRNA family were significantly downregulated. We demonstrate that overexpressing Lin28b in the neural crest can drive NB tumor formation in mice, supporting LIN28B as an important oncogene for NB and potentially for other malignancies. Therapeutic approaches aimed at inhibiting Lin28b or let-7 family re-expression may be useful therapeutic approaches to circumvent MYCN addiction in NB.

Citation Format: Johannes H. Schulte, Jan Molenaar, Sven Lindner, Alexander Schramm, Pieter Mestdagh, Frank Speleman, Rogier Versteeg, Angelika Eggert. LIN28B drives neuroblastoma oncogenesis through let7-MYCN signaling. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4596. doi:10.1158/1538-7445.AM2013-4596

Fast track multidisciplinary approach for gastrointestinal tumours

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Background: The incidence of gastrointestinal (GI) tract tumours in the Netherlands is rising. However, GI oncological medical care is still delayed and fragmented. There is a need for better and faster diagnostic work-up, faster start of treatment, but also for expert multidisciplinary deliberation. Therefore, the GIOCA, Gastro Intestinal Oncological Centre Amsterdam, started in 2009 as a one day fast track multidisciplinary outpatient clinic for patients with GI malignancies. The goal was an admission time (AT, time from referral to consultation) of < 1 week and a run through time (RTT, time from multidisciplinary meeting to start of treatment) of < 3 weeks. The aim of this study was first to evaluate the AT and RTT at GIOCA and secondly to evaluate the subjective impact of this novel strategy on patients burden and satisfaction. Methods: Patients were seen at GIOCA in the morning on a colorectal (CRC ), an oesophago/gastric (OES) or a hepatopancreaticobiliary (HPB) day. That same morning (additional) diagnostics were performed. At the multidisciplinary meeting afterwards, a final diagnosis and treatment plan was made, which was later communicated to the patient. The patient then met all involved specialists. AT and RTT were prospectively recorded for all GIOCA patients. For HPB malignancies, AT and RTT could be compared to historical controls from the preceding year. Patient impact and satisfaction was evaluated using a before/after cohort study design, with a written questionnaire prospectively administered to all GIOCA patients and compared to data obtained 3 months prior to GIOCA start. Results: Analyses of 2009 and 2010 showed the following results: The average AT for CRC, OES and HPB was 7.6, 9.5 and 9 days respectively. The average RTT for CRC, OES and HPB was 20.8, 24 and 25 days respectively. For HPB malignancies, this was 10.4 days (AT) and 59.8 days (RTT) in the year preceding GIOCA. Higher levels of patient satisfaction were obtained in GIOCA patients compared to controls. More than 90% of the patients interviewed would advice the GIOCA outpatient approach to other patients. Conclusions: Progress has been made in the AT and RTT in GI malignancies in GIOCA, but the goals were still not all reached. Patients were very satisfied with this novel approach.

MYCN and ALKF1174L are sufficient to drive neuroblastoma development from neural crest progenitor cells

Neuroblastoma is an embryonal tumor with a heterogeneous clinical course. The tumor is presumed to be derived from the neural crest, but the cells of origin remain to be determined. To date, few recurrent genetic changes contributing to neuroblastoma formation, such as amplification of the MYCN oncogene and activating mutations of the ALK oncogene, have been identified. The possibility to model neuroblastoma in mice allows investigation of the cell of origin hypothesis in further detail. Here we present the evidence that murine neural crest progenitor cells can give rise to neuroblastoma upon transformation with MYCN or ALK(F1174L). For this purpose we used JoMa1, a multipotent neural crest progenitor cell line, which is kept in a viable and undifferentiated state by a tamoxifen-activated c-Myc transgene (c-MycER(T)). Expression of MYCN or ALK(F1174L), one of the oncogenic ALK variants identified in primary neuroblastomas, enabled these cells to grow independently of c-MycER(T) activity in vitro and caused formation of neuroblastoma-like tumors in vivo in contrast to parental JoMa1 cells and JoMa1 cells-expressing TrkA or GFP. Tumorigenicity was enhanced upon serial transplantation of tumor-derived cells, and tumor cells remained susceptible to the MYC-inhibitor, NBT-272, indicating that cell growth depended on functional MYCN. Our findings support neural crest progenitor cells as the precursor cells of neuroblastoma, and indicate that neuroblastomas arise as their malignant progeny.

Dissection of the oncogenic MYCN transcriptional network reveals a large set of clinically relevant cell cycle genes as drivers of neuroblastoma tumorigenesis

Amplification of the oncogenic transcription factor MYCN plays a major role in the pathogenesis of several pediatric cancers, including neuroblastoma, medulloblastoma, and rhabodomyosarcoma. For neuroblastoma, MYCN amplification is the most powerful genetic predictor of poor patient survival, yet the mechanism by which MYCN drives tumorigenesis is only partially understood. To gain an insight into the distribution of MYCN binding and to identify clinically relevant MYCN target genes, we performed an integrated analysis of MYCN ChIP-chip and mRNA expression using the MYCN repressible SHEP-21N neuroblastoma cell line. We hypothesized that genes exclusively MYCN bound in SHEP-21N cells over-expressing MYCN would be enriched for direct targets which contribute to the process of disease progression. Integrated analysis revealed that MYCN drives tumorigenesis predominantly as a positive regulator of target gene transcription. A high proportion of genes (24%) that are MYCN bound and up-regulated in the SHEP-21N model are significantly associated with poor overall patient survival (OS) in a set of 88 tumors. In contrast, the proportion of genes down-regulated when bound by MYCN in the SHEP-21N model and which are significantly associated with poor overall patient survival when under-expressed in primary tumors was significantly lower (5%). Gene ontology analysis determined a highly statistically significant enrichment for cell cycle related genes within the over-expressed MYCN target group which were also associated with poor OS. We conclude that the over-expression of MYCN leads to aberrant binding and over-expression of genes associated with cell cycle regulation which are significantly correlated with poor OS and MYCN amplification.

