Targeted DamID reveals differential binding of mammalian pluripotency factors.

The precise control of gene expression by transcription factor networks is crucial to organismal development. The predominant approach for mapping transcription factor-chromatin interactions has been chromatin immunoprecipitation (ChIP). However, ChIP requires a large number of homogeneous cells and antisera with high specificity. A second approach, DamID, has the drawback that high levels of Dam methylase are toxic. Here, we modify our targeted DamID approach (TaDa) to enable cell type-specific expression in mammalian systems, generating an inducible system (mammalian TaDa or MaTaDa) to identify genome-wide protein/DNA interactions in 100 to 1000 times fewer cells than ChIP-based approaches. We mapped the binding sites of two key pluripotency factors, OCT4 and PRDM14, in mouse embryonic stem cells, epiblast-like cells and primordial germ cell-like cells (PGCLCs). PGCLCs are an important system for elucidating primordial germ cell development in mice. We monitored PRDM14 binding during the specification of PGCLCs, identifying direct targets of PRDM14 that are key to understanding its crucial role in PGCLC development. We show that MaTaDa is a sensitive and accurate method for assessing cell type-specific transcription factor binding in limited numbers of cells

The impact of surgical experience and frequency of practice on perioperative outcomes in pancreatic surgery

Objective We aimed to determine the impact of surgical experience and frequency of practice on perioperative morbidity and mortality in pancreatic surgery. Methods 1281 patients that underwent pancreatic resections from 1993 to 2013 were retrospectively analyzed using logistic regression models. All cases were stratified according to the surgeon’s level of experience, which was based on the number of previously performed pancreatic resections and the extent of received supervision (novice: n  90 / none). Additional stratification was based on the frequency of practice (sporadic: 3 resections > 6 weeks, frequent: 3 resections ≤6 weeks). Results The novice and experienced categories were related to a decreased risk of postoperative pancreatic fistulas (odds ratio [OR] 0.46, 95% confidence interval [CI] 0.26–0.82 and 0.54, 95% CI 0.36–0.82) and in-hospital mortality (OR 0.45, 95% CI 0.17–1.16 and 0.42, 95% CI 0.21–0.83) compared to the intermediate category. Frequent practice was associated with a significantly lower risk of delayed gastric emptying (OR 0.56, 95% CI 0.38–0.83), postpancreatectomy hemorrhage (OR 0.64, 95% CI 0.42–0.98) and in-hospital mortality (OR 0.45, 95% CI 0.24–0.87). Conclusions Our results emphasize the importance of supervision within a pancreatic surgery training program. In addition, our data underline the need of a sufficient patient caseload to ensure frequent practice

Collateral effects of the SARS-CoV-2 pandemic on oncologic surgery in Bavaria

Background The ongoing SARS-COV-2 pandemic has severe implications for people and healthcare systems everywhere. In Germany, worry about the consequences of the pandemic led to the deferral of non-emergency surgeries. Tumor surgery accounts for a large volume in the field of visceral surgery and cannot be considered purely elective. It is not known how the SARS-COV-2 pandemic has changed the surgical volume in tumor patients. Methods Retrospective analysis of the amount of oncological surgeries in three academic visceral surgery departments in Bavaria, Germany, in 2020. Procedures were split into subgroups: Upper Gastrointestinal (Upper GI), Colorectal, Hepato-Pancreato-Biliary (HPB), Peritoneal and Endocrine. Procedures in 2020 were compared to a reference period from January 1st, 2017 to December 31st 2019. Surgical volume was graphically merged with SARS-COV-2 incidence and the number of occupied ICU beds. Results Surgical volume decreased by 7.6% from an average of 924 oncologic surgeries from 2017 to 2019 to 854 in 2020. The decline was temporally associated with the incidence of infections and ICU capacity. Surgical volume did not uniformly increase to pre-pandemic levels in the months following the first pandemic wave with lower SARS-COV-2 incidence and varied according to local incidence levels. The decline was most pronounced in colorectal surgery where procedures declined on average by 26% following the beginning of the pandemic situation. Conclusion The comparison with pre-pandemic years showed a decline in oncologic surgeries in 2020, which could have an impact on lost life years in non-COVID-19 patients. This decline was very different in subgroups which could not be solely explained by the pandemic

A Drosophila immune response against Ras-induced overgrowth

Our goal is to characterize the innate immune response against the early stage of tumor development. For this, animal models where genetic changes in specific cells and tissues can be performed in a controlled way have become increasingly important, including the fruitfly Drosophila melanogaster. Many tumor mutants in Drosophila affect the germline and, as a consequence, also the immune system itself, making it difficult to ascribe their phenotype to a specific tissue. Only during the past decade, mutations have been induced systematically in somatic cells to study the control of tumorous growth by neighboring cells and by immune cells. Here we show that upon ectopic expression of a dominant-active form of the Ras oncogene (RasV12), both imaginal discs and salivary glands are affected. Particularly, the glands increase in size, express metalloproteinases and display apoptotic markers. This leads to a strong cellular response, which has many hallmarks of the granuloma-like encapsulation reaction, usually mounted by the insect against larger foreign objects. RNA sequencing of the fat body reveals a characteristic humoral immune response. In addition we also identify genes that are specifically induced upon expression of RasV12. As a proof-of-principle, we show that one of the induced genes (santa-maria), which encodes a scavenger receptor, modulates damage to the salivary glands. The list of genes we have identified provides a rich source for further functional characterization. Our hope is that this will lead to a better understanding of the earliest stage of innate immune responses against tumors with implications for mammalian immunity

TaDa! Analysing cell type-specific chromatin in vivo with Targeted DamID.

