Accurate detection of tumor-specific gene fusions reveals strongly immunogenic personal neo-antigens.

Cancer-associated gene fusions are a potential source for highly immunogenic neoantigens, but the lack of computational tools for accurate, sensitive identification of personal gene fusions has limited their targeting in personalized cancer immunotherapy. Here we present EasyFuse, a machine learning computational pipeline for detecting cancer-specific gene fusions in transcriptome data obtained from human cancer samples. EasyFuse predicts personal gene fusions with high precision and sensitivity, outperforming previously described tools. By testing immunogenicity with autologous blood lymphocytes from patients with cancer, we detected pre-established CD4+ and CD8+ T cell responses for 10 of 21 (48%) and for 1 of 30 (3%) identified gene fusions, respectively. The high frequency of T cell responses detected in patients with cancer supports the relevance of individual gene fusions as neoantigens that might be targeted in personalized immunotherapies, especially for tumors with low mutation burden.

FGB1 and WSC3 are in planta-induced ß-glucan-binding fungal lectins with different functions.

In the root endophyte Serendipita indica, several lectin-like members of the expanded multigene family of WSC proteins are transcriptionally induced in planta and are potentially involved in ß-glucan remodeling at the fungal cell wall. Using biochemical and cytological approaches we show that one of these lectins, SiWSC3 with three WSC domains, is an integral fungal cell wall component that binds to long-chain ß1-3-glucan but has no affinity for shorter ß1-3- or ß1-6-linked glucose oligomers. Comparative analysis with the previously identified ß-glucan-binding lectin SiFGB1 demonstrated that whereas SiWSC3 does not require ß1-6-linked glucose for efficient binding to branched ß1-3-glucan, SiFGB1 does. In contrast to SiFGB1, the multivalent SiWSC3 lectin can efficiently agglutinate fungal cells and is additionally induced during fungus-fungus confrontation, suggesting different functions for these two ß-glucan-binding lectins. Our results highlight the importance of the ß-glucan cell wall component in plant-fungus interactions and the potential of ß-glucan-binding lectins as specific detection tools for fungi in vivo.

Mining the effector repertoire of the biotrophic fungal pathogen Ustilago hordei during host and non-host infection.

The success of plant-pathogenic fungi mostly relies on their arsenal of virulence factors which are expressed and delivered into the host tissue during colonization. The biotrophic fungal pathogen Ustilago hordei causes covered smut disease on both barley and oat. In this study, we combined cytological, genomics and molecular biological methods to achieve a better understanding of the molecular interactions in the U. hordei-barley pathosystem. Microscopic analysis revealed that U. hordei densely colonizes barley leaves on penetration, in particular the vascular system. Transcriptome analysis of U. hordei at different stages of host infection revealed differential expression of the transcript levels of 273 effector gene candidates. Furthermore, U. hordei transcriptionally activates core effector genes which may suppress even non-host early defence responses. Based on expression profiles and novelty of sequences, knockout studies of 14 effector candidates were performed in U. hordei, which resulted in the identification of four virulence factors required for host colonization. Yeast two-hybrid screening identified potential barley targets for two of the effectors. Overall, this study provides a first systematic analysis of the effector repertoire of U. hordei and identifies four effectors (Uvi1-Uvi4) as virulence factors for the infection of barley.

An apoplastic peptide activates salicylic acid signalling in maize.

Localized control of cell death is crucial for the resistance of plants to pathogens. Papain-like cysteine proteases (PLCPs) regulate plant defence to drive cell death and protection against biotrophic pathogens. In maize (Zea mays), PLCPs are crucial in the orchestration of salicylic acid (SA)-dependent defence signalling. Despite this central role in immunity, it remains unknown how PLCPs are activated, and which downstream signals they induce to trigger plant immunity. Here, we discover an immune signalling peptide, Z. mays immune signalling peptide 1 (Zip1), which is produced after salicylic acid (SA) treatment. In vitro studies demonstrate that PLCPs are required to release bioactive Zip1 from its propeptide precursor. Conversely, Zip1 treatment strongly elicits SA accumulation in leaves. Moreover, transcriptome analyses revealed that Zip1 and SA induce highly overlapping transcriptional changes. Consequently, Zip1 promotes the infection of the necrotrophic fungus Botrytis cinerea, while it reduces virulence of the biotrophic fungus Ustilago maydis. Thus, Zip1 represents the previously missing signal that is released by PLCPs to activate SA defence signalling.

IBS: an illustrator for the presentation and visualization of biological sequences.

UNLABELLED: Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure. AVAILABILITY AND IMPLEMENTATION: The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org. CONTACT: renjian.sysu@gmail.com or xueyu@hust.edu.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a noncompromised plant innate immunity.

During a compatible interaction, the sebacinoid root-associated fungi Piriformospora indica and Sebacina vermifera induce modification of root morphology and enhance shoot growth in Arabidopsis thaliana. The genomic traits common in these two fungi were investigated and compared with those of other root-associated fungi and saprotrophs. The transcriptional responses of the two sebacinoid fungi and of Arabidopsis roots to colonization at three different symbiotic stages were analyzed by custom-designed microarrays. We identified key genomic features characteristic of sebacinoid fungi, such as expansions for gene families involved in hydrolytic activities, carbohydrate-binding and protein-protein interaction. Additionally, we show that colonization of Arabidopsis correlates with the induction of salicylic acid catabolism and accumulation of jasmonate and glucosinolates (GSLs). Genes involved in root developmental processes were specifically induced by S. vermifera at later stages during interaction. Using different Arabidopsis indole-GSLs mutants and measurement of secondary metabolites, we demonstrate the importance of the indolic glucosinolate pathway in the growth restriction of P. indica and S. vermifera and we identify indole-phytoalexins and specifically indole-carboxylic acids derivatives as potential key players in the maintenance of a mutualistic interaction with root endophytes.

