Mutational Signatures Driven by Epigenetic Determinants Enable the Stratification of Patients with Gastric Cancer for Therapeutic Intervention

DNA mismatch repair deficiency (dMMR) is associated with the microsatellite instability (MSI) phenotype and leads to increased mutation load, which in turn may impact anti-tumor immune responses and treatment effectiveness. Various mutational signatures directly linked to dMMR have been described for primary cancers. To investigate which mutational signatures are associated with prognosis in gastric cancer, we performed a de novo extraction of mutational signatures in a cohort of 787 patients. We detected three dMMR-related signatures, one of which clearly discriminates tumors with MLH1 gene silencing caused by promoter hypermethylation (area under the curve = 98%). We then demonstrated that samples with the highest exposure of this signature share features related to better prognosis, encompassing clinical and molecular aspects and altered immune infiltrate composition. Overall, the assessment of the prognostic value and of the impact of modifications in MMR-related genes on shaping specific dMMR mutational signatures provides evidence that classification based on mutational signature exposure enables prognosis stratification.

Mapping the Human Kinome in Response to DNA Damage

We provide a catalog for the effects of the human kinome on cell survival in response to DNA-damaging agents, covering all major DNA repair pathways. By treating 313 kinase-deficient cell lines with ten diverse DNA-damaging agents, including seven commonly used chemotherapeutics, we identified examples of vulnerability and resistance that are kinase specific. To investigate synthetic lethal interactions, we tested the response to carmustine for 25 cell lines by establishing a phenotypic fluorescence-activated cell sorting (FACS) assay designed to validate gene-drug interactions. We show apoptosis, cell cycle changes, and DNA damage and proliferation after alkylation- or crosslink-induced damage. In addition, we reconstitute the cellular sensitivity of DYRK4, EPHB6, MARK3, and PNCK as a proof of principle for our study. Furthermore, using global phosphoproteomics on cells lacking MARK3, we provide evidence for its role in the DNA damage response. Our data suggest that cancers with inactivating mutations in kinases, including MARK3, are particularly vulnerable to alkylating chemotherapeutic agents.

Genome-scale CRISPR screens are efficient in non-homologous end-joining deficient cells

The mutagenic repair of Cas9 generated breaks is thought to predominantly rely on non-homologous end-joining (NHEJ), leading to insertions and deletions within DNA that culminate in gene knock-out (KO). In this study, by taking focused as well as genome-wide approaches, we show that this pathway is dispensable for the repair of such lesions. Genetic ablation of NHEJ is fully compensated for by alternative end joining (alt-EJ), in a POLQ-dependent manner, resulting in a distinct repair signature with larger deletions that may be exploited for large-scale genome editing. Moreover, we show that cells deficient for both NHEJ and alt-EJ were still able to repair CRISPR-mediated DNA double-strand breaks, highlighting how little is yet known about the mechanisms of CRISPR-based genome editing.

Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48

Defects in DNA repair can cause various genetic diseases with severe pathological phenotypes. Fanconi anemia (FA) is a rare disease characterized by bone marrow failure, developmental abnormalities, and increased cancer risk that is caused by defective repair of DNA interstrand crosslinks (ICLs). Here, we identify the deubiquitylating enzyme USP48 as synthetic viable for FA-gene deficiencies by performing genome-wide loss-of-function screens across a panel of human haploid isogenic FA-defective cells (FANCA, FANCC, FANCG, FANCI, FANCD2). Thus, as compared to FA-defective cells alone, FA-deficient cells additionally lacking USP48 are less sensitive to genotoxic stress induced by ICL agents and display enhanced, BRCA1-dependent, clearance of DNA damage. Consequently, USP48 inactivation reduces chromosomal instability of FA-defective cells. Our results highlight a role for USP48 in controlling DNA repair and suggest it as a potential target that could be therapeutically exploited for FA.

Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia

Maintenance of genome integrity via repair of DNA damage is a key biological process required to suppress diseases, including Fanconi anemia (FA). We generated loss-of-function human haploid cells for FA complementation group C (FANCC), a gene encoding a component of the FA core complex, and used genome-wide CRISPR libraries as well as insertional mutagenesis to identify synthetic viable (genetic suppressor) interactions for FA. Here we show that loss of the BLM helicase complex suppresses FANCC phenotypes and we confirm this interaction in cells deficient for FA complementation group I and D2 (FANCI and FANCD2) that function as part of the FA I-D2 complex, indicating that this interaction is not limited to the FA core complex, hence demonstrating that systematic genome-wide screening approaches can be used to reveal genetic viable interactions for DNA repair defects.

