Pangenomics of flax fungal parasite Fusarium oxysporum f. sp. lini.

To assess the genomic diversity of Fusarium oxysporum f. sp. lini strains and compile a comprehensive gene repertoire, we constructed a pangenome using 13 isolates from four different clonal lineages, each exhibiting distinct levels of virulence. Syntenic analyses of two selected genomes revealed significant chromosomal rearrangements unique to each genome. A comprehensive examination of both core and accessory pangenome content and diversity points at an open genome state. Additionally, Gene Ontology (GO) enrichment analysis indicated that non-core pangenome genes are associated with pathogen recognition and immune signaling. Furthermore, the Folini pansecterome, encompassing secreted proteins critical for fungal pathogenicity, primarily consists of three functional classes: effector proteins, CAZYmes, and proteases. These three classes account for approximately 3.5% of the pangenome. Each functional class within the pansecterome was meticulously annotated and characterized with respect to pangenome category distribution, PFAM domain frequency, and strain virulence assessment. This analysis revealed that highly virulent isolates have specific types of PFAM domains that are exclusive to them. Upon examining the repertoire of SIX genes known for virulence in other formae speciales, it was found that all isolates had a similar gene content except for two, which lacked SIX genes entirely.

BSXplorer: analytical framework for exploratory analysis of BS-seq data.

BACKGROUND: Bisulfite sequencing detects and quantifies DNA methylation patterns, contributing to our understanding of gene expression regulation, genome stability maintenance, conservation of epigenetic mechanisms across divergent taxa, epigenetic inheritance and, eventually, phenotypic variation. Graphical representation of methylation data is crucial in exploring epigenetic regulation on a genome-wide scale in both plants and animals. This is especially relevant for non-model organisms with poorly annotated genomes and/or organisms where genome sequences are not yet assembled on chromosome level. Despite being a technology of choice to profile DNA methylation for many years now there are surprisingly few lightweight and robust standalone tools available for efficient graphical analysis of data in non-model systems. This significantly limits evolutionary studies and agrigenomics research. BSXplorer is a tool specifically developed to fill this gap and assist researchers in explorative data analysis and in visualising and interpreting bisulfite sequencing data more easily. RESULTS: BSXplorer provides in-depth graphical analysis of sequencing data encompassing (a) profiling of methylation levels in metagenes or in user-defined regions using line plots and heatmaps, generation of summary statistics charts, (b) enabling comparative analyses of methylation patterns across experimental samples, methylation contexts and species, and (c) identification of modules sharing similar methylation signatures at functional genomic elements. The tool processes methylation data quickly and offers API and CLI capabilities, along with the ability to create high-quality figures suitable for publication. CONCLUSIONS: BSXplorer facilitates efficient methylation data mining, contrasting and visualization, making it an easy-to-use package that is highly useful for epigenetic research.

Pygenomics: manipulating genomic intervals and data files in Python.

SUMMARY: We present pygenomics, a Python package for working with genomic intervals and bioinformatic data files. The package implements interval operations, provides both API and CLI, and supports reading and writing data in widely used bioinformatic formats, including BAM, BED, GFF3, and VCF. The source code of pygenomics is provided with in-source documentation and type annotations and adheres to the functional programming paradigm. These features facilitate seamless integration of pygenomics routines into scripts and pipelines. The package is implemented in pure Python using its standard library only and contains the property-based testing framework. Comparison of pygenomics with other Python bioinformatic packages with relation to features and performance is presented. The performance comparison covers operations with genomic intervals, read alignments, and genomic variants and demonstrates that pygenomics is suitable for computationally effective analysis. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://gitlab.com/gtamazian/pygenomics.

A collection of read depth profiles at structural variant breakpoints.