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.

To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.

Broad compatibility in fungal root symbioses.

Plants associate with a wide range of beneficial fungi in their roots which facilitate plant mineral nutrient uptake in exchange for carbohydrates and other organic metabolites. These associations play a key role in shaping terrestrial ecosystems and are widely believed to have promoted the evolution of land plants. To establish compatibility with their host, root-associated fungi have evolved diverse colonization strategies with distinct morphological, functional and genomic specializations as well as different degrees of interdependence. They include obligate biotrophic arbuscular mycorrhizal (AM), and facultative biotrophic ectomycorrhizal (ECM) interactions but are not restricted to these well-characterized symbioses. There is growing evidence that root endophytic associations, which due to their inconspicuous nature have been often overlooked, can be of mutualistic nature and represent important players in natural and managed environments. Recent research into the biology and genomics of root associations revealed fascinating insight into the phenotypic and trophic plasticity of these fungi and underlined genomic traits associated with biotrophy and saprotrophy. In this review we will consider the commonalities and differences of AM and ECM associations and contrast them with root endophytes.

Host-related metabolic cues affect colonization strategies of a root endophyte.

The mechanisms underpinning broad compatibility in root symbiosis are largely unexplored. The generalist root endophyte Piriformospora indica establishes long-lasting interactions with morphologically and biochemically different hosts, stimulating their growth, alleviating salt stress, and inducing local and systemic resistance to pathogens. Cytological studies and global investigations of fungal transcriptional responses to colonization of barley and Arabidopsis at different symbiotic stages identified host-dependent colonization strategies and host-specifically induced effector candidates. Here, we show that in Arabidopsis, P. indica establishes and maintains biotrophic nutrition within living epidermal cells, whereas in barley the symbiont undergoes a nutritional switch to saprotrophy that is associated with the production of secondary thinner hyphae in dead cortex cells. Consistent with a diversified trophic behavior and with the occurrence of nitrogen deficiency at the onset of saprotrophy in barley, fungal genes encoding hydrolytic enzymes and nutrient transporters were highly induced in this host but not in Arabidopsis. Silencing of the high-affinity ammonium transporter PiAMT1 gene, whose transcripts are accumulating during nitrogen starvation and in barley, resulted in enhanced colonization of this host, whereas it had no effect on the colonization of Arabidopsis. Increased levels of free amino acids and reduced enzymatic activity for the cell-death marker VPE (vacuolar-processing enzyme) in colonized barley roots coincided with an extended biotrophic lifestyle of P. indica upon silencing of PiAMT1. This suggests that PiAmt1 functions as a nitrogen sensor mediating the signal that triggers the in planta activation of the saprotrophic program. Thus, host-related metabolic cues affect the expression of P. indica's alternative lifestyles.

Opprimo ergo sum--evasion and suppression in the root endophytic fungus Piriformospora indica.

The genetically tractable endophytic fungus Piriformospora indica is able to colonize the root cortex of a great variety of different plant species with beneficial effects to its hosts, and it represents a suitable model system to study symbiotic interactions. Recent cytological studies in barley and Arabidopsis showed that, upon penetration of the root, P. indica establishes a biotrophic interaction during which fungal cells are encased by the host plasma membrane. Large-scale transcriptional analyses of fungal and plant responses have shown that perturbance of plant hormone homeostasis and secretion of fungal lectins and other small proteins (effectors) may be involved in the evasion and suppression of host defenses at these early colonization steps. At later stages, P. indica is found more often in moribund host cells where it secretes a large variety of hydrolytic enzymes that degrade proteins. This strategy of colonizing plants is reminiscent of that of hemibiotrophic fungi, although a defined shift to necrotrophy with massive host cell death is missing. Instead, the association with the plant root leads to beneficial effects for the host such as growth promotion, increased resistance to root as well as leaf pathogens, and increased tolerance to abiotic stresses. This review describes current advances in understanding the components of the P. indica endophytic lifestyle from molecular and genomic analyses.

Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica.

Recent sequencing projects have provided deep insight into fungal lifestyle-associated genomic adaptations. Here we report on the 25 Mb genome of the mutualistic root symbiont Piriformospora indica (Sebacinales, Basidiomycota) and provide a global characterization of fungal transcriptional responses associated with the colonization of living and dead barley roots. Extensive comparative analysis of the P. indica genome with other Basidiomycota and Ascomycota fungi that have diverse lifestyle strategies identified features typically associated with both, biotrophism and saprotrophism. The tightly controlled expression of the lifestyle-associated gene sets during the onset of the symbiosis, revealed by microarray analysis, argues for a biphasic root colonization strategy of P. indica. This is supported by a cytological study that shows an early biotrophic growth followed by a cell death-associated phase. About 10% of the fungal genes induced during the biotrophic colonization encoded putative small secreted proteins (SSP), including several lectin-like proteins and members of a P. indica-specific gene family (DELD) with a conserved novel seven-amino acids motif at the C-terminus. Similar to effectors found in other filamentous organisms, the occurrence of the DELDs correlated with the presence of transposable elements in gene-poor repeat-rich regions of the genome. This is the first in depth genomic study describing a mutualistic symbiont with a biphasic lifestyle. Our findings provide a significant advance in understanding development of biotrophic plant symbionts and suggest a series of incremental shifts along the continuum from saprotrophy towards biotrophy in the evolution of mycorrhizal association from decomposer fungi.