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Over the past years, next-generation sequencing (NGS) technologies revolutionized the possibilities in a broad range of application areas. Also in the field of forensic genetics, NGS continuously gained in importance and attentiveness. A significant number of sudden cardiac deaths (SCD) in the young is due to heritable arrhythmia syndromes emphasizing the need of examining the genetic basis in these cases also with regard to the identification of relatives and/or patients being at risk. As a result, high-throughput methods became of increasing value in molecular autopsy investigations enabling the analysis of a broad spectrum of genes.
Most standard protocols are optimized for high-quality samples and frequently not directly applicable to challenging forensic sample material. In the present study, we intended to examine a comprehensive gene panel associated with SCD and inherited arrhythmogenic disorders. We compared three different hybridization-based library preparation technologies in order to implement a suitable NGS workflow for heterogeneous, forensic as well as diagnostic sample material.
The results obtained indicated, that the Illumina technologies Nextera DNA Flex and TruSeq were compatible with samples exhibiting varying levels of degradation. In comparison, the TruSight method also resulted in good sequencing data, but seemed to be more dependent on DNA integrity. The preparation protocols evaluated in our study are not restricted to molecular autopsy investigations and might be helpful for and transferrable to further forensic research applications.
Introduction: Obesity is classified as a global epidemic and judged to be the greatest public health threat in Western countries. The tremendously increasing prevalence rates in children lead to morbidity and mortality in adults. In many countries, prevalence has doubled since the 1980s. Other countries show a continuous increase or stagnate at a very high level. Given these regional differences, this study aims to draw a global world map of childhood obesity research, including regional epidemiological characteristics, to comprehensively assess research influences and needs. Methods: In addition to established bibliometric parameters, this study uses epidemiological data to interpret metadata on childhood obesity research from the Web of Science in combination with state-of-the-art visualization methods, such as density equalizing map projections. Results: It was not until the 1990s that belated recognition of the dangerous effects of childhood obesity led to an increase in the number of publications worldwide. In addition, our findings show that countries’ study output does not correlate with epidemiologic rates of childhood obesity. In contrast, the primary driver of the research efforts on childhood obesity appears to be largely driven government funding structures. Discussion/Conclusion: The geographical differences in the epidemiological background of childhood obesity complicate the implementation of transnational research projects and cross-border prevention programs. Effective realization requires a sound scientific basis, which is facilitated by globally valid approaches. Hence, there is a need for information exchange between researchers, policy makers, and private initiatives worldwide.
Hematopoietic stem cell transplantation (HSCT) has been proposed as a promising therapeutic opportunity to improve immunity and prevent hematologic malignancies in Ataxia-telangiectasia (A-T). However, experience in the transplantation strategy for A-T patients is still scarce. The aim of this study was to investigate whether different approaches of HSCT are feasible in regard to graft versus host response and sufficient concerning functional immune reconstitution. Atm-deficient mice were treated with a clinically relevant non-myeloablative host-conditioning regimen and transplanted with CD90.2-depleted, green fluorescent protein (GFP)-expressing, and ataxia telangiectasia mutated (ATM)-competent bone marrow donor cells in a syngeneic, haploidentical or allogeneic setting. Like syngeneic HSCT, haploidentical HSCT, but not allogeneic HSCT extended the lifespan of Atm-deficient mice through the reduction of thymic tumors and normalized T-cell numbers. Donor-derived splenocytes isolated from transplanted Atm-deficient mice filled the gap of cell loss in the naïve T-cell population and raised CD4 cell functionality up to wild-type level. Interestingly, HSCT using heterozygous donor cells let to a significantly improved survival of Atm-deficient mice and increased CD4 cell numbers as well as CD4 cell functionality equivalent to HSCT using with wild-type donor cells. Our data provided evidence that haploidentical HSCT could be a feasible strategy for A-T, possibly even if the donor is heterozygous for ATM. However, this basic research cannot substitute any research in humans.