SWaveform, a newly created open genome-wide resource for read depth signal in the vicinity of structural variant (SV) breakpoints, aims to boost development of computational tools and algorithms for discovery of genomic rearrangement events from sequencing data. SVs are a dominant force shaping genomes and substantially contributing to genetic diversity. Still, there are challenges in reliable and efficient genotyping of SVs from whole genome sequencing data, thus delaying translation into clinical applications and wasting valuable resources. SWaveform includes a database containing ~7 M of read depth profiles at SV breakpoints extracted from 911 sequencing samples generated by the Human Genome Diversity Project, generalised patterns of the signal at breakpoints, an interface for navigation and download, as well as a toolbox for local deployment with user's data. The dataset can be of immense value to bioinformatics and engineering communities as it empowers smooth application of intelligent signal processing and machine learning techniques for discovery of genomic rearrangement events and thus opens the floodgates for development of innovative algorithms and software.

Long non-coding RNA-derived peptides are immunogenic and drive a potent anti-tumour response.

Protein arginine methyltransferase (PRMT) 5 is over-expressed in a variety of cancers and the master transcription regulator E2F1 is an important methylation target. We have explored the role of PRMT5 and E2F1 in regulating the non-coding genome and report here a striking effect on long non-coding (lnc) RNA gene expression. Moreover, many MHC class I protein-associated peptides were derived from small open reading frames in the lncRNA genes. Pharmacological inhibition of PRMT5 or adjusting E2F1 levels qualitatively altered the repertoire of lncRNA-derived peptide antigens displayed by tumour cells. When presented to the immune system as either ex vivo-loaded dendritic cells or expressed from a viral vector, lncRNA-derived peptides drove a potent antigen-specific CD8 T lymphocyte response, which translated into a significant delay in tumour growth. Thus, lncRNA genes encode immunogenic peptides that can be deployed as a cancer vaccine.

Transcriptomic Analysis of Flowering Time Genes in Cultivated Chickpea and Wild Cicer.

Chickpea (Cicer arietinum L.) is a major grain legume and a good source of plant-based protein. However, comprehensive knowledge of flowering time control in Cicer is lacking. In this study, we acquire high-throughput transcriptome sequencing data and analyze changes in gene expression during floral transition in the early flowering cultivar ICCV 96029, later flowering C. arietinum accessions, and two wild species, C. reticulatum and C. echinospermum. We identify Cicer orthologs of A. thaliana flowering time genes and analyze differential expression of 278 genes between four species/accessions, three tissue types, and two conditions. Our results show that the differences in gene expression between ICCV 96029 and other cultivated chickpea accessions are vernalization-dependent. In addition, we highlight the role of FTa3, an ortholog of FLOWERING LOCUS T in Arabidopsis, in the vernalization response of cultivated chickpea. A common set of differentially expressed genes was found for all comparisons between wild species and cultivars. The direction of expression change for different copies of the FT-INTERACTING PROTEIN 1 gene was variable in different comparisons, which suggests complex mechanisms of FT protein transport. Our study makes a contribution to the understanding of flowering time control in Cicer, and can provide genetic strategies to further improve this important agronomic trait.

An account of Fusarium wilt resistance in flax Linum usitatissimum: The disease severity data.

A collection of flax accessions maintained by the Russian Federal Research Center for Bast Fiber Crops was characterized to evaluate its resistance to Fusarium wilt. 297 samples representing different morphotypes and selection status were infected with highly virulent MI39 strain of Fusarium oxysporum f. sp. lini. Evaluation of disease symptoms was performed at the full emergence stage in a greenhouse. The experiment lasted for 3 successive years. The disease severity index (DSI) record was obtained for every genotype in each year of the experiment. The data set was produced in a framework of a project focused on both a) deciphering the mechanisms of plant immunity, and b) development of flax cultivars resistant to Fusarium wilt. The data is available via Figshare repository.

The Genetic Landscape of Fiber Flax.