Pre-operative Simulation of the Appropriate C-arm Position Using Computed Tomography Post-processing Software Reduces Radiation and Contrast Medium Exposure During EVAR Procedures

OBJECTIVE/BACKGROUND

The aim was to evaluate the feasibility and efficacy of a new method for pre-operative calculation of an appropriate C-arm position for iliac bifurcation visualisation during endovascular aortic repair (EVAR) procedures by using three dimensional computed tomography angiography (CTA) post-processing software.

METHODS

Post-processing software was used to simulate C-arm angulations in two dimensions (oblique, cranial/caudal) for appropriate visualisation of distal landing zones at the iliac bifurcation during EVAR. Retrospectively, 27 consecutive EVAR patients (25 men, mean ± SD age 73 ± 7 years) were identified; one group of patients (NEW; n = 12 [23 iliac bifurcations]) was compared after implementation of the new method with a group of patients who received a historic method (OLD; n = 15 [23 iliac bifurcations]), treated with EVAR before the method was applied.

RESULTS

In the OLD group, a median of 2.0 (interquartile range [IQR] 1-3) digital subtraction angiography runs were needed per iliac bifurcation versus 1.0 (IQR 1-1) runs in the NEW group (p = .007). The median dose area products per iliac bifurcation were 11951 mGy*cm² (IQR 7308-16663 mGy*cm²) for the NEW, and 39394 mGy*cm² (IQR 19066-53702 mGy*cm²) for the OLD group, respectively (p = .001). The median volume of contrast per iliac bifurcation was 13.0 mL (IQR: 13-13 mL) in the NEW and 26 mL (IQR 13-39 mL) in the OLD group (p = .007).

CONCLUSION

Pre-operative simulation of the appropriate C-arm angulation in two dimensions using dedicated computed tomography angiography post-processing software is feasible and significantly reduces radiation and contrast medium exposure.

A Comprehensive Analysis of the Dynamic Response to Aphidicolin-Mediated Replication Stress Uncovers Targets for ATM and ATMIN

The cellular response to replication stress requires the DNA-damage-responsive kinase ATM and its cofactor ATMIN; however, the roles of this signaling pathway following replication stress are unclear. To identify the functions of ATM and ATMIN in response to replication stress, we utilized both transcriptomics and quantitative mass-spectrometry-based phosphoproteomics. We found that replication stress induced by aphidicolin triggered widespread changes in both gene expression and protein phosphorylation patterns. These changes gave rise to distinct early and late replication stress responses. Furthermore, our analysis revealed previously unknown targets of ATM and ATMIN downstream of replication stress. We demonstrate ATMIN-dependent phosphorylation of H2AX and of CRMP2, a protein previously implicated in Alzheimer's disease but not in the DNA damage response. Overall, our dataset provides a comprehensive resource for discovering the cellular responses to replication stress and, potentially, associated pathologies.

DNA Repair Cofactors ATMIN and NBS1 Are Required to Suppress T Cell Activation

Proper development of the immune system is an intricate process dependent on many factors, including an intact DNA damage response. The DNA double-strand break signaling kinase ATM and its cofactor NBS1 are required during T cell development and for the maintenance of genomic stability. The role of a second ATM cofactor, ATMIN (also known as ASCIZ) in T cells is much less clear, and whether ATMIN and NBS1 function in synergy in T cells is unknown. Here, we investigate the roles of ATMIN and NBS1, either alone or in combination, using murine models. We show loss of NBS1 led to a developmental block at the double-positive stage of T cell development, as well as reduced TCRα recombination, that was unexpectedly neither exacerbated nor alleviated by concomitant loss of ATMIN. In contrast, loss of both ATMIN and NBS1 enhanced DNA damage that drove spontaneous peripheral T cell hyperactivation, proliferation as well as excessive production of proinflammatory cytokines and chemokines, leading to a highly inflammatory environment. Intriguingly, the disease causing T cells were largely proficient for both ATMIN and NBS1. In vivo this resulted in severe intestinal inflammation, colitis and premature death. Our findings reveal a novel model for an intestinal bowel disease phenotype that occurs upon combined loss of the DNA repair cofactors ATMIN and NBS1.

