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To investigate clonal hematopoiesis associated gene mutations in vitro and to unravel the direct impact on the human stem and progenitor cell (HSPC) compartment, we targeted healthy, young hematopoietic progenitor cells, derived from umbilical cord blood samples, with CRISPR/Cas9 technology. Site-specific mutations were introduced in defined regions of DNMT3A, TET2, and ASXL1 in CD34+ progenitor cells that were subsequently analyzed in short-term as well as long-term in vitro culture assays to assess self-renewal and differentiation capacities. Colony-forming unit (CFU) assays revealed enhanced self-renewal of TET2 mutated (TET2mut) cells, whereas ASXL1mut as well as DNMT3Amut cells did not reveal significant changes in short-term culture. Strikingly, enhanced colony formation could be detected in long-term culture experiments in all mutants, indicating increased self-renewal capacities. While we could also demonstrate preferential clonal expansion of distinct cell clones for all mutants, the clonal composition after long-term culture revealed a mutation-specific impact on HSPCs. Thus, by using primary umbilical cord blood cells, we were able to investigate epigenetic driver mutations without confounding factors like age or a complex mutational landscape, and our findings provide evidence for a direct impact of clonal hematopoiesis-associated mutations on self-renewal and clonal composition of human stem and progenitor cells.

Pancreatic ductal adenocarcinoma (PDAC) has generally a poor prognosis, but recent data suggest that there are molecular subtypes differing in clinical outcome. This study examines the association between histopathologic heterogeneity, genetic profile, and survival. Tumor histology from 177 resected PDAC patients with follow-up data was subclassified according to predominant growth pattern, and four key genes were analyzed. PDACs were classified as conventional (51%), combined with a predominant component (41%), variants and special carcinomas (8%). Patients with combined PDACs and a dominant cribriform component survived longer than patients with conventional or other combined PDACs. Genetic alterations in at least two out of four genes were found in 95% of the patients ( KRAS 93%, TP53 79%, CDKN2A/p16 75%, SMAD4 37%). Patients with less than four mutations survived significantly longer (p = 0.04) than those with alterations in all four genes. Patients with either wildtype KRAS or CDKN2A/p16 lived significantly longer than those with alterations in these genes (p = 0.018 and p = 0.006, respectively). Our data suggest that the number of altered genes, the mutational status of KRAS and certain morphological subtypes correlate with the outcome of patients with PDAC. Future pathology reporting of PDAC should therefore include the KRAS status and a detailed morphological description.

Evidence for umbilical cord blood (UCB) cell therapies as a potential intervention for neurological diseases is emerging. To date, most existing trials worked with allogenic cells, as the collection of autologous UCB from high-risk patients is challenging. In obstetric emergencies the collection cannot be planned. In preterm infants, late cord clamping and anatomic conditions may reduce the availability. The aim of the present study was to assess the feasibility of UCB collection in neonates at increased risk of brain damage. Infants from four high-risk groups were included: newborns with perinatal hypoxemia, gestational age (GA) ≤30 + 0 weeks and/or birthweight <1,500 g, intrauterine growth restriction (IUGR), or monochorionic twins with twin-to-twin transfusion syndrome (TTTS). Feasibility of collection, quantity and quality of obtained UCB [total nucleated cell count (TNC), volume, sterility, and cell viability], and neonatal outcome were assessed. UCB collection was successful in 141 of 177 enrolled patients (hypoxemia n = 10; GA ≤30 + 0 weeks n = 54; IUGR n = 71; TTTS n = 6). Twenty-six cases were missed. The amount of missed cases per month declined over the time. Volume of collected UCB ranged widely (median: 24.5 ml, range: 5.0–102 ml) and contained a median of 0.77 × 108 TNC (range: 0.01–13.0 × 108). TNC and UCB volume correlated significantly with GA. A total of 10.7% (19/177) of included neonates developed brain lesions. To conclude, collection of UCB in neonates at high risk of brain damage is feasible with a multidisciplinary approach and intensive training. High prevalence of brain damage makes UCB collection worthwhile. Collected autologous UCB from mature neonates harbors a sufficient cell count for potential therapy. However, quality and quantity of obtained UCB are critical for potential therapy in preterm infants. Therefore, for extremely preterm infants alternative cell sources such as UCB tissue should be investigated for autologous treatment options because of the low yield of UCB.

Somatostatin receptor 2A expression is a feature of well-differentiated neuroendocrine neoplasms and is important for their diagnosis and therapy. Little is known about somatostatin receptor 2A expression in poorly differentiated neuroendocrine neoplasms in relation to TP53 and RB1 status and how these features may contribute to the separation of well from poorly differentiated neuroendocrine neoplasms with a proliferation index above 20%. This study investigates the expression of somatostatin receptors, p53 and Rb1, and TP53 alterations in pancreatic and extrapancreatic well and poorly differentiated neuroendocrine neoplasms (Ki67-index >20%). Thirty-seven poorly differentiated neuroendocrine neoplasms of pancreatic (n=12) and extrapancreatic origin (n=25) as well as 10 well-differentiated neuroendocrine neoplasms of the pancreas (n=9) and rectum (n=1) with a Ki67-index >20% were immunostained for synaptophysin, chromogranin A, Ki67, CD56, p53, Rb1, ATRX, DAXX, progesterone receptor, somatostatin receptor 2A, somatostatin receptor 5, and cytokeratin 20, and sequenced for TP53, exons 5–9. Somatostatin receptor 2A was positive in 6/37 of poorly differentiated and in 8/10 of well-differentiated neuroendocrine neoplasms. One well-differentiated and two poorly differentiated neuroendocrine neoplasms expressed somatostatin receptor 5. Abnormal nuclear p53 and Rb1 staining was found in 29/37 and 22/37 poorly differentiated neuroendocrine neoplasms, respectively, whereas all well-differentiated neuroendocrine neoplasms showed normal p53 and Rb1 expression. TP53 gene alterations were restricted to poorly differentiated neuroendocrine neoplasms (24/34) and correlated well with p53 expression. All cases were progesterone receptor negative. Somatostatin receptor 2A expression is not limited to well-differentiated neuroendocrine neoplasms but also occurs in 16% of poorly differentiated neuroendocrine neoplasms from various sites. Most poorly differentiated neuroendocrine neoplasms are characterized by TP53 alterations and Rb1 loss, usually in the absence of somatostatin receptor 2A expression. In the pancreas, these criteria contribute to separate well-differentiated neuroendocrine neoplasms with a Ki67-index above 20% from poorly differentiated neuroendocrine neoplasms.

