Inhibition of 53BP1 favors homology-dependent DNA repair and increases CRISPR-Cas9 genome-editing efficiency

Programmable nucleases, such as Cas9, are used for precise genome editing by homology-dependent repair (HDR)^1–3. However, HDR efficiency is constrained by competition from other double-strand break (DSB) repair pathways, including non-homologous end-joining (NHEJ)⁴. We report the discovery of a genetically encoded inhibitor of 53BP1 that increases the efficiency of HDR-dependent genome editing in human and mouse cells. 53BP1 is a key regulator of DSB repair pathway choice in eukaryotic cells^{4, 5} and functions to favor NHEJ over HDR by suppressing end resection, which is the rate-limiting step in the initiation of HDR. We screened an existing combinatorial library of engineered ubiquitin variants⁶ for inhibitors of 53BP1. Expression of one variant, named i53 (inhibitor of 53BP1), in human and mouse cells blocked accumulation of 53BP1 at sites of DNA damage and improved gene targeting and chromosomal gene conversion with either double-stranded DNA or single-stranded oligonucleotide donors by up to 5.6-fold. Inhibition of 53BP1 is a robust method to increase efficiency of HDR-based precise genome editing.

Emergent biomarker derived from next-generation sequencing to identify pain patients requiring uncommonly high opioid doses

Next-generation sequencing (NGS) provides unrestricted access to the genome, but it produces 'big data' exceeding in amount and complexity the classical analytical approaches. We introduce a bioinformatics-based classifying biomarker that uses emergent properties in genetics to separate pain patients requiring extremely high opioid doses from controls. Following precisely calculated selection of the 34 most informative markers in the OPRM1, OPRK1, OPRD1 and SIGMAR1 genes, pattern of genotypes belonging to either patient group could be derived using a k-nearest neighbor (kNN) classifier that provided a diagnostic accuracy of 80.6±4%. This outperformed alternative classifiers such as reportedly functional opioid receptor gene variants or complex biomarkers obtained via multiple regression or decision tree analysis. The accumulation of several genetic variants with only minor functional influences may result in a qualitative consequence affecting complex phenotypes, pointing at emergent properties in genetics.

Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia

In the search for genes that define critical steps of relapse in pediatric T-cell acute lymphoblastic leukemia (T-ALL) and can serve as prognostic markers, we performed targeted sequencing of 313 leukemia-related genes in 214 patients: 67 samples collected at the time of relapse and 147 at initial diagnosis. As relapse-specific genetic events, we identified activating mutations in NT5C2 (P=0.0001, Fisher's exact test), inactivation of TP53 (P=0.0007, Fisher's exact test) and duplication of chr17:q11.2-24.3 (P=0.0068, Fisher's exact test) in 32/67 of T-ALL relapse samples. Alterations of TP53 were frequently homozygous events, which significantly correlated with higher rates of copy number alterations in other genes compared with wild-type TP53 (P=0.0004, Mann–Whitney's test). We subsequently focused on mutations with prognostic impact and identified genes governing DNA integrity (TP53, n=8; USP7, n=4; MSH6, n=4), having key roles in the RAS signaling pathway (KRAS, NRAS, n=8), as well as IL7R (n=4) and CNOT3 (n=4) to be exclusively mutated in fatal relapses. These markers recognize 24/49 patients with a second event. In 17 of these patients with mostly refractory relapse and dire need for efficient treatment, we identified candidate targets for personalized therapy with p53 reactivating compounds, MEK inhibitors or JAK/STAT-inhibitors that may be incorporated in future treatment strategies.

[Pain therapy with metamizole after ambulatory surgery?]

One third of operations are performed on an outpatient basis in Germany, but methods of postoperative pain therapy are less studied. We observed 126 patients with ambulatory and planned surgery in the field of orthopedics and trauma surgery. They were treated with the analgesic metamizole intra- and postoperatively and completed the patients' questionnaire QUIPS on the first postoperative day. In all, 79 patients (61.7%) reported current pain ≥4 on the numerical rating scale (NRS); 84 (66.6%) had restrictions in mobility, 48 (38.1%) described sleep disorders, and 26 (20.6%) wished for more or stronger analgesics. However, 91 (72.2%) of our patients were satisfied with the their pain therapy. Chances are that the treatment of nociceptive pain during movement with NSAID or COX-2-inhibitors is more successful. Further investigations should follow.