The emergence of neuronal diversity during development of the nervous system relies on dynamic changes in the epigenetic landscape of neural stem cells and their progeny. Targeted DamID (TaDa) is proving invaluable in identifying the genome-wide binding sites of chromatin-associated proteins in vivo, without fixation, cell isolation, or immunoprecipitation. The simplicity and efficiency of the technique have led to an ever-expanding TaDa toolbox. These tools enable profiling of gene expression and chromatin accessibility, as well as the identification of the genome-wide binding sites of chromatin complexes, transcription factors and RNAs. Here, we review these new developments, with particular emphasis on the use of TaDa in studying neuronal specification

Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells

Transposable elements are an abundant source of transcription factor binding sites, and favorable genomic integration may lead to their recruitment by the host genome for gene regulatory functions. However, it is unclear how frequent co-option of transposable elements as regulatory elements is, to which regulatory programs they contribute and how they compare to regulatory elements devoid of transposable elements. Here, we report a transcription initiation-centric, in-depth characterization of the transposon-derived regulatory landscape of mouse embryonic stem cells. We demonstrate that a substantial number of transposable element insertions, in particular endogenous retroviral elements, are associated with open chromatin regions that are divergently transcribed into unstable RNAs in a cell-type specific manner, and that these elements contribute to a sizable proportion of active enhancers and gene promoters. We further show that transposon subfamilies contribute differently and distinctly to the pluripotency regulatory program through their repertoires of transcription factor binding site sequences, shedding light on the formation of regulatory programs and the origins of regulatory elements

Continuous or interrupted suture technique for hepaticojejunostomy? A national survey

Abstract Background Hepaticojejunostomy is commonly used in hepato-bilio-pancreatic surgery and a crucial step in many surgical procedures, including pancreaticoduodenectomy. The most frequently used techniques are the interrupted suture and the continuous suture technique. Currently, there is no data available in regard to the utilization of these techniques. Methods In total, 102 hospitals in Germany were invited between September and November 2017 to participate in this survey. Using a paper-based questionnaire, data were collected on surgical technique and complication rates of hepaticojejunostomies. Results A total of 77 of the 102 addressed hospitals (76%) participated in the survey. On average, each hospital performed 71 hepaticojejunostomies per year - most often in the context of pancreaticoduodenectomy (71%). 24 (31%) hospitals exclusively use an interrupted suture technique, 7 (9%) hospitals solely a continuous suture technique, 3 (4%) hospitals perform a combination of continuous and interrupted suture technique and 43 (56%) hospitals decide on one of both techniques depending on intraoperative findings. According to the participants in this survey, the continuous suture technique is significantly faster than the interrupted suture technique in hepaticojejunostomy (p = 0,015). There were no significant differences in the overall complication rate (p = 0,902) and insufficiency rate (p = 1,000). Conclusions In Germany, there is a heterogeneity in the technique used to create a hepaticojejunostomy. As our survey suggests that the use of continuous suture technique may offer an advantage in time without jeopardizing patient outcomes, the different techniques should be compared in a randomized controlled study

Cinematic Rendering in Anatomy: A Crossover Study Comparing a Novel 3D Reconstruction Technique to Conventional Computed Tomography

Integration of medical imaging into preclinical anatomy courses is already underway in many medical schools. However, interpretation of two‐dimensional grayscale images is difficult and conventional volume rendering techniques provide only images of limited quality. In this regard, a more photorealistic visualization provided by Cinematic Rendering (CR) may be more suitable for anatomical education. A randomized, two‐period crossover study was conducted from July to December 2018, at the University Hospital of Erlangen, Germany to compare CR and conventional computed tomography (CT) imaging for speed and comprehension of anatomy. Sixteen students were randomized into two assessment sequences. During each assessment period, participants had to answer 15 anatomy‐related questions that were divided into three categories: parenchymal, musculoskeletal, and vascular anatomy. After a washout period of 14 days, assessments were crossed over to the respective second reconstruction technique. The mean interperiod differences for the time to answer differed significantly between the CR–CT sequence (−204.21 ± 156.0 seconds) and the CT–CR sequence (243.33 ± 113.83 seconds; P < 0.001). Overall time reduction by CR was 65.56%. Cinematic Rendering visualization of musculoskeletal and vascular anatomy was higher rated compared to CT visualization (P < 0.001 and P = 0.003), whereas CT visualization of parenchymal anatomy received a higher scoring than CR visualization (P < 0.001). No carryover effects were observed. A questionnaire revealed that students consider CR to be beneficial for medical education. These results suggest that CR has a potential to enhance knowledge acquisition and transfer from medical imaging data in medical education