An Autochthonous Mouse Model of Myd88- and BCL2-Driven Diffuse Large B-cell Lymphoma Reveals Actionable Molecular Vulnerabilities

Diffuse large B-cell lymphoma is the most common non-Hodgkin`s lymphoma and accounts for 30-40% of newly diagnosed lymphoma. DLBCL can be subdivided in the activated B-cell-like (ABC) and the germinal center B-cell-like (GCB) DLBCL. Large-scale sequencing efforts showed a large overlap between ABC-and GCB-DLBCL. Therefore two research groups recently published new genetic based approaches to classify DLBCL into distinct clusters. The most aggressive cluster in regards to clinical outcome and resistance to first line treatment is the MCD/C5-DLBCL, enriched with former ascribed ABC-DLBCL cases. Two of the most common aberrations in MCD/C5-DLBCL are a copy-number gain of BCL2and a point mutation in MYD88.In this study we present a detailed characterization of our Myd88-and BCL2-driven MCD/C5-DLBCL mouse model. We characterized the mouse model using immune phenotyping, RNA sequencing and whole exome sequencing. We could show that the lymphomas derived from our mouse model resemble genetic features of human MCD/C5-DLBCL. We detected that Myd88and BCL2induce splenomegaly and germinal center formation in vivo. This indicates that the oncogenic Myd88and BCL2overexpression might cooperate in lymphomagenesis. Furthermore we could detect an actionable dependenceof the murine MCD/C5-DLBCL model on BCL2. This BCL2dependence was also shown in human MCD/C5-DLBCL cell lines. Moreover, the human MCD/C5-DLBCL in comparison to the human non-MCD/C5-DLBCL showed a higher expression of PD-L1. Therefore we used our MCD/C5-DLBCL mouse model as preclinical tool to test a combined blockade of BCL2 and PD-1. We observed a significant synergistic effect of the combined treatment in comparison to the single agents and the vehicle control with regard to overall survival and tumor growth control, which could be shown by MRI monitoring.Altogether, we demonstrated that our Myd88/BCL2-driven mouse model resembles many features of the human MCD/C5-DLBCL. Further we could use our MCD/C5-DLBCL mouse model as a preclinical tool to detect actionable molecular vulnerabilities and to test new treatment regimens. Based on the detected cooperation of mutant Myd88and BCL2in murine lymphomagenesis, we were able to show a synergistic effect of combined BCL2 and PD-1 blockade in murine MCD/C5-DLBCL. These data indicate that it could be a reasonable approach to test a combined BCL2/PD-1 blockade inrelapsed or refractory patients