Here, we show CRISPR/Cas9-based targeted somatic multiplexmutagenesis and its application for high-throughput analysis of gene function in mice. Using hepatic single guide RNA (sgRNA) delivery, we targeted large gene sets to induce hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC). We observed Darwinian selection of target genes, which suppress tumorigenesis in the respective cellular/tissue context, such asPtenorCdkn2a,and conversely found low frequency ofBrca1/2alterations, explaining mutational spectra in human ICC/HCC. Our studies show that multiplexed CRISPR/Cas9 can be used for recessive genetic screening or high-throughput cancer gene validation in mice. The analysis of CRISPR/Cas9-induced tumors provided support for a major role of chromatin modifiers in hepatobiliary tumorigenesis, including that of ARID family proteins, which have recently been reported to be mutated in ICC/HCC. We have also comprehensively characterized the frequency and size of chromosomal alterations induced by combinatorial sgRNA delivery and describe related limitations of CRISPR/Cas9 multiplexing, as well as opportunities for chromosome engineering in the context of hepatobiliary tumorigenesis. Our study describes novel approaches to model and study cancer in a high-throughput multiplexed format that will facilitate the functional annotation of cancer genomes.

Background Lenalidomide is a thalidomide analogue with immunomodulatory and anti-angiogenic properties that include altering cytokine production, activating T cells, and augmenting natural killer cell function. Lenalidomide is approved by the U.S. Food and Drug Administration (FDA) for single-agent treatment of myelodysplastic syndromes associated with a 5q deletion and as a combination therapy with dexamethasone for the treatment of multiple myeloma. Methods All prospective phase I–III clinical trials and preclinical data published until October 2011 and relevant literature were reviewed. Results In phase I and/or II studies of single-agent lenalidomide in patients with advanced cancer, responses were reported in patients with prostate, thyroid, hepatocellular, pancreatic, and renal cancer and melanoma. The most common toxicities were hematologic, and in the first clinical trials, thrombotic events were noted. When anticoagulation prophylaxis and exclusion of patients with a history of thrombosis were implemented, thrombotic complications became uncommon. Conclusion Monitoring of blood counts and for evidence of thromboembolic events is essential for patients treated with lenalidomide. Ongoing trials of lenalidomide combination therapy offer a treatment option for patients with advanced cancer and will better define the role of lenalidomide in solid tumors.

This dissertation develops a new methodology for interrogating the complex and material milieu of late medieval English literary production. Rather than take either the text or its author as the basic unit of literary significance, this project instead argues that the codex is the basic unit of literary significance in any study of medieval literary culture. Furthermore, since in most cases the codex is not an autographed copy of the author’s original work, each manuscript and its copy or variant of a given text are equally viable witnesses to the medieval literary phenomenon, and must be taken into account as part of the work of literature itself. In examining a manuscript corpus as the literary phenomenon, then, manuscripts themselves bear witness to a literary culture of selection, compilation, recapitulation and mediation that operates by way of a register of multivariate interactions users can have with manuscript objects. In order to develop tools for “reading” and interpreting this larger, more complex, integrated and material literary phenomenon, this work defines a method of “aggregate reading” with data visualization. “Aggregate reading” is a cross-over between Franco Moretti’s “distant reading,” which distills large literary phenomena into simplified structures and forms, and Heather Love’s “surface reading,” which operates on description and a proliferation of detail to make the “texture” of a phenomenon more visible. Aggregate reading relies both upon the distillation of graphs, maps, structures and forms and upon the proliferation of descriptions—either narrative or graphical—in order to make legible patterns within the larger literary phenomenon that give it meaning. This work takes the manuscript corpus of Piers Plowman as a case study, analyzing its fifty-two different codices and their textual variants in a number of statistical, computational, and literary ways. In addition to describing of the manuscript corpus, a holistic project heretofore unattempted in detail, this dissertation argues that the manuscripts themselves present a literary context in which to read the work of literature. This context is established by the set of other works, images, and objects with which the poem circulates in manuscript form. Repeated patterns within the corpus context allow this project to redefine the genre of the poem itself as an object facilitating pious and imaginative meditation. An examination of the devotional, meditative, and contemplative works in the corpus reveals that the poem traveled more with works by contemplative writer Richard Rolle more than any others, indicating that the poem itself was used as a contemplative machine, like other works in its manuscripts. A look at the second largest collocational trend in the manuscript corpus, the poem’s circulation with travel literatures and histories, indicates that the poem is less of a narrative dream vision—as it has long been classified—and more of an imaginative itinerary, developed for a meditative way-making among the commonplaces of medieval catechism and doctrine. The end result is that aggregate reading not only redefines the parameters of the literary object as part of material-textual discourse, but it also reveals a rich network of textual and material interactions with the work of literature that matter—that change the articulation of exactly what this work is and what it does.