Matthew A. Parker

The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma.

Pediatric high-grade glioma (HGG) is a devastating disease with a less than 20% survival rate 2 years after diagnosis. We analyzed 127 pediatric HGGs, including diffuse intrinsic pontine gliomas (DIPGs) and non-brainstem HGGs (NBS-HGGs), by whole-genome, whole-exome and/or transcriptome sequencing. We identified recurrent somatic mutations in ACVR1 exclusively in DIPGs (32%), in addition to previously reported frequent somatic mutations in histone H3 genes, TP53 and ATRX, in both DIPGs and NBS-HGGs. Structural variants generating fusion genes were found in 47% of DIPGs and NBS-HGGs, with recurrent fusions involving the neurotrophin receptor genes NTRK1, NTRK2 and NTRK3 in 40% of NBS-HGGs in infants. Mutations targeting receptor tyrosine kinase–RAS-PI3K signaling, histone modification or chromatin remodeling, and cell cycle regulation were found in 68%, 73% and 59% of pediatric HGGs, respectively, including in DIPGs and NBS-HGGs. This comprehensive analysis provides insights into the unique and shared pathways driving pediatric HGG within and outside the brainstem.

C11orf95 – RELA fusions drive oncogenic NF-κB signalling in ependymoma

Members of the nuclear factor-κB (NF-κB) family of transcriptional regulators are central mediators of the cellular inflammatory response. Although constitutive NF-κB signalling is present in most human tumours, mutations in pathway members are rare, complicating efforts to understand and block aberrant NF-κB activity in cancer. Here we show that more than two-thirds of supratentorial ependymomas contain oncogenic fusions between RELA, the principal effector of canonical NF-κB signalling, and an uncharacterized gene, C11orf95. In each case, C11orf95–RELA fusions resulted from chromothripsis involving chromosome 11q13.1. C11orf95–RELA fusion proteins translocated spontaneously to the nucleus to activate NF-κB target genes, and rapidly transformed neural stem cells—the cell of origin of ependymoma—to form these tumours in mice. Our data identify a highly recurrent genetic alteration of RELA in human cancer, and the C11orf95–RELA fusion protein as a potential therapeutic target in supratentorial ependymoma.

Local population differentiation for compatibility in an annual legume and its host-specific fungal pathogen

Severe attack by the fungal pathogen Synchytrium decipiens frequently occurs in natural populations of the annual plant Amphicarpaea bracteata (Leguminosae) in eastern North America. Field transplant experiments indicate that there is significant population differentiation in the plant‐fungus association over distances of 1 km or greater: plants transplanted back into their population of origin become heavily infected, while foreign plants from populations 1 or 100 km away experience little or no infection, even though these foreign plants are subject to heavy fungal attack in their native populations. To investigate the fine structure of population differentiation, progeny of A. bracteata plants collected at six sites at 30 m intervals along a transect were inoculated with a single strain of S. decipiens in a controlled environment. Fungal lesions were initiated in all 36 plant progeny groups tested, yet there was highly significant, 5‐fold variation among plants from different sites in the mean number of fungal lesions developing per plant. In addition, all fungal lesions aborted without maturing spores on all plants from one site on the transect. Fungal lesion abortion rates averaged only 9% on plants from the other five sites. Such local population differentiation in plant‐pathogen compatibility may be related to A. bracteatas high degree of self‐pollination. Limited long‐distance recombination in A. bracteata due to self‐pollination and spatially restricted pollen flow may be a major factor preventing the evolution of increased plant resistance to fungal attack.

The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes

Studies of paediatric cancers have shown a high frequency of mutation across epigenetic regulators. Here we sequence 633 genes, encoding the majority of known epigenetic regulatory proteins, in over 1,000 paediatric tumours to define the landscape of somatic mutations in epigenetic regulators in paediatric cancer. Our results demonstrate a marked variation in the frequency of gene mutations across 21 different paediatric cancer subtypes, with the highest frequency of mutations detected in high-grade gliomas, T-lineage acute lymphoblastic leukaemia and medulloblastoma, and a paucity of mutations in low-grade glioma and retinoblastoma. The most frequently mutated genes are H3F3A, PHF6, ATRX, KDM6A, SMARCA4, ASXL2, CREBBP, EZH2, MLL2, USP7, ASXL1, NSD2, SETD2, SMC1A and ZMYM3. We identify novel loss-of-function mutations in the ubiquitin-specific processing protease 7 (USP7) in paediatric leukaemia, which result in decreased deubiquitination activity. Collectively, our results help to define the landscape of mutations in epigenetic regulatory genes in paediatric cancer and yield a valuable new database for investigating the role of epigenetic dysregulations in cancer.

The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias.

Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia with a poor prognosis. To define its mutational landscape, we performed whole-genome, exome, RNA and targeted DNA sequencing on 65 infants (47 MLL-R and 18 non–MLL-R cases) and 20 older children (MLL-R cases) with leukemia. Our data show that infant MLL-R ALL has one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations. Despite this paucity of mutations, we detected activating mutations in kinase-PI3K-RAS signaling pathway components in 47% of cases. Surprisingly, these mutations were often subclonal and were frequently lost at relapse. In contrast to infant cases, MLL-R leukemia in older children had more somatic mutations (mean of 6.5 mutations/case versus 1.3 mutations/case, P = 7.15 × 10−5) and had frequent mutations (45%) in epigenetic regulators, a category of genes that, with the exception of MLL, was rarely mutated in infant MLL-R ALL.