AMS Radiocarbon analysis of Greenhouse gases: Method development and application

The northern circumpolar permafrost regions are warming faster compared to the global mean. As a result, the duration of annual thaw seasons is increasing, so that the permafrost is subjected to increasingly deep thaw. Within the permafrost zones large amounts of carbon were buried over thousands of years and previously freeze locked due to the cold climate. These carbon sinks are affected by the consequences of global warming and become available for microbial degradation, and thereby potentially turning from carbon sinks into carbon pools. As a result of the microbial degradation of organic matter, the greenhouse gases carbon dioxide and methane are released into the atmosphere, amplifying the global warming, and forcing a positive climate feedback. Among the permafrost deposits, Pleistocene sediments, termed Yedoma, are especially vulnerable to climate change induced rapid thaw and subject to thermoerosion because of their high ice-content. While chemical characterizations of permafrost organic matter and laboratory incubation experiments give information about the degradability of Yedoma organic matter, actual field-studies documenting the extent and exact sources of greenhouse gas release are limited. The analysis of carbon isotopes (13C, 14C) can be used to estimate the age of the permafrost organic matter that is being degraded into greenhouse gases and trace their sources. This is done by collecting carbon dioxide during either field expeditions or during analogue laboratory incubation experiments. Samples are handled in laboratory vacuum rigs, during which the amount of carbon dioxide is quantified and purified from other gases that have been collected along the carbon dioxide. While these methods are overall established and reliable, the analyses are, however, sensitive towards contamination from exogenous carbon sources. The sensitivity towards contamination is amplified towards increasingly smaller sample sizes, down to a few micrograms of carbon. Thus, assessments are necessary to quantify how much contamination is introduced during the preparation of carbon dioxide samples for isotopic analysis and to determine what is the smallest sample size that still delivers meaningful results. The aims of this thesis were to evaluate the laboratory methods applied for the isotopic analysis of carbon dioxide and apply these methods and sampling devices to a field study investigating the degradability of freshly thawed Yedoma organic matter. The evaluation of our existing laboratory methods to handle carbon dioxide demonstrated that routine measurements can safely be performed on samples as small as 20 μg C. Samples as small as 2.5 μg C can also be analyzed, however the associated uncertainty is very large and prevents the analysis of 14C-depleted samples. Further, new methods for the isotopic analysis of methane via accelerator mass spectrometry were established. This required the development of a workflow and pre-treatment routine to convert methane samples to carbon dioxide. After establishing a satisfying conversion rate, first test runs of different standards and gas mixtures further allowed the identification and quantification of sources of exogenous carbon, potentially contaminating samples. During the application study, carbon dioxide emissions were collected along with Yedoma sediment samples from an active retrogressive thaw slump in the Lena River Delta in Siberia. The sediment samples were incubated in the laboratory for a 1.5-year aerobic incubation experiment, during which the amount of produced carbon dioxide was closely monitored and sampled at fixed intervals. The carbon isotopy of the carbon dioxide sampled during the field campaign was compared with the carbon dioxide produced during the incubation experiment and a mass balance approach was applied to identify carbon sources based on isotopic values. The results show that labile organic matter pools are being degraded first and that their contribution to carbon dioxide emissions is decreasing after the initial thaw. Mostly ancient organic matter is being degraded at sites where Pleistocene-aged Yedoma is exposed, the admixture of Pleistocene Yedoma sediments with younger Holocene sediments through erosion does not favor the degradation of ancient organic matter through positive priming. Instead, younger substrates are degraded preferentially, if available. Most surprisingly, the results of the mass balance approach suggest, that a significant proportion of the carbon dioxide, that was released during the field measurement as well as during the laboratory incubation, was derived from inorganic carbon. The release of carbon dioxide from inorganic carbon is likely favored by low pH values and organic acids contained in the thaw slump sediments. The results of the carbon isotope analysis further suggest that a fraction of the carbon dioxide derived from secondary carbonates. Therefore, it is hypothesized that these secondary carbonates precipitated from microbially respired carbon dioxide and thus would not contribute to a net positive carbon emission budget

Fatty acid bioconversion in harpacticoid copepods in a changing environment : a transcriptomic approach

By 2100, global warming is predicted to significantly reduce the capacity of marine primary producers for long-chain polyunsaturated fatty acid (LC-PUFA) synthesis. Primary consumers such as harpacticoid copepods (Crustacea) might mitigate the resulting adverse effects on the food web by increased LC-PUFA bioconversion. Here, we present a high-quality de novo transcriptome assembly of the copepodPlatychelipus littoralis, exposed to changes in both temperature (+3 degrees C) and dietary LC-PUFA availability. Using this transcriptome, we detected multiple transcripts putatively coding for LC-PUFA-bioconverting front-end fatty acid (FA) desaturases and elongases, and performed phylogenetic analyses to identify their relationship with sequences of other (crustacean) taxa. While temperature affected the absolute FA concentrations in copepods, LC-PUFA levels remained unaltered even when copepods were fed an LC-PUFA-deficient diet. While this suggests plasticity of LC-PUFA bioconversion withinP. littoralis, none of the putative front-end desaturase or elongase transcripts was differentially expressed under the applied treatments. Nevertheless, the transcriptome presented here provides a sound basis for future ecophysiological research on harpacticoid copepods. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'

Array-based DNA methylation profiling of primary lymphomas of the central nervous system

<p>Abstract</p> <p>Background</p> <p>Although primary lymphomas of the central nervous system (PCNSL) and extracerebral diffuse large B-cell lymphoma (DLBCL) cannot be distinguished histologically, it is still a matter of debate whether PCNSL differ from systemic DLBCL with respect to their molecular features and pathogenesis. Analysis of the DNA methylation pattern might provide further data distinguishing these entities at a molecular level.</p> <p>Methods</p> <p>Using an array-based technology we have assessed the DNA methylation status of 1,505 individual CpG loci in five PCNSL and compared the results to DNA methylation profiles of 49 DLBCL and ten hematopoietic controls.</p> <p>Results</p> <p>We identified 194 genes differentially methylated between PCNSL and normal controls. Interestingly, Polycomb target genes and genes with promoters showing a high CpG content were significantly enriched in the group of genes hypermethylated in PCNSL. However, PCNSL and systemic DLBCL did not differ in their methylation pattern.</p> <p>Conclusions</p> <p>Based on the data presented here, PCNSL and DLBCL do not differ in their DNA methylation pattern. Thus, DNA methylation analysis does not support a separation of PCNSL and DLBCL into individual entities. However, PCNSL and DLBCL differ in their DNA methylation pattern from non- malignant controls.</p