Introduction: Ischemic and hemorrhagic strokes in the brainstem and cerebellum with injury to the functional loop of the Guillain-Mollaret triangle (GMT) can trigger a series of events that result in secondary trans-synaptic neurodegeneration of the inferior olivary nucleus. In an unknown percentage of patients, this leads to a condition called hypertrophic olivary degeneration (HOD). Characteristic clinical symptoms of HOD progress slowly over months and consist of a rhythmic palatal tremor, vertical pendular nystagmus, and Holmes tremor of the upper limbs. Diffusion Tensor Imaging (DTI) with tractography is a promising method to identify functional pathway lesions along the cerebello-thalamo-cortical connectivity and to generate a deeper understanding of the HOD pathophysiology. The incidence of HOD development following stroke and the timeline of clinical symptoms have not yet been determined in prospective studies—a prerequisite for the surveillance of patients at risk. Methods and Analysis: Patients with ischemic and hemorrhagic strokes in the brainstem and cerebellum with a topo-anatomical relation to the GMT are recruited within certified stroke units of the Interdisciplinary Neurovascular Network of the Rhine-Main. Matching lesions are identified using a predefined MRI template. Eligible patients are prospectively followed up and present at 4 and 8 months after the index event. During study visits, a clinical neurological examination and brain MRI, including high-resolution T2-, proton-density-weighted imaging, and DTI tractography, are performed. Fiberoptic endoscopic evaluation of swallowing is optional if palatal tremor is encountered. Study Outcomes: The primary endpoint of this prospective clinical multicenter study is to determine the frequency of radiological HOD development in patients with a posterior fossa stroke affecting the GMT at 8 months after the index event. Secondary endpoints are identification of (1) the timeline and relevance of clinical symptoms, (2) lesion localizations more prone to HOD occurrence, and (3) the best MR-imaging regimen for HOD identification. Additionally, (4) DTI tractography data are used to analyze individual pathway lesions. The aim is to contribute to the epidemiological and pathophysiological understanding of HOD and hereby facilitate future research on therapeutic and prophylactic measures.
Interactions of drugs with the classical epigenetic mechanism of DNA methylation or histone modification are increasingly being elucidated mechanistically and used to develop novel classes of epigenetic therapeutics. A data science approach is used to synthesize current knowledge on the pharmacological implications of epigenetic regulation of gene expression. Computer-aided knowledge discovery for epigenetic implications of current approved or investigational drugs was performed by querying information from multiple publicly available gold-standard sources to (i) identify enzymes involved in classical epigenetic processes, (ii) screen original biomedical scientific publications including bibliometric analyses, (iii) identify drugs that interact with epigenetic enzymes, including their additional non-epigenetic targets, and (iv) analyze computational functional genomics of drugs with epigenetic interactions. PubMed database search yielded 3051 hits on epigenetics and drugs, starting in 1992 and peaking in 2016. Annual citations increased to a plateau in 2000 and show a downward trend since 2008. Approved and investigational drugs in the DrugBank database included 122 compounds that interacted with 68 unique epigenetic enzymes. Additional molecular functions modulated by these drugs included other enzyme interactions, whereas modulation of ion channels or G-protein-coupled receptors were underrepresented. Epigenetic interactions included (i) drug-induced modulation of DNA methylation, (ii) drug-induced modulation of histone conformations, and (iii) epigenetic modulation of drug effects by interference with pharmacokinetics or pharmacodynamics. Interactions of epigenetic molecular functions and drugs are mutual. Recent research activities on the discovery and development of novel epigenetic therapeutics have passed successfully, whereas epigenetic effects of non-epigenetic drugs or epigenetically induced changes in the targets of common drugs have not yet received the necessary systematic attention in the context of pharmacological plasticity.
Epoxides and diols of polyunsaturated fatty acids (PUFAs) are bioactive and can influence processes such as tumor cell proliferation and angiogenesis. Studies with inhibitors of the soluble epoxide hydrolase (sEH) in animals overexpressing cytochrome P450 enzymes or following the systemic administration of specific epoxides revealed a markedly increased incidence of tumor metastases. To determine whether PUFA epoxides increased metastases in a model of spontaneous breast cancer, sEH-/- mice were crossed onto the polyoma middle T oncogene (PyMT) background. We found that the deletion of the sEH accelerated the growth of primary tumors and increased both the tumor macrophage count and angiogenesis. There were small differences in the epoxide/diol content of tumors, particularly in epoxyoctadecamonoenic acid versus dihydroxyoctadecenoic acid, and marked changes in the expression of proteins linked with cell proliferation and metabolism. However, there was no consequence of sEH inhibition on the formation of metastases in the lymph node or lung. Taken together, our results confirm previous reports of increased tumor growth in animals lacking sEH but fail to substantiate reports of enhanced lymph node or pulmonary metastases.