Genetic diversity in a breeding program is essential to overcome modern-day environmental challenges faced by humanity and produce robust, resilient crop cultivars with improved agronomic characteristics, as well as to trace crop domestication history. Flax (Linum usitatissimum), one of the first crops domesticated by mankind, has been traditionally cultivated for fiber as well as for medicinal purposes and as a nutritional product. The origins of fiber flax are hidden in the mists of time and can be hypothetically traced back to either the Indo-Afghan region or Fertile Crescent. To shed new light on fiber flax genetic diversity and breeding history, in this study, we presented a comprehensive analysis of the core collection of flax (306 accessions) of different morphotypes and geographic origins maintained by the Russian Federal Research Center for Bast Fiber Crops. We observed significant population differentiation between oilseed and fiber morphotypes, as well as mapped genomic regions affected by recent breeding efforts. We also sought to unravel the origins of kryazhs, Russian heritage landraces, and their genetic relatedness to modern fiber flax cultivars. For the first time, our results provide strong genetic evidence in favor of the hypothesis on kryazh's mixed origin from both the Indo-Afghan diversity center and Fertile Crescent. Finally, we showed predominant contribution from Russian landraces and kryazhs into the ancestry of modern fiber flax varieties. Taken together, these findings may have practical implications on the development of new improved flax varieties with desirable traits that give farmers greater choice in crop management and meet the aspirations of breeders.

Stochastic Effects in Retrotransposon Dynamics Revealed by Modeling under Competition for Cellular Resources.

Transposons are genomic elements that can relocate within a host genome using a 'cut'- or 'copy-and-paste' mechanism. They make up a significant part of many genomes, serve as a driving force for genome evolution, and are linked with Mendelian diseases and cancers. Interactions between two specific retrotransposon types, autonomous (e.g., LINE1/L1) and nonautonomous (e.g., Alu), may lead to fluctuations in the number of these transposons in the genome over multiple cell generations. We developed and examined a simple model of retrotransposon dynamics under conditions where transposon replication machinery competed for cellular resources: namely, free ribosomes and available energy (i.e., ATP molecules). Such competition is likely to occur in stress conditions that a malfunctioning cell may experience as a result of a malignant transformation. The modeling revealed that the number of actively replicating LINE1 and Alu elements in a cell decreases with the increasing competition for resources; however, stochastic effects interfere with this simple trend. We stochastically simulated the transposon dynamics in a cell population and showed that the population splits into pools with drastically different transposon behaviors. The early extinction of active Alu elements resulted in a larger number of LINE1 copies occurring in the first pool, as there was no competition between the two types of transposons in this pool. In the other pool, the competition process remained and the number of L1 copies was kept small. As the level of available resources reached a critical value, both types of dynamics demonstrated an increase in noise levels, and both the period and the amplitude of predator-prey oscillations rose in one of the cell pools. We hypothesized that the presented dynamical effects associated with the impact of the competition for cellular resources inflicted on the dynamics of retrotransposable elements could be used as a characteristic feature to assess a cell state, or to control the transposon activity.

Genomic Regions Associated with Fusarium Wilt Resistance in Flax.

Modern flax cultivars are susceptible to many diseases; arguably, the most economically damaging of these is the Fusarium wilt fungal disease. Over the past decades international flax breeding initiatives resulted in the development of resistant cultivars. However, much remains to be learned about the mechanisms of resistance to Fusarium infection in flax. As a first step to uncover the genetic factors associated with resistance to Fusarium wilt disease, we performed a genome-wide association study (GWAS) using 297 accessions from the collection of the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. These genotypes were infected with a highly pathogenic Fusarium oxysporum f.sp. lini MI39 strain; the wilt symptoms were documented in the course of three successive years. Six different single-locus models implemented in GAPIT3 R package were applied to a selected subset of 72,526 SNPs. A total of 15 QTNs (Quantitative Trait Nucleotides) were detected during at least two years of observation, while eight QTNs were found during all three years of the experiment. Of these, ten QTNs occupied a region of 640 Kb at the start of chromosome 1, while the remaining QTNs mapped to chromosomes 8, 11 and 13. All stable QTNs demonstrate a statistically significant allelic effect across 3 years of the experiment. Importantly, several QTNs spanned regions that harbored genes involved in the pathogen recognition and plant immunity response, including the KIP1-like protein (Lus10025717) and NBS-LRR protein (Lus10025852). Our results provide novel insights into the genetic architecture of flax resistance to Fusarium wilt and pinpoint potential candidate genes for further in-depth studies.

A comprehensive dataset of flax (Linum uitatissimum L.) phenotypes.

