Generative neural networks separate common and specific transcriptional responses

Genome-wide transcriptome profiling identifies genes that are prone to differential expression across contexts ("common DEGs"), as well as specific changes relevant to the experimental manipulation. Distinguishing common DEGs from those that are specifically changed in a context of interest will allow more efficient inference of relevant mechanisms and a more systematic understanding of the biological process under scrutiny. Currently, common changes can only be identified through the laborious manual curation of highly controlled experiments, an inordinately time-consuming and impractical endeavor. Here we pioneer a method for identifying common patterns using generative neural networks. This method produces a background set of transcriptomic experiments from which a gene and pathway-specific null distribution can be generated. By comparing the set of differentially expressed genes found in a target experiment against the background set, common results can easily be separated from specific ones. This "Specific cOntext Pattern Highlighting In Expression data" (SOPHIE) method is broadly applicable to new platforms or any species with a large collection of unannotated gene expression data. We apply SOPHIE to diverse datasets including human, including human cancer, and bacterial datasets. SOPHIE recapitulates previously described common DEGs, and our molecular validation indicates it detects highly specific, but low magnitude, biologically relevant, transcriptional changes. SOPHIE's measure of specificity can complement log fold change activity generated from traditional differential expression analyses by, for example, filtering the set of changed genes to identify those that are specifically relevant to the experimental condition of interest. Consequently, these results can inform future research directions.

Markers for monitoring hydrogen peroxide resistance in the salmon louse, Lepeophtheirus salmonis

Background: Hydrogen peroxide (H2O2) is one of the delousing agents used to control sea lice infestations in salmonid aquaculture. However, some Lepeophtheirus salmonis populations have developed resistance towards H2O2. An increased gene expression and activity of catalase, an enzyme that breaks down H2O2, have been detected in resistant lice, being therefore introduced as a resistance marker in the salmon industry. In the present study the aim was to validate the use of catalase expression as a marker and to identify new markers related to H2O2 resistance in L. salmonis.Methods: A sensitive and an H2O2 resistant laboratory strain (P0 generation, not exposed to H2O2 for several years) were batch crossed to generate a cohort with a wide range of H2O2 sensitivities (F2 generation). F2 adult females were then exposed to H2O2 to separate sensitive and resistant individuals. Those F2 lice, the P0 lice and field-collected resistant lice (exposed to H2O2 in the field) were used in an RNA sequencing study.Results: Catalase was up-regulated in resistant lice exposed to H2O2 compared to sensitive lice. This was, however, not the case for unexposed resistant P0 lice. Several other genes were found differentially expressed between sensitive and resistant lice, but most of them seemed to be related to H2O2 exposure. However, five genes were consistently up- or down- regulated in the resistant lice independent of exposure history. The up-regulated genes were: one gene in the DNA polymerase family, one gene encoding a Nesprin-like protein and an unannotated gene encoding a small protein. The down-regulated genes encoded endoplasmic reticulum resident protein 29 and an aquaporin (Glp1_v2).Conclusions: Catalase expression seems to be induced by H2O2 exposure, since it was not up-regulated in unexposed resistant lice. This may pose a challenge for its use as a resistance marker. The five new genes associated with resistance are put forward as potential good, complementary markers. The most promising was Glp1_v2, an aquaglyceroporin that may serve as a passing channel for H2O2. Lower channel number can reduce the influx or distribution of H2O2 in the salmon louse, being directly involved in the resistance mechanism.

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

The most commonly employed mammalian model organism is the laboratory mouse. A wide variety of genetically diverse inbred mouse strains, representing distinct physiological states, disease susceptibilities, and biological mechanisms have been developed over the last century. We report full length draft de novo genome assemblies for 16 of the most widely used inbred strains and reveal for the first time extensive strain-specific haplotype variation. We identify and characterise 2,567 regions on the current Genome Reference Consortium mouse reference genome exhibiting the greatest sequence diversity between strains. These regions are enriched for genes involved in defence and immunity, and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. Several immune related loci, some in previously identified QTLs for disease response have novel haplotypes not present in the reference that may explain the phenotype. We used these genomes to improve the mouse reference genome resulting in the completion of 10 new gene structures, and 62 new coding loci were added to the reference genome annotation. Notably this high quality collection of genomes revealed a previously unannotated gene (Efcab3-like) encoding 5,874 amino acids, one of the largest known in the rodent lineage. Interestingly, Efcab3-like−/− mice exhibit severe size anomalies in four regions of the brain suggesting a mechanism of Efcab3-like regulating brain development.