Abstract 61: A mouse model for small round cell tumors induced by the Ewing sarcoma oncogene EWS/FLI1

Ewing Sarcoma is a malignant bone tumor in children and young adults. Upon current multimodal therapy only ∼60% of patients are long term survivors. Due to the rarity of the disease, however, only few novel agents can be tested in clinical trials. An animal model closely recapitulating the human disease would be highly needed to more rapidly explore new therapies. Ewing sarcoma is driven by the EWS/FLI1 (EF) chimeric oncogene, an aberrant Ets transcription factor that is toxic to many cell types, but tolerated by mesenchymal stem cells (MSC). Ewing sarcoma is postulated to develop from mesenchymal progenitor cells (MPC), but transgenic approaches tolerating EF expression lack behind. EF expression was shown to induce a differentiation block in MSC but does not drive full transformation. Thus, it was hypothesized that cooperating mutations are required for sarcomagenesis. We challenged this concept in a conditional mouse model in which EWS/FLI1 is activated early during endochondral bone formation by a Prx1-driven Cre recombinase (EFPrx1). EFPrx1 mice follows Mendelian ratio, but newborns suffocated due to a malformed rib cage. Bone formation was blocked at an early chondrocytic stage. EFPrx1 mice lacked limb bones, had reduced calvaria, craniofacial abnormalities and polydactyly. We found that EF expression blocked differentiation of MSC at the pre-hypertrophic chondrocyte stage due to blocked TGF-β and enhanced Hedgehog signaling (down regulated tgfβrI/II, smad1/5, dlx5 and upregulated gli1/2 and caspase 3 mRNA expression). Moreover, EF expression blocked sox9, runx2 and osterix expression. These genes are important for bone differentian. We established MSC-like cells (MSCL) from EFPrx1 mice that self-renewed, but full transformation was absent.

We ought to test if the timing of EF induction plays a role, therefor we tested many time points later that the time point described before and we found that when Prx1Cre expression and consequently EWS/FLI1 induction was delayed to a time point after birth using a tamoxifen inducible system, a significant fraction of mice developed solid tumors up to 4 months after Tamoxifen induction. The histo-pathology of the tumors resembled PAS and VIMENTIN positive small round cell tumors, and genetically an EWS/FLI1 signature was seen similar to a patient-derived Ewing sarcoma gene expression pattern. These data suggest that EWS/FLI1 can drive oncogenesis without the need for additional genetic aberrations. We propose that this transgenic mouse model could resemble a faithful model for a solid EWS/FLI1 induced tumor phenocopying human Ewing sarcoma.

Citation Format: Tahereh Javaheri, Barbara Sax, Harini Nivarthi, Eleni Tomazou, Mario Mikula, Jan Pencik, Zahra Kazemi, Maximilian Kauer, Marc Wiedner, Jan Tuckermann, Michaela Schlederer, Lukas Kenner, Reinhold Erben, Malkolm Logan, Christine Hartmann, Heinrich Kovar, Richard Moriggl. A mouse model for small round cell tumors induced by the Ewing sarcoma oncogene EWS/FLI1. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 61. doi:10.1158/1538-7445.AM2014-61

Skin graft fixation in severe burns: use of topical negative pressure

Over the last 50 years, the evolution of burn care has led to a significant decrease in mortality. The biggest impact on survival has been the change in the approach to burn surgery. Early excision and grafting has become a standard of care for the majority of patients with deep burns; the survival of a given patient suffering from major burns is invariably linked to the take rate and survival of skin grafts. The application of topical negative pressure (TNP) therapy devices has demonstrated improved graft take in comparison to conventional dressing methods alone. The aim of this study was to analyze the impact of TNP therapy on skin graft fixation in large burns. In all patients, we applied TNP dressings covering a %TBSA of >25. The following parameters were recorded and documented using BurnCase 3D: age, gender, %TBSA, burn depth, hospital length-of-stay, Baux score, survival, as well as duration and incidence of TNP dressings. After a burn depth adapted wound debridement, coverage was simultaneously performed using split-thickness skin grafts, which were fixed with staples and covered with fatty gauzes and TNP foam. The TNP foam was again fixed with staples to prevent displacement and finally covered with the supplied transparent adhesive film. A continuous subatmospheric pressure between 75-120 mm Hg was applied (VAC®, KCI, Vienna, Austria). The first dressing change was performed on day 4. Thirty-six out of 37 patients, suffering from full thickness burns, were discharged with complete wound closure; only one patient succumbed to their injuries. The overall skin graft take rate was over 95%. In conclusion, we consider that split thickness skin graft fixation by TNP is an efficient method in major burns, notably in areas with irregular wound surfaces or subject to movement (e.g. joint proximity), and is worth considering for the treatment of aged patients.

