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Long non-coding RNAs are a very versatile class of molecules that can have important roles in regulating a cells function, including regulating other genes on the transcriptional level. One of these mechanisms is that RNA can directly interact with DNA thereby recruiting additional components such as proteins to these sites via an RNA:dsDNA triplex formation. We genetically deleted the triplex forming sequence (FendrrBox) from the lncRNA Fendrr in mice and found that this FendrrBox is partially required for Fendrr function in vivo. We found that the loss of the triplex forming site in developing lungs causes a dysregulation of gene programs associated with lung fibrosis. A set of these genes contain a triplex site directly at their promoter and are expressed in lung fibroblasts. We biophysically confirmed the formation of an RNA:dsDNA triplex with target promoters in vitro. We found that Fendrr with the Wnt signalling pathway regulates these genes, implicating that Fendrr synergizes with Wnt signalling in lung fibrosis.
Large-scale molecular profiling studies in recent years have shown that central nervous system (CNS) tumors display a much greater heterogeneity in terms of molecularly distinct entities, cellular origins and genetic drivers than anticipated from histological assessment. DNA methylation profiling has emerged as a useful tool for robust tumor classification, providing new insights into these heterogeneous molecular classes. This is particularly true for rare CNS tumors with a broad morphological spectrum, which are not possible to assign as separate entities based on histological similarity alone. Here, we describe a molecularly distinct subset of predominantly pediatric CNS neoplasms (n = 60) that harbor PATZ1 fusions. The original histological diagnoses of these tumors covered a wide spectrum of tumor types and malignancy grades. While the single most common diagnosis was glioblastoma (GBM), clinical data of the PATZ1-fused tumors showed a better prognosis than typical GBM, despite frequent relapses. RNA sequencing revealed recurrent MN1:PATZ1 or EWSR1:PATZ1 fusions related to (often extensive) copy number variations on chromosome 22, where PATZ1 and the two fusion partners are located. These fusions have individually been reported in a number of glial/glioneuronal tumors, as well as extracranial sarcomas. We show here that they are more common than previously acknowledged, and together define a biologically distinct CNS tumor type with high expression of neural development markers such as PAX2, GATA2 and IGF2. Drug screening performed on the MN1:PATZ1 fusion-bearing KS-1 brain tumor cell line revealed preliminary candidates for further study. In summary, PATZ1 fusions define a molecular class of histologically polyphenotypic neuroepithelial tumors, which show an intermediate prognosis under current treatment regimens.
We report the case of a 62-year-old man with chronic pancreatitis who presented with increasing abdominal pain. Sonography, magnetic resonance imaging, contrast-enhanced computed tomography, and ultimately catheter angiography demonstrated a pancreatic pseudocyst that had eroded into the splenoportal venous confluence, mimicking an arterial aneurysm. The diagnostic was confirmed at the time of surgical treatment. This case demonstrates the use of imaging to diagnose complications of pancreatitis, and the difficulty of distinguishing an eroding pseudocyst from an arterial aneurysm.
Persistent neuropathic pain is a frequent consequence of peripheral nerve injuries, particularly in the elderly. Using the IntelliCage we studied if sciatic nerve injury obstructed learning and memory in young and aged mice, each in wild type and progranulin deficient mice, which develop premature signs of brain aging. Both young and aged mice developed long-term nerve injury-evoked hyperalgesia and allodynia. In both genotypes, aged mice with neuropathic pain showed high error rates in place avoidance acquisition tasks. However, once learnt, these aged mice with neuropathic pain showed a significantly stronger maintenance of the aversive memory. Nerve injury did not affect place preference behavior in neither genotype, neither in young nor aged mice. However, nerve injury in progranulin deficient mice impaired the learning of spatial sequences of awarded places, particularly in the aged mice. This task required a discrimination of clockwise and anti-clockwise sequences. The chaining failure occurred only in progranulin deficient mice after nerve injury, but not in sham operated or wildtype mice, suggesting that progranulin was particularly important for compensatory adaptations after nerve injury. In contrast, all aged mice with neuropathic pain, irrespective of the genotype, had a long maintenance of aversive memory suggesting a negative alliance and possibly mutual aggravation of chronic neuropathic pain and aversive memory at old age.