[Emergency departments--2016 update]

Acute medical care in hospital emergency departments has experienced rapid development in recent years and gained increasing importance not only from a professional medical point of view but also from an economic and health policy perspective. The present article therefore provides an update on the situation of emergency departments in Germany. Care in emergency departments is provided with an increasing tendency to patients of all ages presenting with varying primary symptoms, complaints, illnesses and injury patterns. In the process, patients reach the emergency department by various routes and structural provision. Cross-sectional communication and cooperation, prioritization and organization of emergency management and especially medical staff qualifications increasingly play a decisive role in this process. The range of necessary knowledge and skills far exceeds the scope of prehospital medical emergency care and the working environment differs substantially. In addition to existing structural and economic problems, the latest developments, as well as future proposals for the design of in-hospital emergency medical care in interdisciplinary emergency departments are described.

[Air rescue missions at night: Data analysis of primary and secondary missions by the DRF air rescue service in 2014]

The advantages that are inherent to the air ambulance service are shown in a reduction in mortality of critically ill or injured patients. The air ambulance service ensures quick and efficient medical care to a patient as well as the immediate transport of patients to a suitable hospital. In addition, primary air rescue has proved to be effective as a support for the standard ground-based ambulance services in some regions of Germany during the night. Under certain conditions, such as the strict adherence to established, practiced and coordinated procedures, air rescue at night does not have a significantly higher risk compared to operations in daytime. Particular requirements should be imposed for air rescue operations at night: a strict indication system for alerting, 4-man helicopter crews solely during the night as well as pilots (and copilots) with the correct qualifications and experience in dealing with night vision devices on a regular basis. Moreover, the helicopters need to be suitable and approved for night flying including cabin upgrades and the appropriate medical technology equipment. To increase the benefits of air rescue for specific diseases and injuries, a nationwide review of the processes is needed to further develop the primary air rescue service.

[Management of the Therapy of Pulmonary Sequestration: A Retrospective Multicentre Study]

BACKGROUND

Pulmonary sequestration is a rare pulmonary malformation whose complex pathogenesis is not completely understood. Extrapulmonary sequestrations are always hereditary malformations and are usually diagnosed during childhood. Some intralobar sequestrations in adults, by contrast, seem to be acquired. The clinical presentation is non-specific and often misinterpreted, which results in delayed diagnosis. Surgical resection continues to be the gold standard. Despite the low incidence, new technologies developed in the past few decades, e.g. preoperative interventional angiology procedures and video-assisted lung resection, have changed the management of the disease.

METHODS

A prospective data collection was performed on adult patients who had undergone surgical resection of a pulmonary sequestration in four different centres during a period of 23 years. These data were retrospectively analysed.

RESULTS

A total of 14 patients with intralobar sequestrations (n = 11, 79 % left lower lobe) underwent surgical resection. The male/female ratio was 8/6 (median age 50 years). Non-specific pulmonary symptoms such as recurrent infections had a high prevalence (n = 6, 42 %). Two patients had haemoptysis. Three patients were asymptomatic. All patients had a chest CT, 7 patients had an additional abdominal CT, while 10 underwent angiography. Preoperative embolization was performed in 5 of these patients (branches of the thoracic aorta: in 2 cases, branches of abdominal aorta: in 2 cases, and branches of both: in 1 case). Resection was mostly performed with an open surgical approach (n = 12, 86 %). Most patients had a non-anatomic pulmonary resection (n = 8, 57 %). In 7 patients, a microbiologic examination revealed a superinfection with Streptococcus pneumoniae, while 1 patient had an invasive mycosis with Candida albicans.

CONCLUSION

In patients with non-specific pulmonary symptoms and undetermined lesions, especially in the lower lobes, pulmonary sequestrations must be considered in the differential diagnostic evaluation even in adult and elderly patients. If there are no contraindications, surgical removal is basically recommended and may be minimally-invasive in selected cases. The planning of the resection can be facilitated by preoperative evaluation of the arterial supply (branches of the thoracic or abdominal aorta, or both). In cases with haemoptysis or blood supply over the abdominal aorta, preoperative embolization is indicated.

Diversity of assessing circulating tumor cells (CTCs) emphasizes need for standardization: a CTC Guide to design and report trials

Hematogenous spreading of tumor cells from primary tumors is a crucial step in the cascade to metastasis, the latter being the most limiting factor for patients' survival prognosis. Therefore, circulating tumor cells (CTCs) have become a field of intensive research. However, the process of isolation and identification of CTCs lacks standardization. This article presents an overview of 71 CTC studies reported in PUBMED since 2000 and focusing on colorectal cancer. These studies are evaluated regarding standardization of CTC isolation and identification, marker proteins used, study population and blood sample quality management, clinical performance, and quality measures. Overall, standardization of CTC assessment seems insufficient. Thus, comparability of CTC studies is hampered and results should be interpreted carefully. We here propose a standardized CTC guideline (CTC Guide) to prospectively design and report studies/trials in a harmonized form. Despite the current interstudy heterogeneity, the data indicate that CTC detection is of clinical relevance and CTCs should be considered as a surrogate prognostic marker. Many studies indicate the high potential for CTCs as prognostic markers, e.g., in colorectal cancer treatment. However, standardized, large-scale multicenter validation studies are still needed to pave the way for clinical implementation of CTC detection that could ameliorate individualized medicine regimes.