ATMIN is required for the ATM-mediated signaling and recruitment of 53BP1 to DNA damage sites upon replication stress

Unresolved replication intermediates can block the progression of replication forks and become converted into DNA lesions, hence exacerbating genomic instability. The p53-binding protein 1 (53BP1) forms nuclear bodies at sites of unrepaired DNA lesions to shield these regions against erosion, in a manner dependent on the DNA damage kinase ATM. The molecular mechanism by which ATM is activated upon replicative stress to localize the 53BP1 protection complex is unknown. Here we show that the ATM-INteracting protein ATMIN (also known as ASCIZ) is partially required for 53BP1 localization upon replicative stress. Additionally, we demonstrate that ATM activation is impaired in cells lacking ATMIN and we define that ATMIN is required for initiating ATM signaling following replicative stress. Furthermore, loss of ATMIN leads to chromosomal segregation defects. Together these data reveal that chromatin integrity depends on ATMIN upon exposure to replication-induced stress.

The properties of the "ideal" donor site dressing: results of a worldwide online survey

Split skin grafting is a widely used technique for reconstructing skin defects. Although a vast number of different coverage options for donor sites have become available in daily clinical practice, no optimum dressing material has been found to date. For this reason, we conducted a globally-distributed online survey to poll for the properties of such an "ideal" donor site dressing, possibly leading to an improved clinically-driven direction of future wound dressing developments. A total of 69 respondents from 34 countries took part in the questionnaire, resulting in a response rate of 13.8% (69/500) over a 1-month period. The majority of respondents rated the characteristics of an "ideal" donor site dressing to be either "essential" or "desirable" as follows: lack of adhesion to the wound bed ("essential": 31/69, 44.9%; "desirable": 30/69, 43.5%); pain-free dressing changes ("essential": 38/69, 55.1%; "desirable": 30/69, 43.5%); absorbency ("essential": 27/69, 39.1%; "desirable": 33/69, 47.8%); ease of removal ("essential": 37/69, 53.6%; "desirable": 27/69, 39.13%). With regard to the desired frequency of dressing changes, respondents preferred "no dressing change until the donor site has healed" (51/69, 73.9%) in the majority of cases, followed by "twice weekly" (10/69, 14.5%), "alternate days" (5/69, 7.2%) and "daily" (3/69, 4.3%). With regard to the design of the dressing material, the majority of participants preferred a one-piece (composite) dressing product (44/69, 63.8%). The majority of respondents also denied the current availability of an "ideal" donor site dressing (49/69, 71%). The strength of this study was the remarkable geographic distribution of responses; all parts of the world were included and participated. We believe that this globally conducted online survey has polled for the properties of the "ideal" donor site dressing and possibly will lead to an improved clinically-driven direction of future wound dressing development.

Ischemic brain injury: a consortium analysis of key factors involved in mesenchymal stem cell-mediated inflammatory reduction

Increasing global birth rate, coupled with the aging population surviving into their eighth decade has lead to increased incidence diseases, hitherto designated as rare. Brain related ischemia, at birth, or later in life, during, for example stroke, is increasing in global prevalence. Reactive microglia can contribute to neuronal damage as well as compromising transplantion. One potential treatment strategy is cellular therapy, using mesenchymal stem cells (hMSCs), which possess immunomodulatory and cell repair properties. For effective clinical therapy, mechanisms of action must be understood better. Here multicentre international laboratories assessed this question together investigating application of hMSCs neural involvement, with interest in the role of reactive microglia. Modulation by hMSCs in our in vivo and in vitro study shows they decrease markers of microglial activation (lower ED1 and Iba) and astrogliosis (lower GFAP) following transplantation in an ouabain-induced brain ischemia rat model and in organotypic hippocampal cultures. The anti-inflammatory effect in vitro was demonstrated to be CD200 ligand dependent with ligand expression shown to be increased by IL-4 stimulation. hMSC transplant reduced rat microglial STAT3 gene expression and reduced activation of Y705 phosphorylated STAT3, but STAT3 in the hMSCs themselves was elevated upon grafting. Surprisingly, activity was dependent on heterodimerisation with STAT1 activated by IL-4 and Oncostatin M. Our study paves the way to preclinical stages of a clinical trial with hMSC, and suggests a non-canonical JAK-STAT signaling of unphosphorylated STAT3 in immunomodulatory effects of hMSCs.

