Molecular and clinical diversity in primary central nervous system lymphoma.

BACKGROUND: Primary central nervous system lymphoma (PCNSL) is a rare and distinct entity within diffuse large B-cell lymphoma presenting with variable response rates probably to underlying molecular heterogeneity. PATIENTS AND METHODS: To identify and characterize PCNSL heterogeneity and facilitate clinical translation, we carried out a comprehensive multi-omic analysis [whole-exome sequencing, RNA sequencing (RNA-seq), methylation sequencing, and clinical features] in a discovery cohort of 147 fresh-frozen (FF) immunocompetent PCNSLs and a validation cohort of formalin-fixed, paraffin-embedded (FFPE) 93 PCNSLs with RNA-seq and clinico-radiological data. RESULTS: Consensus clustering of multi-omic data uncovered concordant classification of four robust, non-overlapping, prognostically significant clusters (CS). The CS1 and CS2 groups presented an immune-cold hypermethylated profile but a distinct clinical behavior. The 'immune-hot' CS4 group, enriched with mutations increasing the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) and nuclear factor-κB activity, had the most favorable clinical outcome, while the heterogeneous-immune CS3 group had the worse prognosis probably due to its association with meningeal infiltration and enriched HIST1H1E mutations. CS1 was characterized by high Polycomb repressive complex 2 activity and CDKN2A/B loss leading to higher proliferation activity. Integrated analysis on proposed targets suggests potential use of immune checkpoint inhibitors/JAK1 inhibitors for CS4, cyclin D-Cdk4,6 plus phosphoinositide 3-kinase (PI3K) inhibitors for CS1, lenalidomide/demethylating drugs for CS2, and enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) inhibitors for CS3. We developed an algorithm to identify the PCNSL subtypes using RNA-seq data from either FFPE or FF tissue. CONCLUSIONS: The integration of genome-wide data from multi-omic data revealed four molecular patterns in PCNSL with a distinctive prognostic impact that provides a basis for future clinical stratification and subtype-based targeted interventions.

Cooperation in Microbial Populations: Theory and Experimental Model Systems.

Cooperative behavior, the costly provision of benefits to others, is common across all domains of life. This review article discusses cooperative behavior in the microbial world, mediated by the exchange of extracellular products called public goods. We focus on model species for which the production of a public good and the related growth disadvantage for the producing cells are well described. To unveil the biological and ecological factors promoting the emergence and stability of cooperative traits we take an interdisciplinary perspective and review insights gained from both mathematical models and well-controlled experimental model systems. Ecologically, we include crucial aspects of the microbial life cycle into our analysis and particularly consider population structures where ensembles of local communities (subpopulations) continuously emerge, grow, and disappear again. Biologically, we explicitly consider the synthesis and regulation of public good production. The discussion of the theoretical approaches includes general evolutionary concepts, population dynamics, and evolutionary game theory. As a specific but generic biological example, we consider populations of Pseudomonas putida and its regulation and use of pyoverdines, iron scavenging molecules, as public goods. The review closes with an overview on cooperation in spatially extended systems and also provides a critical assessment of the insights gained from the experimental and theoretical studies discussed. Current challenges and important new research opportunities are discussed, including the biochemical regulation of public goods, more realistic ecological scenarios resembling native environments, cell-to-cell signaling, and multispecies communities.

Impacts of invading N2-fixing Acacia species on patterns of nutrient cycling in two Cape ecosystems: evidence from soil incubation studies and 15N natural abundance values.

This study examines the impacts of woody, N2-fixing invasive Acacia spp. on the patterns of nutrient cycling in two invaded ecosystems of differing nutrient status in the Cape floristic region. Patterns of soil nutrient mineralization were measured by a field incubation method while the significance of the fixation process in altering nutrient cycling was assessed by the δ15N natural abundance technique. The results confirm earlier reports that invasion by woody shrubs results in organic matter and nutrient enrichment of surface soils of both ecosystems. However, patterns of nutrient availability (phosphorus and nitrogen) were not necessarily enhanced. In the more fertile strandveld both phosphorus and nitrogen (significant at P<0.10) showed trends towards enhanced annual mineralization rates upon invasion, while in the low nutrient fynbos system only phosphorus followed this trend. It is unclear whether this differential response is a consequence of plant- or soil-derived feedbacks on the decomposition processes in each system. The δ15N values of the soils from the invaded sites of both ecosystems indicated a strong influence of the alien species on the soil nitrogen component. However, as with other studies of natural ecosystems, the contribution of nitrogen from fixation could not be readily quantified with the δ15N natural abundance method because of problems in selecting suitable non-N2-fixing reference plants. A technique of disrupting nodule structure and function, by fumigation with O2, to obtain the δ15N value of a non-N2-fixing speciment of the study species was tried and found to overcome some of the problems associated with the lack of suitable reference plants. With this technique it was possible to detect the almost total dependence of A. saligna on N2-fixation in the fynbos soils with their low nitrogen mineralization rates. In the strandveld ecosystem with much higher soil nitrogen release rates A. cyclops was only partly dependent on fixation (about half) for its nitrogen. The nutrient enrichment of both ecosystems and trends towards enhanced rates of nutrient mineralization could have profound implications on the long-term success of alien invader clearing operations and the restoration of the indigenous flora at these sites.