Abrogation of Niche Signals Discovered New Genes Regulating Homing, Expansion and homeostasis of Multiple Myeloma Cells

Abstract 5080 Introduction: Multiple myeloma (MM) cells depend on the bone marrow (BM) niche signals for their viability. Thus, tracing the earliest molecular changes in response to the lost of niche signals can disclose new homing related interactions. Methods: BM aspirates were collected in heparinized syringes and samples were flesh frozen at different time points. GEP (Affymetrix 1.0 st) was performed for 8 cases with massive BM infiltration with plasma cells. The GEP was also analyzed at different time points following spreading of cultured BM cells from the same patients (maintained in culture for several days). Results: Spontaneous induction of genes started within few minutes following aspiration, peaking in hours and persisting for at least 12 hours (Tables 1). RT-PCR results along several time points following BM aspiration from a representative case are presented in Table 2. Interestingly, the induction of genes reverted entirely in cultured conditions imposing cell-cell-matrix contact. However, spreading of the cultured cells re-induced these genes similar to that followed BM aspiration. Furthermore, in comparison of the GEP of cultured cells (frozen immediately after spreading) Vs the GEP from samples taken immediately after BM aspiration, an absolutely different repertoire of genes showed significant changes (Table 3): Conclusions: 1. BM cells from MM patients respond immediately to changing microenvironment, with prompt upregulation of genes active in tumor expansion (FOS, AREG, JUN, PTGS2). However, such constitutive upregulation plus elevation of tumor suppressor genes (like NR4A2) is intolerable if not reverted by cell-cell-matrix contact. 2. In culture, BM cells from MM patients respond with dramatic upregulation of genes supporting neovascularisation (IL8, PLA27, MMP12, CXCL5), matrix (SPP1, FN1) and osteoclasts. 3. Most interestingly, in culture there is also downregulation of 20 genes critical to mitosis, especially relating to spindle machinery (KIF members, NUF2, TUBB1, ASPM, CENPE, CENPF) suggesting that the failure of long-term culture of primary MM cells results from mitotic crisis. This may also explain the lobulation of primary MM cell nuclei observed. 4. The unannotated gene MOP-1 has a role in MM homing. Disclosures: No relevant conflicts of interest to declare.

Identification of the Origin of Transfer (oriT) and a New Gene Required for Mobilization of the SXT/R391 Family of Integrating Conjugative Elements

ABSTRACT Integrating conjugative elements (ICEs) are self-transmissible, mobile elements that are widespread among bacteria. Following their excision from the chromosome, ICEs transfer by conjugation, a process initiated by a single-stranded DNA break at a specific locus called the origin of transfer (oriT). The SXT/R391 family of ICEs includes SXTMO10, R391, and more than 25 related ICEs found in gammaproteobacteria. A previous study mapped the oriT locus of SXTMO10 to a 550-bp intergenic region between traD and s043. We suspected that this was not the correct oriT locus, because the identical traD-s043 region in R391 and other SXT/R391 family ICEs was annotated as a gene of an unknown function. Here, we investigated the location and structure of the oriT locus in the ICEs of the SXT/R391 family and demonstrated that oriT SXT corresponds to a 299-bp sequence that contains multiple imperfect direct and inverted repeats and is located in the intergenic region between s003 and rumB′. The oriT SXT locus is well conserved among SXT/R391 ICEs, like R391, R997, and pMERPH, and cross-recognition of oriT SXT and oriT R391 by R391 and SXTMO10 was demonstrated. Furthermore, we identified a previously unannotated gene, mobI, located immediately downstream from oriT SXT, which proved to be essential for SXTMO10 transfer and SXTMO10-mediated chromosomal DNA mobilization. Deletion of mobI did not impair the SXTMO10-dependent transfer of the mobilizable plasmid CloDF13, suggesting that mobI has no role in the assembly of the SXTMO10 mating pair apparatus. Instead, mobI appears to be involved in the recognition of oriT SXT.