Pathogens and sex in plants

SummaryExtant theories that attribute the evolution of sex to pathogen attack depend on the assumption that pathogens are narrowly specialized, so that high fitness on one host genotype results in poor fitness on hosts with other allele combinations. This assumption is necessary in order for frequency-dependent selection to produce sustained cycling of gametic disequilibrium across the hosts disease resistance loci, which makes recombination advantageous. However, a review of numerous genetic studies on plant disease resistance failed to uncover a single example consistent with this assumption. Instead, the empirical results provide strong support for a different pattern of pathogen specificity, in which adaptation by pathogens to one resistance allele does not preclude high fitness on alternate host genotypes lacking that allele. Modification of traditional models for pathogen-mediated evolution of sex showed that for conditions close to the empirical pattern of genotypic specificity, sex is almost never favoured. For plants, these results cast doubt on current theories arguing that pathogens are the primary selective agent responsible for sexual reproduction.

Coexistence of Burkholderia, Cupriavidus, and Rhizobium sp. Nodule Bacteria on two Mimosa spp. in Costa Rica

ABSTRACT rRNA gene sequencing and PCR assays indicated that 215 isolates of root nodule bacteria from two Mimosa species at three sites in Costa Rica belonged to the genera Burkholderia, Cupriavidus, and Rhizobium. This is the first report of Cupriavidus sp. nodule symbionts for Mimosa populations within their native geographic range in the neotropics. Burkholderia spp. predominated among samples from Mimosa pigra (86% of isolates), while there was a more even distribution of Cupriavidus, Burkholderia, and Rhizobium spp. on Mimosa pudica (38, 37, and 25% of isolates, respectively). All Cupriavidus and Burkholderia genotypes tested formed root nodules and fixed nitrogen on both M. pigra and M. pudica, and sequencing of rRNA genes in strains reisolated from nodules verified identity with inoculant strains. Inoculation tests further indicated that both Cupriavidus and Burkholderia spp. resulted in significantly higher plant growth and nodule nitrogenase activity (as measured by acetylene reduction assays) relative to plant performance with strains of Rhizobium. Given the prevalence of Burkholderia and Cupriavidus spp. on these Mimosa legumes and the widespread distribution of these plants both within and outside the neotropics, it is likely that both β-proteobacterial genera are more ubiquitous as root nodule symbionts than previously believed.

Mutualism in Metapopulations of Legumes and Rhizobia

Coevolution in mutualisms may result in a stable mosaic pattern of spatial differentiation, with regions occupied by different coadapted pairs of mutualists each being resistant to invasion by organisms with alternative phenotypes. The evolution of geographic mosaic patterns was analyzed for symbioses of legume plants and root‐nodule bacteria (rhizobia), where plants are commonly polymorphic for genes affecting mutualism specificity. Typically, some alleles confer broad compatibility, and others restrict the set of bacterial genotypes accepted by plants as mutualist partners. Metapopulation simulation models with genetic assumptions matching the observed form of symbiotic specificity show that selection can generate a stable geographic mosaic if certain conditions are satisfied regarding competitive abilities, fitness benefits from mutualism, and migration rates. The structure of geographic variation in natural populations of the annual legume Amphicarpaea bracteata, together with patterns of variation in symbiotic fitness, is consistent with the interpretation that a mosaic pattern of differentiation may exist. Experimental and observational studies necessary to test more rigorously for mosaic distributions are outlined.

DIVERGENCE IN SYMBIOTIC COMPATIBILITY IN A LEGUME-BRADYRHIZOBIUM MUTUALISM

Geographic variation in the mutualism between the legume Amphicarpaea bracteata and its nitrogen‐fixing root nodule bacteria (Bradyrhizobium sp.) was analyzed by sampling genotypes from 11 sites separated by distances ranging from 0.6 km to more than 1000 km. Cross inoculation experiments revealed that plants were genetically differentiated in traits determining compatibility with mutualist partners from different sites. Combinations of plant and bacterial genotypes native to the same local habitat yielded 26% higher plant growth relative to non‐native combinations (range across 4 experiments; 9% to 48%). Among non‐native symbioses, plant growth was unrelated to the geographic distance between sites of plant and bacterial origin. However, compatibility varied significantly with the genetic distance among host populations (inferred by multilocus enzyme electrophoresis): genetically similar plants from separate sites showed superior growth with each others mutualist partners. Nevertheless, the tree structure of population genetic similarity was not congruent in plants versus bacteria. This implies that adaptive variation in symbiotic compatibility has evolved without strictly parallel divergence in the two species.

Conflicting phylogeographic patterns in rRNA and nifD indicate regionally restricted gene transfer in Bradyrhizobium

Major differences in evolutionary relationships of the 16S rRNA gene and the nitrogenase alpha-subunit gene (nifD) were observed among 38 strains of Bradyrhizobium sp. nodule bacteria from North America, Central America, Asia and Australia. Two lineages were evident in the 16S rRNA phylogeny representing strains related to Bradyrhizobium japonicum (29 isolates) or Bradyrhizobium elkanii (9 isolates). Both clades were distributed across most or all of the geographic regions sampled. By contrast, in the nifD tree almost all isolates were placed into one of three groups each exclusively composed of taxa from a single geographic region (North Temperate, Central America or Australia). Isolates that were closely related or identical in gene sequence at one locus often had divergent sequences at the other locus and a partition homogeneity test indicated that the 16S rRNA and nifD phylogenies were significantly incongruent. No evidence for any gene duplication of nifD was found by Southern hybridization analysis on a subset of the strains, so unrecognized paralogy is not likely to be responsible for the discrepancy between 16S rRNA and nifD tree topologies. These results are consistent with a model whereby geographic areas were initially colonized by several diverse 16S rRNA lineages, with subsequent horizontal gene transfer of nifD leading to increased nifD sequence homogeneity within each regional population.