Objectives: Bladder neck contracture (BNC) is a bothersome complication following endoscopic treatment for benign prostatic hyperplasia (BPH). The objective of our study was to give a more realistic insight into contemporary endoscopic BNC treatment and to evaluate and identify risk factors associated with inferior outcome. Material and Methods: We identified patients who underwent transurethral treatment for BNC secondary to previous endoscopic therapy for BPH between March 2009 and October 2016. Patients with vesico-urethral anastomotic stenosis after radical prostatectomy were excluded. Digital charts were reviewed for re-admissions and re-visits at our institutions and patients were contacted personally for follow-up. Our non-validated questionnaire assessed previous urologic therapies (including radiotherapy, endoscopic, and open surgery), time to eventual further therapy in case of BNC recurrence, and the modality of recurrence management. Results: Of 60 patients, 49 (82%) and 11 (18%) underwent transurethral bladder neck resection and incision, respectively. Initial BPH therapy was transurethral resection of the prostate (TURP) in 54 (90%) and holmium laser enucleation of the prostate (HoLEP) in six (10%) patients. Median time from prior therapy was 8.5 (IQR 5.3–14) months and differed significantly in those with (6.5 months; IQR 4–10) and those without BNC recurrence (10 months; IQR 6–20; p = 0.046). Thirty-three patients (55%) underwent initial endoscopic treatment, and 27 (45%) repeated endoscopic treatment for BNC. In initially-treated patients, time since BPH surgery differed significantly between those with a recurrence (median 7.5 months; IQR 6–9) compared to those treated successfully (median 12 months; IQR 9–25; p = 0.01). In patients with repeated treatment, median time from prior BNC therapy did not differ between those with (4.5 months; IQR 2–12) and those without a recurrence (6 months; IQR 6–10; p = 0.6). Overall, BNC treatment was successful in 32 patients (53%). The observed success rate of BNC treatment was significantly higher after HoLEP compared to TURP (100% vs. 48%; p = 0.026). Type of BNC treatment, number of BNC treatment, and age at surgery did not influence the outcome. Conclusions: A longer time interval between previous BPH therapy and subsequent BNC incidence seems to favorably affect treatment success of endoscopic BNC treatment, and transurethral resection and incision appear equally effective. Granted the relatively small sample size, BNC treatment success seems to be higher after HoLEP compared to TURP, which warrants validation in larger cohorts.
Purpose: To stratify differences in visual semantic and quantitative imaging features in intensive care patients with nonspecific mastoid effusions versus patients with acute mastoiditis (AM) requiring surgical treatment. Methods: We included 48 patients (male, 28; female, 20; mean age, 59.5 ± 18.1 years) with mastoid opacification (AM, n = 24; control, n = 24) who underwent clinically indicated cerebral CT between 12/2007 and 07/2018 in this retrospective study. Semantic features described the extend and asymmetry of mastoid and middle-ear cavity opacification and complications like erosive changes. Minimum, maximum and mean Hounsfield unit (HU) values were obtained as quantitative features. We analyzed the features employing univariate testing. Results: Compared to intensive care patients, AM patients revealed asymmetric mastoid or middle-ear cavity opacification (likelihood-ratio (LR) < 0.001). Applying a dedicated threshold of the extent of opacification, AM patients reached significance levels of LR = 0.042 and 0.002 for mastoid and middle-ear cavity opacification. AM cases showed higher maximum and mean HU values (p = 0.009, p = 0.024). Conclusions: We revealed that the extent and asymmetry of mastoid and middle-ear cavity opacification differs significantly between AM patients and intensive care patients. Multicenter research is needed to expand our cohort and possibly pave the way to build a non-invasive predictive model for AM in the future.