A collection of flax accessions from Russian Federal Research Center for Bast Fiber Crops was characterised to evaluate its phenotypic diversity. 406 samples representing different morphotypes were selected for thorough quantitative assessment of various agronomic traits. We measured height, length of technical part of the stem, technical part weight, inflorescence length, number of bolls and seeds per plant, 1000 seed weight, the diameter of the stem, the number of internodes and finally, distance between internodes. The fiber quality was estimated by calculating stem slenderness, stem taperingness and elementary fiber length. The dataset was produced in a framework of a project focused on characterization of diversity of flax genotypes and phenotypes, as well as on identification of genomic regions associated with various traits, it is hosted on Figshare.

A Genomic Blueprint of Flax Fungal Parasite Fusarium oxysporum f. sp. lini.

Fusarium wilt of flax is an aggressive disease caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini. It is a challenging pathogen presenting a constant threat to flax production industry worldwide. Previously, we reported chromosome-level assemblies of 5 highly pathogenic F. oxysporum f. sp. lini strains. We sought to characterize the genomic architecture of the fungus and outline evolutionary mechanisms shaping the pathogen genome. Here, we reveal the complex multi-compartmentalized genome organization and uncover its diverse evolutionary dynamics, which boosts genetic diversity and facilitates host adaptation. In addition, our results suggest that host of functions implicated in the life cycle of mobile genetic elements are main contributors to dissimilarity between proteomes of different Fusaria. Finally, our experiments demonstrate that mobile genetics elements are expressed in planta upon infection, alluding to their role in pathogenicity. On the whole, these results pave the way for further in-depth studies of evolutionary forces shaping the host-pathogen interaction.

Immune modulation underpins the anti-cancer activity of HDAC inhibitors.

Aberrant protein acetylation is strongly linked to tumorigenesis, and modulating acetylation through targeting histone deacetylase (HDAC) with small-molecule inhibitors has been the focus of clinical trials. However, clinical success on solid tumours, such as colorectal cancer (CRC), has been limited, in part because the cancer-relevant mechanisms through which HDAC inhibitors act remain largely unknown. Here, we have explored, at the genome-wide expression level, the effects of a novel HDAC inhibitor CXD101. In human CRC cell lines, a diverse set of differentially expressed genes were up- and downregulated upon CXD101 treatment. Functional profiling of the expression data highlighted immune-relevant concepts related to antigen processing and natural killer cell-mediated cytotoxicity. Similar profiles were apparent when gene expression was investigated in murine colon26 CRC cells treated with CXD101. Significantly, these changes were also apparent in syngeneic colon26 tumours growing in vivo. The ability of CXD101 to affect immune-relevant gene expression coincided with changes in the tumour microenvironment (TME), especially in the subgroups of CD4 and CD8 tumour-infiltrating T lymphocytes. The altered TME reflected enhanced antitumour activity when CXD101 was combined with immune checkpoint inhibitors (ICIs), such as anti-PD-1 and anti-CTLA4. The ability of CXD101 to reinstate immune-relevant gene expression in the TME and act together with ICIs provides a powerful rationale for exploring the combination therapy in human cancers.

A genome-wide association study identifies a gene network associated with paranoid schizophrenia and antipsychotics-induced tardive dyskinesia.

In the present study we conducted a genome-wide association study (GWAS) in a cohort of 505 patients with paranoid schizophrenia (SCZ), of which 95 had tardive dyskinesia (TD), and 503 healthy controls. Using data generated by the PsychENCODE Consortium (PEC) and other bioinformatic databases, we revealed a gene network, implicated in neurodevelopment and brain function, associated with both these disorders. Almost all these genes are in gene or isoform co-expression PEC network modules important for the functioning of the brain; the activity of these networks is also altered in SCZ, bipolar disorder and autism spectrum disorders. The associated PEC network modules are enriched for gene ontology terms relevant to the brain development and function (CNS development, neuron development, axon ensheathment, synapse, synaptic vesicle cycle, and signaling receptor activity) and to the immune system (inflammatory response). Results of the present study suggest that orofacial and limbtruncal types of TD seem to share the molecular network with SCZ. Paranoid SCZ and abnormal involuntary movements that indicate the orofacial type of TD are associated with the same genomic loci on chromosomes 3p22.2, 8q21.13, and 13q14.2. The limbtruncal type of TD is associated with a locus on chromosome 3p13 where the best functional candidate is FOXP1, a high-confidence SCZ gene. The results of this study shed light on common pathogenic mechanisms for SCZ and TD, and indicate that the pathogenesis of the orofacial and limbtruncal types of TD might be driven by interacting genes implicated in neurodevelopment.