Biotic and Abiotic Drivers of Topsoil Organic Carbon Concentration in Drylands Have Similar Effects at Regional and Global Scales

Drylands contain 25% of the world’s soil organic carbon (SOC), which is controlled by many factors, both abiotic and biotic. Thus, understanding how these factors control SOC concentration can help to design more sustainable land-use practices in drylands aiming to foster and preserve SOC storage, something particularly important to fight ongoing global warming. We use two independent, largescale databases with contrasting geographic coverage (236 sites in global drylands and 185 sites in Patagonia, Argentina) to evaluate the relative importance of abiotic (precipitation, temperature and soil texture) and biotic (primary productivity) factors as drivers of SOC concentration in drylands at global and regional scales. We found that biotic and abiotic factors had similar effects on SOC concentration across regional and global scales: Maximum temperature and sand content had negative effects, while precipitation and plant productivity exerted positive effects. Our findings provide empirical evidence that increases in temperature and reductions in rainfall, as forecasted by climatic models in many drylands worldwide, promote declines in SOC both directly and indirectly via the reduction in plant productivity. This has important implications for the conservation of drylands under climate change; land management should seek to enhance plant productivity as a tool to offset the negative impact of climate change on SOC storage and on associated ecosystem services.Estación Experimental Agropecuaria BarilocheFil: Gaitan, Juan Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; Argentina. Universidad Nacional de Luján. Departamento de Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Maestre, Fernando T. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; EspañaFil: Bran, Donaldo Eduardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; ArgentinaFil: Buono, Gustavo Gabriel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Chubut; ArgentinaFil: Dougill, Andrew J. University of Leeds. School of Earth and Environment; Reino UnidoFil: Garcia Martinez, Guillermo Carlos. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Esquel; ArgentinaFil: Ferrante, Daniela. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; ArgentinaFil: Guuroh, Reginald Tang. CSIR-Forestry Research Institute of Ghana; GhanaFil: Linstadter, Anja. University of Cologne. Botanical Institute; AlemaniaFil: Massara Paletto, Virginia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Chubut; ArgentinaFil: Thomas, Andrew David. Aberystwyth University. Department of Geography and Earth Sciences; Reino UnidoFil: Oliva, Gabriel Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentin

Mouse models of diffuse large B cell lymphoma

Diffuse large B cell lymphoma (DLBCL) is a genetically highly heterogeneous disease. Yet, to date, the vast majority of patients receive standardized frontline chemo-immune-therapy consisting of an anthracycline backbone. Using these regimens, approximately 65% of patients can be cured, whereas the remaining 35% of patients will face relapsed or refractory disease, which, even in the era of CAR-T cells, is difficult to treat. To systematically tackle this high medical need, it is important to design, generate and deploy suitable in vivo model systems that capture disease biology, heterogeneity and drug response. Recently published, large comprehensive genomic characterization studies, which defined molecular sub-groups of DLBCL, provide an ideal framework for the generation of autochthonous mouse models, as well as an ideal benchmark for cell line-derived or patient-derived mouse models of DLBCL. Here we discuss the current state of the art in the field of mouse modelling of human DLBCL, with a particular focus on disease biology and genetically defined molecular vulnerabilities, as well as potential targeting strategies