BACKGROUND: The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements.
RESULTS: The method proposed here is specifically designed for the analysis of perturbation responses. It combines different scores to capture fast and transient dynamics as well as slow expression changes, and performs well in the presence of low replicate numbers and irregular sampling times. The results are given in the form of tables including links to figures showing the expression dynamics of the respective transcript. These allow to quickly recognise the relevance of detection, to identify possible false positives and to discriminate early and late changes in gene expression. An extension of the method allows the analysis of the expression dynamics of functional groups of genes, providing a quick overview of the cellular response. The performance of this package was tested on microarray data derived from lung cancer cells stimulated with epidermal growth factor (EGF).
CONCLUSION: Here we describe a new, efficient method for the analysis of sparse and heterogeneous time course data with high detection sensitivity and transparency. It is implemented as R package TTCA (transcript time course analysis) and can be installed from the Comprehensive R Archive Network, CRAN. The source code is provided with the Additional file 1.
Acute myeloid leukemia (AML) is a malignant disorder derived from neoplastic myeloid progenitor cells characterized by abnormal proliferation and differentiation. Although novel therapeutics have recently been introduced, AML remains a therapeutic challenge with insufficient cure rates. In the last years, immune-directed therapies such as chimeric antigen receptor (CAR)-T cells were introduced, which showed outstanding clinical activity against B-cell malignancies including acute lymphoblastic leukemia (ALL). However, the application of CAR-T cells appears to be challenging due to the enormous molecular heterogeneity of the disease and potential long-term suppression of hematopoiesis. Here we report on the generation of CD33-targeted CAR-modified natural killer (NK) cells by transduction of blood-derived primary NK cells using baboon envelope pseudotyped lentiviral vectors (BaEV-LVs). Transduced cells displayed stable CAR-expression, unimpeded proliferation, and increased cytotoxic activity against CD33-positive OCI-AML2 and primary AML cells in vitro. Furthermore, CD33-CAR-NK cells strongly reduced leukemic burden and prevented bone marrow engraftment of leukemic cells in OCI-AML2 xenograft mouse models without observable side effects.
Chimeric antigen receptor (CAR)-T cell therapies are on the verge of becoming powerful immunotherapeutic tools for combating hematological diseases confronted with pressing medical needs. Lately, CAR-NK cell therapies have also come into focus as novel therapeutic options to address hurdles related to CAR-T cell therapies, such as therapy-induced side effects. Currently, more than 500 CAR-T and 17 CAR-NK cell trials are being conducted worldwide including the four CAR-T cell products Kymriah, Yescarta, Tecartus and Breyanzi, which are already available on the market. Most CAR-T cell-based gene therapy products that are under clinical evaluation consist of autologous enriched T cells, whereas CAR-NK cell-based approaches can be generated from allogeneic donors. Besides modification based on a second-generation CAR, more advanced CAR-immune cell therapeutics are being tested, which utilize precise insertion of genes to circumvent graft-versus-host disease (GvHD) or employ a dual targeting approach and adapter CARs in order to avoid therapy resistance caused by antigen loss. In this review, we are going to take a closer look at the commercial CAR-T cell therapies, as well as on CAR-T and CAR-NK cell products, which are currently under evaluation in clinical trials, that are being conducted in Germany.
The etiology of many diseases results from the dysregulation of inflammation. Understanding the molecular mechanisms controlling the inflammatory response is essential to formulate therapeutic strategies for the treatment of inflammatory conditions. In fact, substantial research has unveiled important aspects of the inflammatory machinery, both at the cellular and molecular levels. Recently, sphingolipids (Sph) have emerged as signaling molecules that regulate many cell functions, and ample evidence emphasizes their role in the regulation of inflammatory responses. ...