PRMT5 promotes cancer cell migration and invasion through the E2F pathway.

The pRb-E2F pathway is a critical point of regulation in the cell cycle and loss of control of the pathway is a hallmark of cancer. E2F1 is the major target through which pRb exerts its effects and arginine methylation by PRMT5 plays a key role in dictating E2F1 activity. Here we have explored the functional role of the PRMT5-E2F1 axis and highlight its influence on different aspects of cancer cell biology including viability, migration, invasion and adherence. Through a genome-wide expression analysis, we identified a distinct set of genes under the control of PRMT5 and E2F1, including some highly regulated genes, which influence cell migration, invasio and adherence through a PRMT5-dependent mechanism. Most significantly, a coincidence was apparent between the expression of PRMT5 and E2F1 in human tumours, and elevated levels of PRMT5 and E2F1 correlated with poor prognosis disease. Our results suggest a causal relationship between PRMT5 and E2F1 in driving the malignant phenotype and thereby highlight an important pathway for therapeutic intervention.

The Genome Sequence of Five Highly Pathogenic Isolates of Fusarium oxysporum f. sp. lini.

Fusarium wilt is the most destructive fungal disease in flax, limiting flax cultivation in all the main flax and linseed growing countries. The causative agent is seedborne and soilborne fungus F. oxysporum f. sp. lini. Here, we report, for the first time, genome assemblies of five highly pathogenic isolates of Fusarium oxysporum f. sp. lini, namely monoisolate 39 and strains F329, F324, F282, F287. In addition, syntenic analysis provided a powerful approach to distinguish between core and lineage-specific parts of the genome. These results lay a solid foundation for comparative genomics studies of plant fungal pathogens, evolution of pathogenicity, and virulence factors underlying the dynamics of host-pathogen interactions, thus eventually offering solutions to Fusarium disease control.

Current challenges and possible future developments in personalized psychiatry with an emphasis on psychotic disorders.

A personalized medicine approach seems to be particularly applicable to psychiatry. Indeed, considering mental illness as deregulation, unique to each patient, of molecular pathways, governing the development and functioning of the brain, seems to be the most justified way to understand and treat disorders of this medical category. In order to extract correct information about the implicated molecular pathways, data can be drawn from sampling phenotypic and genetic biomarkers and then analyzed by a machine learning algorithm. This review describes current difficulties in the field of personalized psychiatry and gives several examples of possibly actionable biomarkers of psychotic and other psychiatric disorders, including several examples of genetic studies relevant to personalized psychiatry. Most of these biomarkers are not yet ready to be introduced in clinical practice. In a next step, a perspective on the path personalized psychiatry may take in the future is given, paying particular attention to machine learning algorithms that can be used with the goal of handling multidimensional datasets.

Arginine methylation expands the regulatory mechanisms and extends the genomic landscape under E2F control.

E2F is a family of master transcription regulators involved in mediating diverse cell fates. Here, we show that residue-specific arginine methylation (meR) by PRMT5 enables E2F1 to regulate many genes at the level of alternative RNA splicing, rather than through its classical transcription-based mechanism. The p100/TSN tudor domain protein reads the meR mark on chromatin-bound E2F1, allowing snRNA components of the splicing machinery to assemble with E2F1. A large set of RNAs including spliced variants associate with E2F1 by virtue of the methyl mark. By focusing on the deSUMOylase SENP7 gene, which we identified as an E2F target gene, we establish that alternative splicing is functionally important for E2F1 activity. Our results reveal an unexpected consequence of arginine methylation, where reader-writer interplay widens the mechanism of control by E2F1, from transcription factor to regulator of alternative RNA splicing, thereby extending the genomic landscape under E2F1 control.

Development and validation of response markers to predict survival and pleurodesis success in patients with malignant pleural effusion (PROMISE): a multicohort analysis.