Background: To test the value of immunohistochemistry (IHC) staining in prostate biopsies for changes in biopsy results and its impact on treatment decision-making. Methods: Between January 2017–June 2020, all patients undergoing prostate biopsies were identified and evaluated regarding additional IHC staining for diagnostic purpose. Final pathologic results after radical prostatectomy (RP) were analyzed regarding the effect of IHC at biopsy. Results: Of 606 biopsies, 350 (58.7%) received additional IHC staining. Of those, prostate cancer (PCa) was found in 208 patients (59.4%); while in 142 patients (40.6%), PCa could be ruled out through IHC. IHC patients harbored significantly more often Gleason 6 in biopsy (p < 0.01) and less suspicious baseline characteristics than patients without IHC. Of 185 patients with positive IHC and PCa detection, IHC led to a change in biopsy results in 81 (43.8%) patients. Of these patients with changes in biopsy results due to IHC, 42 (51.9%) underwent RP with 59.5% harboring ≥pT3 and/or Gleason 7–10. Conclusions: Patients with IHC stains had less suspicious characteristics than patients without IHC. Moreover, in patients with positive IHC and PCa detection, a change in biopsy results was observed in >40%. Patients with changes in biopsy results partly underwent RP, in which 60% harbored significant PCa.
Correct cellular function is ensured by a complex network of proteins and enzymes, regulating protein synthesis and degradation. This protein network, maintaining the so-called protein homeostasis, regulates those processes on multiple levels, producing new or degrading old proteins to cope with changing intra- and extracellular environments. Disturbance of this tightly regulated machinery can have severe effects on the cell and can lead to a variety of pathologies on organism level. Diseases including cancer, neurodegeneration and infections are associated with causative or consequent alterations in protein homeostasis. To understand the pathologies of these diseases, it is therefore critical to examine how perturbations of protein homeostasis affect cellular pathways and physiology. In the recent years, analysis of protein homeostasis networks has resulted in the development of novel therapeutic approaches. However, for many factors it remains unclear how the cell is affected, if they are disturbed. Protein synthesis and degradation represent immediate responses of the cell to changes and need to be studied in the right timeframe, making them difficult to access by common methodology. In this work we developed a new mass spectrometry (MS) based method to study protein synthesis and degradation on a system-wide scale. Multiplexed enhanced protein dynamic (mePROD) MS was developed, overcoming these limitations by special sample mixing and novel data analysis protocols. MePROD thereby enables the measurement of rapid and transient (e.g. minutes) changes in protein synthesis of thousands of proteins. During responses of the cell to stressors (e.g. protein misfolding, oxidation or infection), two major pathways regulate the protein synthesis: the Integrated Stress Response (ISR) and mammalian target of rapamycin (mTOR). Both pathways have been connected with various diseases in the past and are common therapy targets. Although both pathways target protein synthesis in stress responses, the set of targets regulated by these pathways was believed to differ. Through the new mePROD MS method we could measure a comprehensive comparison of both pathways for the first time, revealing comparable system-wide patterns of regulation between the two pathways. This changed the current view on the regulation elicited by these pathways and furthermore represents a useful resource for the whole field of research. We could further develop the mePROD method and decrease MS measurement time needed to obtain an in-depth dataset. Through implementation of logic based instrument methods, it was possible to enhance the number of measured proteins by approximately three-fold within the same measurement time.
The dynamics of protein synthesis and degradation are frequently modulated by pathogens infecting the cell to promote pathogen replication. At the same time, the cell counteracts the infection by modulating protein dynamics as well. To develop useful therapy approaches to fight infections, it therefore is necessary to understand the complex changes within the host cell during infections on a system-wide scale. In 2019, a novel coronavirus spread around the world, causing a world-wide health-crisis. To better understand this novel virus and its infection of the host cell we conducted a study applying the mePROD methodology and classical proteomics to characterize the dynamic changes during the infection course in vitro. We discovered that the infection remodeled a diverse set of host cell pathways (e.g. mRNA splicing, glycolysis, DNA synthesis and protein homeostasis) and thereby showed possible targets for antiviral therapy. By targeted inhibition of these pathways, we could observe that these pathways indeed are necessary for SARS-CoV-2 replication and their inhibition could reduce viral load in the cells. Another experimental approach focused on the dynamic changes of protein modification, namely phosphorylation, after infection with SARS-CoV-2. Here, we could show the very important participation of growth factor signaling pathways in viral proliferation. Both studies together revealed critical pathways that are needed for the viral proliferation and hence are promising candidates for further therapies. Subsequent targeting of these pathways by either already approved drugs (Ribavirin and Sorafenib) or drugs in clinical trials (2-deoxyglucose, Pladienolide-B, NMS-873, Pictilisib, Omipalisib, RO5126766 and Lonafarnib) could block viral replication in vitro and suggests important clinical approaches targeting SARS-COV-2 infection.