Flow-induced correlation effects within a linear chain in a polymer melt

A framework for a consistent description of the flow-induced correlation effects within a linear polymer chain in a melt is proposed. The formalism shows how correlations between chain segments in the flow can be incorporated into a hierarchy of distribution functions for tangent vectors. The present model allows one to take into account all the major relaxation mechanisms. Special cases of the derived set of equations are shown to yield existing models and shed some light on the connection between them. Consequences of several assumptions widely used in the literature are analyzed within the developed framework.

A molecular model for cohesive slip at polymer melt/solid interfaces

A molecular model is proposed which predicts wall slip by disentanglement of polymer chains adsorbed on a wall from those in the polymer bulk. The dynamics of the near-wall boundary layer is found to be governed by a nonlinear equation of motion, which accounts for such mechanisms on surface chains as convection, retraction, constraint release, and thermal fluctuations. This equation is valid over a wide range of grafting regimes, including those in which interactions between neighboring adsorbed molecules become essential. It is not closed since the dynamics of adsorbed chains is shown to be coupled to that of polymer chains in the bulk via constraint release. The constitutive equations for the layer and bulk, together with continuity of stress and velocity, are found to form a closed system of equations which governs the dynamics of the whole "bulk+boundary layer" ensemble. Its solution provides a stick-slip law in terms of the molecular parameters and extruder geometry. The model is quantitative and contains only those parameters that can be measured directly, or extracted from independent rheological measurements. The model predictions show a good agreement with available experimental data.

Prediction of survival in patients with head and neck cancer

BACKGROUND

In patients with head and neck squamous cell carcinoma (HNSCC) the estimated prognosis is usually based on the TNM classification. The relative weight of the three contributing parameters is often not completely clear. Moreover, the impact of other important clinical variables such as age, gender, prior malignancies, etc is very difficult to substantiate in daily clinical practice. The Cox-regression model allows us to estimate the effect of different variables simultaneously. The purpose of this study was to design a model for application in new HNSCC patients. In our historical data-base of patients with HNSCC, patient, treatment, and follow-up data are stored by trained oncological data managers. With these hospital-based data, we developed a statistical model for risk assessment and prediction of overall survival. This model serves in clinical decision making and appropriate counseling of patients with HNSCC.

PATIENTS AND METHODS

All patients with HNSCC of the oral cavity, the pharynx, and the larynx diagnosed in our hospital between 1981 and 1998 were included. In these 1396 patients, the prognostic value of site of the primary tumor, age at diagnosis, gender, T-, N-, and M-stage, and prior malignancies were studied univariately by Kaplan-Meier curves and the log-rank test. The Cox-regression model was used to investigate the effect of these variables simultaneously on overall survival and to develop a prediction model for individual patients.

RESULTS

In the univariate analyses, all variables except gender contributed significantly to overall survival. Their contribution remained significant in the multivariate Cox model. Based on the relative risks and the baseline survival curve, the expected survival for a new HNSCC patient can be calculated.

CONCLUSIONS

It is possible to predict survival probabilities in a new patient with HNSCC based on historical results from a data-set analyzed with the Cox-regression model. The model is supplied with hospital-based data. Our model can be extended by other prognostic factors such as co-morbidity, histological data, molecular biology markers, etc. The results of the Cox-regression may be used in patient counseling, clinical decision making, and quality maintenance.

Grazing impact oscillations

An impact oscillator is a periodically driven system that hits a wall when its amplitude exceeds a critical value. We study impact oscillations where collisions with the wall are with near-zero velocity (grazing impacts). A characteristic feature of grazing impact dynamics is a geometrically converging series of transitions from a nonimpacting period-1 orbit to period-M orbits that impact once per period with M=1,2,ellipsis. In an experiment we explore the dynamics in the vicinity of these period-adding transitions. The experiment is a mechanical impact oscillator with a precisely controlled driving strength. Although the excitation of many high-order harmonics in the experiment appeared unavoidable, we characterize it with only three parameters. Despite the simplicity of this description, good agreement with numerical simulations of an impacting harmonic oscillator was found. Grazing impact dynamics can be described by mappings that have a square-root singularity. We evaluate several mappings, both for instantaneous impacts and for impacts that involve soft collisions with a yielding wall. As the square-root singularity appears persistent in the reduction of the dynamics to mappings, and because impact dynamics appears insensitive to experimental nonidealities, the characteristic bifurcation scenario should be observed in a wide class of experimental systems.