Inheritance of Barley yellow dwarf virus resistance in maize

Barley yellow dwarf (BYD) is one of the economically most important virus diseases in cereals. Due to increasing winter temperatures it is expected that BYD will become an increasing problem in maize cultivation. In earlier studies, it was reported that BYD has a negative impact on plant performance of maize. BYD virus (BYDV) is transmitted by aphids and the best control of the virus is the development of resistant maize cultivars. Therefore, the first objectives of my thesis research were to (i) determine phenotypic and genotypic variation in five segregating populations and in a broad germplasm set of maize with respect to BYDV tolerance and resistance as well as to (ii) quantify the influence of BYDV infection on the plant traits plant height, ear height, and flowering time. I observed a negative impact of BYDV infection on maize plant traits which shows that the development of resistant maize cultivars is of high importance for maize cultivation. Furthermore, in the connected biparental populations as well as in the association mapping population, I observed a high genotypic variance with regard to BYDV resistance which is the requirement for successful breeding and the identification of genome regions which contribute to BYDV resistance. The evaluation of BYDV resistance by the inoculation with BYDV and by double antibody sandwich enzyme-linked immunosorbent assay (DASELISA) is dificult to be included in the breeding process. Therefore, molecular markers are of high importance for the improvement of BYDV resistance by breeding. Therefore, the objective of this study was the (iii) identification of genome regions which are involved in the BYDV resistance by a genome wide association study (GWAS). For the BYDV resistance traits, significantly (&#945;=0.01) associated SNPs were identified in the GWAS on chromosome 10 and 4. The SNPs identified for virus extinction on chromosome 10 explained in a simultaneous fit 25% of the phenotypic variance and were located in gene regions which were in other plants described to be involved in resistance mechanisms. This suggests that BYDV resistance is inherited oligogenically and that genes involved in general resistance mechanisms are also involved in BYDV resistance in maize. GWAS has the advantage that a large number of alleles per locus can be surveyed simultaneously, and because historical recombinations can be used, the mapping resolution is higher compared to classical linkage mapping. Nevertheless, genes contributing to phenotypic variation which show a low allele frequency can remain undetected. Due to a balanced allele frequency in segregating populations, linkage mapping has the advantage of higher QTL detection power compared to GWAS. Therefore, the objective of this study was to (iv) validate the genome regions with a linkage analysis in connected biparental crosses. The genome region on chromosome 10 which was identified in the GWAS to be linked to BYDV resistance could be validated in the linkage mapping study with connected populations as well as in the single populations. Furthermore, the QTL on chromosome 10 colocalized with the QTL identified in controlled greenhouse conditions. In earlier studies, QTL for other virus resistances were identified on chromosome 10. This suggests that these genes are involved in multiple virus resistances. The identified genome regions explain 45% of the phenotypic variance and are, therefore, promising for the use in MAS. The broad genotypic variation with regard to BYDV resistance, observed in my thesis research, provided a good basis for the successful identification of molecular markers which are associated with BYDV resistance in maize. The markers identified in my study by GWAS were validated by a linkage mapping approach and are promising for the use in marker assisted selection on BYDV resistance in maize breeding.Die Gerstengelbverzwergung (Barley yellow dwarf, BYD) gehört wirtschaftlich zu den wichtigsten Viruskrankheiten im Getreide. Aufgrund steigender Wintertemperaturen wird auch in Mais erwartet, dass die BYD in Zukunft ein wachsendes Problem wird, zumal aus bisherigen Studien bekannt ist, dass die BYD einen negativen Einfluss auf Mais hat. Die effektivste Methode zur Bekämpfung des BYD Virus (BYDV), welches von Aphiden übertragen wird, ist die Züchtung von resistenten Maissorten. Deshalb waren die ersten Ziele meiner Doktorarbeit (i) die Erfassung der genotypischen Variation für die BYDV-Resistenz in fünf spaltenden Populationen und in einem diversen Mais-Set, sowie (ii) die Beobachtung des Einflusses der BYDV-Infektion auf die Pflanzenmerkmale, Pflanzenhöhe, Kolbenhöhe und den Blühzeitpunkt. In der aktuellen Studie wurde beobachtet, dass eine BYDV-Infektion einen negativen Einfluss auf Pflanzenmerkmale von Mais hat - was die Relevanz einer Verbesserung der BYDV-Resistenz hervorhebt. Des Weiteren wurde sowohl in den verbundenen spaltenden Populationen als auch in der Assoziationskartierungspopulation eine hohe genotypische Variation für die BYDV Resistenz beobachtet. Diese stellt eine wichtige Voraussetzung für eine erfolgreiche Assoziationskartierung dar. Die Evaluierung hinsichtlich der BYDV-Resistenz ist schwer in den Züchtungsprozess zu integrieren, da die Virus-Inokulation mit Blattläusen und die Bestimmung des Virusgehalts durch DAS-ELISA sehr aufwändig sind. Für die züchterische Verbesserung der BYDV-Resistenz sind molekulare Marker von gröer Bedeutung. Deshalb war ein weiteres Ziel der Arbeit (iii) in einer genomweiten Assoziationskartierung (GWAS) Genomregionen zu identifizieren, die an der BYDV-Resistenz in Mais beteiligt sind. In der GWAS wurden signifikante (&#945;=0.01) SNPs auf Chromosom 4 und 10 für die BYDV-Resistenzmerkmale identifiziert. Die SNPs die auf Chromosom 10 für die Virusextinktion identifiziert wurden, erklären zusammen 25% der phänotypischen Varianz. Dieser Genombereich wurde schon in anderen Pflanzen als für Resistenzmechanismen zuständig beschrieben. Die Ergebnisse der aktuellen Studie lassen deshalb vermuten, dass die BYDV-Resistenz oligogen vererbt wird und, dass Gene, die in generelle Resistenzmechanismen involviert sind, auch an der BYDV-Resistenz in Mais beteiligt sind. Die GWAS hat den Vorteil, dass eine gro&#946;e Anzahl von Allelen pro Locus gleichzeitig untersucht werden können. Da in verbundenen Populationen eine höhere Rekombination stattgefunden hat, ist die Auflösung, verglichen zur klassischen quantitative trait locus (QTL) Kartierung, höher. Trotzdem können Gene, die zu einer gröen phänotypischen Variation füuhren, unentdeckt bleiben, wenn sie eine niedrige Allel Frequenz aufweisen. Durch die ausgeglichene Allelfrequenz in biparentalen Populationen hat die klassische QTL-Analyse eine höhere Power weitere QTL zu detektieren als eine GWAS. Deshalb war ein weiteres Ziel dieser Arbeit (iv) die Validierung der Genomregionen in einer QTL-Analyse mit verbundenen Populationen. Die Genomregion auf Chromosom 10, die in der GWAS identifiziert wurde, konnte in der QTL-Analyse mit verbundenen Populationen und in QTL- Analysen mit Einzel-Populationen validiert werden. Darüber hinaus kolokalisieren diese QTL mit den QTL, die in kontrollierten Gewächshausbedingungen identifiziert wurden. Au&#946;erdem lassen die Ergebnisse vermuten, dass die Gene auch an der Ausprägung anderer Virus-Resistenzen beteiligt sind. Da diese Genomregionen 45% der phänotypischen Varianz erklären, sind sie vielversprechend für die Marker-gestützte Selektion. Die hohe genotypische Varianz, die in meiner Arbeit beobachtet wurde, stellte eine gute Gundlage für die Identifizierung von molekularen Markern dar, die mit der BYDV Resistenz assoziiert sind. Diese Marker, welche mit einer GWAS identifiziert wurden, konnten mit einer QTL Kartierung verifiziert werden und sind vielversprechend für die markergestützte Selektion auf BYDV Resistenz in der Maiszüchtung