Stent insertion is an established technique of endoscopic retrograde cholangiopancreatography (ERCP) to treat symptomatic malignant or benign biliary strictures, and stent placement is accomplished by using the over-the-wire (OTW) method. In some cases, however, it might be challenging and sometimes time consuming to pass a complex biliary stricture with the guidewire. Stent-exchange technique with a guidewire left in place during stent removal might therefore be helpful to guarantee successful and time-sparing interventions.
A simple method is presented to remove the stent with the guidewire left in place, using the OTW stent-exchange method in ERCP. This technique simplifies stent OTW exchange by using a simple endoscopy snare. This article is part of an expert video encyclopedia.
Small bowel endoscopy is indicated for patients with an unidentified bleeding site in esophagogastroduodenoscopy and ileocolonoscopy and symptoms of intestinal blood loss or unexplained anemia. In approximately two-thirds of these cases, capsule endoscopy (CE) detects a lesion within the small bowel that explains the patient's symptoms. In few cases, though, lesions outside of the small bowel might be revealed by CE. Therefore, attention to all intestines that are visualized by CE might be necessary not to overlook bleeding sites that had not been discovered by prior flexible endoscopy.
Here the case of a 71-year-old male patient with unexplained anemia is presented by the authors. Small-bowel CE revealed minor bleeding from a neoplastic mass in the cecum. The final diagnosis of an adenocarcinoma of the ascending colon was established after the patient underwent a right hemicolectomy. This article is part of an expert video encyclopedia.
Small bowel endoscopy is indicated for patients with an unidentified bleeding site in esophago-gastro-duodenoscopy and ileo-colonoscopy and symptoms of intestinal blood loss or unexplained anemia. In approximately two-thirds of these cases, capsule endoscopy (CE) detects a lesion within the small bowel that explains the patient's symptoms. In few cases, though, lesions outside of the small bowel might be revealed by CE. Therefore, attention to all intestines that are visualized by CE might be necessary not to overlook bleeding sites that had not been discovered by prior flexible endoscopy.
The authors present the case of a 71-year-old male patient who presented to their outpatient clinic for unexplained anemia. Small bowel CE revealed minor bleeding from an adenocarcinoma in the cecum. This article is part of an expert video encyclopedia.
Operatively altered anatomy might provide a challenge for endoscopic retrograde cholangiopancreatography. However, with the support of the balloon-assisted enteroscopy technique the access route to the biliary system even in long-limb Roux-Y anastomosis is feasible in most cases.
In this video case report, an 81-year-old woman was symptomatic for stone obstruction of the common bile duct (CBD). Complete gastrectomy had been performed in this patient for stomach cancer many years earlier. Balloon-assisted enteroscopy was used for retrograde access of the duodenum via a Roux-Y anastomosis. There was major difficulty in intubating the CBD via the native papilla in this case because access was prevented by the tangential approach of the enteroscope. After performing an incomplete papillectomy, the insertion of a guidewire into the CBD was feasible and the bile duct stone was removed. This article is part of an expert video encyclopedia.
Here the authors report the case of an elderly woman who had upper abdominal pain, upper gastrointestinal hemorrhage, and jaundice (a symptomatic triad termed the ‘Quincke’ triad) a few days after endoscopic sphincterotomy. Abdominal ultrasonography demonstrated an echo-rich filling of the choledochus consistent with hemobilia. Endoscopic retrograde cholangiography was immediately performed and blood clots were removed from the common bile duct. A nasobiliary catheter was placed to irrigate the bile duct for prevention of recurring obstruction of the bile ducts from blood clots. Further follow-up of the patient was uneventful. This article is part of an expert video encyclopedia.
Small bowel tumors are detected in approximately 10% of patients with small bowel endoscopies for obscure or overt mid-intestinal bleeding. Small bowel tumors may be of malignant or benign etiology. Malignant etiologies include adenocarcinoma, neuroendocrine tumors, or lymphoma, whereas benign lesions are typically lipomas, inflammatory polyps, or adenomas. Within the group of nonneoplastic lesions inflammatory polyps are most frequent. Significant bleeding and bowel obstruction due to intussusception might occur, and surgical or endoscopic treatment has been reported for symptomatic patients. A case is demonstrated with an inflammatory fibroid polyp detected by capsule endoscopy and confirmed by balloon enteroscopy. This article is part of an expert video encyclopedia.