BACKGROUND: The prevalence of malignant pleural effusion is increasing worldwide, but prognostic biomarkers to plan treatment and to understand the underlying mechanisms of disease progression remain unidentified. The PROMISE study was designed with the objectives to discover, validate, and prospectively assess biomarkers of survival and pleurodesis response in malignant pleural effusion and build a score that predicts survival. METHODS: In this multicohort study, we used five separate and independent datasets from randomised controlled trials to investigate potential biomarkers of survival and pleurodesis. Mass spectrometry-based discovery was used to investigate pleural fluid samples for differential protein expression in patients from the discovery group with different survival and pleurodesis outcomes. Clinical, radiological, and biological variables were entered into least absolute shrinkage and selection operator regression to build a model that predicts 3-month mortality. We evaluated the model using internal and external validation. FINDINGS: 17 biomarker candidates of survival and seven of pleurodesis were identified in the discovery dataset. Three independent datasets (n=502) were used for biomarker validation. All pleurodesis biomarkers failed, and gelsolin, macrophage migration inhibitory factor, versican, and tissue inhibitor of metalloproteinases 1 (TIMP1) emerged as accurate predictors of survival. Eight variables (haemoglobin, C-reactive protein, white blood cell count, Eastern Cooperative Oncology Group performance status, cancer type, pleural fluid TIMP1 concentrations, and previous chemotherapy or radiotherapy) were validated and used to develop a survival score. Internal validation with bootstrap resampling and external validation with 162 patients from two independent datasets showed good discrimination (C statistic values of 0·78 [95% CI 0·72-0·83] for internal validation and 0·89 [0·84-0·93] for external validation of the clinical PROMISE score). INTERPRETATION: To our knowledge, the PROMISE score is the first prospectively validated prognostic model for malignant pleural effusion that combines biological and clinical parameters to accurately estimate 3-month mortality. It is a robust, clinically relevant prognostic score that can be applied immediately, provide important information on patient prognosis, and guide the selection of appropriate management strategies. FUNDING: European Respiratory Society, Medical Research Funding-University of Oxford, Slater & Gordon Research Fund, and Oxfordshire Health Services Research Committee Research Grants.

Anti-neuraminidase antibodies against pandemic A/H1N1 influenza viruses in healthy and influenza-infected individuals.

The main objective of the study was to evaluate neuraminidase inhibiting (NI) antibodies against A/H1N1pdm09 influenza viruses in the community as a whole and after infection. We evaluated NI serum antibodies against A/California/07/09(H1N1)pdm and A/South Africa/3626/2013(H1N1)pdm in 134 blood donors of different ages using enzyme-linked lectin assay and in 15 paired sera from convalescents with laboratory confirmed influenza. The neuraminidase (NA) proteins of both A/H1N1pdm09 viruses had minimal genetic divergence, but demonstrated different enzymatic and antigenic properties. 5.2% of individuals had NI antibody titers ≥1:20 against A/South Africa/3626/2013(H1N1)pdm compared to 53% of those who were positive to A/California/07/2009(H1N1)pdm NA. 2% of individuals had detectable NI titers against A/South Africa/3626/13(H1N1)pdm and 47.3% were positive to A/California/07/2009(H1N1)pdm NA among participants negative to hemagglutinin (HA) of A/H1N1pdm09 but positive to seasonal A/H1N1. The lowest NI antibody levels to both A/H1N1pdm09 viruses were detected in individuals born between 1956 and 1968. Our data suggest that NI antibodies against A/South Africa/3626/13 (H1N1)pdm found in the blood donors could have resulted from direct infection with a new antigenic A/H1N1pdm09 variant rather than from cross-reaction as a result of contact with previously circulating seasonal A/H1N1 variants. The immune responses against HA and NA were formed simultaneously right after natural infection with A/H1N1pdm09. NI antibodies correlated with virus-neutralizing antibodies when acquired shortly after influenza infection. A group of middle-aged patients with the lowest level of anti-NA antibodies against A/California/07/2009 (H1N1)pdm was identified, indicating the highest-priority vaccination against A/H1N1pdm09 viruses.