Embryonic stem cells facilitate the isolation of persistent clonal cardiovascular progenitor cell lines and leukemia inhibitor factor maintains their self-renewal and myocardial differentiation potential in vitro

Compelling evidence for the existence of somatic stem cells in the heart of different mammalian species has been provided by numerous groups; however, so far it has not been possible to maintain these cells as self-renewing and phenotypically stable clonal cell lines in vitro. Thus, we sought to identify a surrogate stem cell niche for the isolation and persistent maintenance of stable clonal cardiovascular progenitor cell lines, enabling us to study the mechanism of self-renewal and differentiation in these cells. Using postnatal murine hearts with a selectable marker as the stem cell source and embryonic stem cells and leukemia inhibitory factor (LIF)-secreting fibroblasts as a surrogate niche, we succeeded in the isolation of stable clonal cardiovascular progenitor cell lines. These cell lines self-renew in an LIF-dependent manner. They express both stemness transcription factors Oct4, Sox2, and Nanog and early myocardial transcription factors Nkx2.5, GATA4, and Isl-1 at the same time. Upon LIF deprivation, they exclusively differentiate to functional cardiomyocytes and endothelial and smooth muscle cells, suggesting that these cells are mesodermal intermediates already committed to the cardiogenic lineage. Cardiovascular progenitor cell lines can be maintained for at least 149 passages over 7 years without phenotypic changes, in the presence of LIF-secreting fibroblasts. Isolation of wild-type cardiovascular progenitor cell lines from adolescent and old mice has finally demonstrated the general feasibility of this strategy for the isolation of phenotypically stable somatic stem cell lines.

[Clinical experiences using the Versajet system in burns: indications and applications]

Early debridement and early skin grafting are the "Gold standard" in the surgical treatment of burns. There are different debridement methods available. Concerning the treatment of burns, surgical-sharp debridement, laser ablation and hydrosurgery system are used. While in full thickness burns the sharp debridement is advisable, the Versajet shows its benefits in the treatment of partial thickness burns. Especially for debridement of difficult to treat areas - face, neck, lips, fingers, interdigital spaces, convex and concave areas the Versajet System shows its benefits. With the Versajet System, tissue excision is precise; moreover it helps to avoid the damage of viable tissue and its vascular supply.

Arterial and venous cytokine response to cardiopulmonary bypass for low risk CABG and relation to hemodynamics

During and after cardiopulmonary bypass (CPB), cytokines may affect cardiac performance and the immune response and are therefore of diagnostic and therapeutic interest. We have used EIA/EASIA kits to measure arterial and venous levels of interleukin-1-beta (IL-1-beta), IL-2, IL-2 receptor (IL-2-R), IL-6, tumor necrosis factor (TNF)-alpha and interferon (IFN)-gamma in 12 men and 3 women (mean age 59.4 +/- 8.5 years, mean left ventricular ejection fraction 66 +/- 11%, average of 2.5 +/- 0.64 vessels affected by disease) undergoing elective coronary artery bypass grafting (CABG). On average each patient received 3 +/- 0.85 bypass grafts and required a postoperative maximum dopamine-dose of 3.8 micrograms/kg per min. Mean CPB and operation times were 60 +/- 21 min, and 132 +/- 16 min, respectively. During CPB, the venous levels of IL-2 temporarily decreased from 234 to 0 (p < 0.05) pg/ml and arterial and venous levels of IL-2-R temporarily decreased from 28 to 16, and 36 to 18 pM (p < 0.05), respectively. After termination of CPB, there was an increase in the arterial and venous levels of IL-6 from below 3 to 253 and 277 pg/ml (p < 0.05) and TNF-alpha from 1.1 to 5.7 and 0.7 to 4.0 pg/ml, respectively (p < 0.05). Tumor necrosis factor-alpha-increases peaked 30 min, and IL-6 increases peaked 4 h after termination of CPB. Twenty-four hours after the end of CPB, IL-6 showed a tendency to return to baseline, but still remained significantly elevated.(ABSTRACT TRUNCATED AT 250 WORDS)