The small bowel is essential to sustain alimentation and small bowel Crohn's disease (CD) may severely limit its function. Small bowel imaging is a crucial element in diagnosing small
bowel CD, and treatment control with imaging is increasingly used to optimize the patients outcome. Thereby, capsule endoscopy, Balloon-assisted enteroscopy, and Magnetic resonance imaging have become key players to manage CD patients. In this review, role of small bowel imaging is detailed discussed for use in diagnosing and managing Crohn's disease patients.
Endoscopic retrograde cholangiopancreatography (ERCP) offers an effective interventional option for treating symptomatic chronic pancreatitis. Endoscopic pancreatic sphincterotomy is performed to facilitated endoscopic treatment. Pancreatic duct strictures can be treated by inserting plastic stents, and a 10 Fr endoprosthesis is adequate in many cases. Before stent insertion, hydrostatic balloon dilation is needed in some cases. Pancreatic stones can be removed with a dormia basket, but combining ERCP and extracorporeal shockwave lithotripsy (ESWL) is often most effective.
Standard and advanced endoscopic treatment approaches are delineated in this article and include stricture dilation with a Soehendra retriever, cSEMS placement and multi-stenting.
Celiac disease (CD) is an immune-mediated enteropathy that is characterized by intraepithelial lymphocytosis, crypt hyperplasia, and villous atrophy. Prevalence is high and has been estimated to range between 0.5% and 1.5%. Capsule endoscopy (CE) has a sensitivity and specificity of approximately 90%. CD is an important differential diagnosis for diagnostic workup for anemia, malabsorption, or diarrhea, and must be recognized reliably by the investigator. Moreover, CE is the preferred method to screen for complications in CD, such as enteropathy-associated T-cell lymphoma, ulcerative jejunitis, and small bowel adenocarcinoma. This article is part of an expert video encyclopedia.
Peutz–Jeghers syndrome (PJS) is a rare autosomal-dominant inherited disorder characterized by gastrointestinal hamartomas, mucocutaneous pigmentation, and an elevated cancer risk. Moreover, intussusception risk may be as high as 50% at the age of 20 years and is caused by large polyps. There is some evidence that endoscopic surveillance of PJS patients with removal of small intestinal polyps with a diameter of more than 15 mm efficiently prevents intussusceptions. In recent years, capsule endoscopy (CE) has largely replaced small-bowel radiography techniques to screen for small-bowel polyps. Magnetic resonance imaging may be equally efficient as CE for screening of large polyps. Balloon enteroscopy may be used for endoscopic snare resection of polyps. This article is part of an expert video encyclopedia.
The author presents the case of a patient with severe bleeding from a duodenal ulcer that could not be controlled by endoscopic application of metal clips and injection of fibrin glue. Angiographic embolization with placement of coils into the feeding vessel stopped the bleeding. However, 3 days later, a fistula emerged from coil material penetrating into the dorsal duodenum and a peritoneal leakage developed. The fistula was completely closed by placing an over-the-scope clip on the enteral opening of the fistula. This article is part of an expert video encyclopedia.
Small-bowel tumors are rare and account for approximately 5% of all gastrointestinal tumors. Approximately 65% of small-bowel tumors are malignant, and approximately 40% of these tumors are adenocarcinomas. Similar to colorectal adenocarcinoma, premalignant adenomas of the small bowel may progress to carcinoma. This occurs both sporadically and in the context of hereditary tumor syndromes such as familial adenomatous polyposis or hereditary nonpolyposis colorectal cancer (Lynch syndrome). Herein cases with small-bowel adenocarcinomas visualized with both capsule endoscopy and double-balloon enteroscopy are presented. This article is part of an expert video encyclopedia.