Formation of mineral-associated organic matter in temperate soils is primarily controlled by mineral type and modified by land use and management intensity

Formation of mineral-associated organic matter (MAOM) supports the accumulation and stabilization of carbon (C) in soil, and thus, is a key factor in the global C cycle. Little is known about the interplay of mineral type, land use and management intensity in MAOM formation, especially on subdecadal time scales. We exposed mineral containers with goethite or illite, the most abundant iron oxide and phyllosilicate clay in temperate soils, for 5 years in topsoils of 150 forest and 150 grassland sites in three regions across Germany. Results show that irrespective of land use and management intensity, more C accumulated on goethite than illite (on average 0.23 ± 0.10 and 0.06 ± 0.03 mg m−2 mineral surface respectively). Carbon accumulation across regions was consistently higher in coniferous forests than in deciduous forests and grasslands. Structural equation models further showed that thinning and harvesting reduced MAOM formation in forests. Formation of MAOM in grasslands was not affected by grazing. Fertilization had opposite effects on MAOM formation, with the positive effect being mediated by enhanced plant productivity and the negative effect by reduced plant species richness. This highlights the caveat of applying fertilizers as a strategy to increase soil C stocks in temperate grasslands. Overall, we demonstrate that the rate and amount of MAOM formation in soil is primarily driven by mineral type, and can be modulated by land use and management intensity even on subdecadal time scales. Our results suggest that temperate soils dominated by oxides have a higher capacity to accumulate and store C than those dominated by phyllosilicate clays, even under circumneutral pH conditions. Therefore, adopting land use and management practices that increase C inputs into oxide-rich soils that are under their capacity to store C may offer great potential to enhance near-term soil C sequestration

Relating Profile Wall Root-Length Density Estimates to Monolith Root-Length Density Measurements of Cover Crops

Different methods have been proposed for in situ root-length density (RLD) measurement. One widely employed is the time-consuming sampling of soil cores or monoliths (MO). The profile wall (PW) method is a less precise, but faster and less laborious alternative. However, depth-differentiated functions to convert PW RLD estimates to MO RLD measurements have not yet been reported. In this study, we perform a regression analysis to relate PW results to MO results and determine whether calibration is possible for distinct crop groups (grasses, brassicas and legumes) consisting of pure and mixed stands, and whether soil depth affects this calibration. The methods were applied over two years to all crop groups and their absolute and cumulative RLD were compared using a linear (LR) and multiple linear (MLR) regression. PW RLD was found to highly underestimate MO RLD in absolute values and in highly rooted areas. However, a close agreement between both methods was found for cumulative root-length (RL) when applying MLR, highlighting the influence of soil depth. The level of agreement between methods varied strongly with depth. Therefore, the application of PW as the main RLD estimation method can provide reliable estimates of cumulative root distribution traits of cover crops.Peer Reviewe