Predictors of Morbidity and Mortality in Esophageal Perforation: Retrospective Study of 80 Patients

Background and Aims:

Esophageal perforation is a life-threatening disease. Factors impacting morbidity and mortality include the cause and site of the perforation, the time to diagnosis, and the therapeutic procedure. This study aimed to identify risk factors for morbidity and mortality after esophageal perforation.

Patients and Methods:

This retrospective study analyzed data collected from all patients treated for esophageal perforation at the Department of Surgery, University of Schleswig–Holstein, Luebeck Campus, from January 1986 through December 2011.

Results:

Altogether, 80 patients (52 men, 28 women; mean age 65 years) were treated. The cause of perforation was intraluminal in 44 (55%) (group A) and extraluminal in 2 (3%) (group B). Spontaneous perforations were observed in 12 (15%) (group C). Perforations were due to a preexisting esophageal disease in 22 (28%) (group D). The survival rate was higher for group A (82%) than for groups B (50%), C (57%), and D (59%). The distal third of the esophagus had the highest prevalence of perforations (49, 61%) independent of the cause. Mortality, however, was independent of the perforation site. Perforations were diagnosed within 24 h in 57% (n = 46) of patients, associated with a statistically significant lower mortality rate (p = 0.035). Altogether, 40 patients underwent non-operative treatment, and among those 27 had endoscopic treatment. Emergency thoracic surgery was performed in 40 patients: direct suture of the defect (n = 26), partial esophageal resection (n = 11), other (n = 3). Significantly higher morbidity (p = 0.007) and prolonged hospitalization (p < 0.0001) was observed among patients who underwent emergency surgery. Mortality was higher in the surgical group (14/40) than in the non-operative treatment group (9/40) but without statistical significance.

Conclusion:

Intraluminal perforations, rapid initiation of therapy, and non-operative treatment were associated with favorable outcomes. The perforation site did not have an impact on outcomes. Esophageal resection was associated with high mortality.

Abstract PR03: High-resolution detection of fitness genes and genotype-specific cancer vulnerabilities with CRISPR-Cas9 screens

Genetic knockouts are a fundamental tool for elucidating gene function in model organisms and hold great potential for finding therapeutic targets for diseases such as cancer. The advance that pooled CRISPR-Cas9 library technology brings to human genetics sets the stage for identifying cellular fitness genes which operate either globally or specifically within a particular genetic background or environmental context. To extend the catalogue of human core and context-dependent fitness genes, we have developed the TKO (Toronto KnockOut) library, a second-generation gRNA library of 176,500 guides targeting 17,661 human protein coding genes. We used the library to screen five human cell lines, representing a cross-section of wild type and cancer tissues, to identify genes whose knockouts induced significant fitness defects. We consistently discover fivefold more fitness genes than were previously observed using systematic RNA interference, including many genes at moderate expression levels that are largely refractory to RNAi methods. We expand the known set of human core fitness genes more than fourfold to 1,580 genes, and identify dozens of essential protein complexes, both known and novel, whose heterozygous copy loss in chromosomally unstable cancers may induce a therapeutic window. We further characterize novel fitness genes of unknown function and find that they all likely exist in protein complexes with other essential genes. TKO screens accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds. We also identified a surprising and specific dependency on mitochondrial activity, which strongly supports the idea that oxidative phosphorylation dependency - a clear exception to the Warburg effect - is a targetable weakness of some tumors. Our findings demonstrate that the CRISPR-Cas9 system fundamentally alters the landscape for systematic genetics in human cells through rigorous identification of cell line essential genes, affording a high-resolution view of the genetic vulnerabilities of a cell that may represent therapeutic opportunities in cancer and that might conceivably contribute to cell plasticity and tumor progression.

Citation Format: Traver Hart, Megha Chandrashekhar, Michael Aregger, Zachary Steinhart, Kevin R. Brown, Graham Macleod, Monika Mis, Michal Zimmermann, Amelie Fradet-Turcotte, Song Sun, Peter Driks, Sachdev Sidhu, Frederick P. Roth, Olivia S. Rissland, Daniel Durocher, Stephane Angers, Jason Moffat. High-resolution detection of fitness genes and genotype-specific cancer vulnerabilities with CRISPR-Cas9 screens. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr PR03.