Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package.

Analyzing different omics data types independently is often too restrictive to allow for detection of subtle, but consistent, variations that are coherently supported based upon different assays. Integrating multi-omics data in one model can increase statistical power. However, designing such a model is challenging because different omics are measured at different levels. We developed the iNETgrate package ( https://bioconductor.org/packages/iNETgrate/ ) that efficiently integrates transcriptome and DNA methylation data in a single gene network. Applying iNETgrate on five independent datasets improved prognostication compared to common clinical gold standards and a patient similarity network approach.

"iNETgrate": integrating DNA methylation and gene expression data in a single gene network.

Integrating multi-omics data in one model can increase statistical power. However, designing such a model is challenging because different omics are measured at different levels. We developed the iNETgrate package (https://bioconductor.org/packages/iNETgrate/) that efficiently integrates transcriptome and DNA methylation data in a single gene network. Applying iNETgrate on five independent datasets improved prognostication compared to common clinical gold standards and a patient similarity network approach.

DNA methylation analysis improves the prognostication of acute myeloid leukemia.

Integration of orthogonal data could provide new opportunities to pinpoint the underlying molecular mechanisms of hematologic disorders. Using a novel gene network approach, we integrated DNA methylation data from The Cancer Genome Atlas (n = 194 cases) with the corresponding gene expression profile. Our integrated gene network analysis classified AML patients into low-, intermediate-, and high-risk groups. The identified high-risk group had significantly shorter overall survival compared to the low-risk group (p-value ≤10-11). Specifically, our approach identified a particular subgroup of nine high-risk AML cases that died within 2 years after diagnosis. These high-risk cases otherwise would be incorrectly classified as intermediate-risk solely based on cytogenetics, mutation profiles, and common molecular characteristics of AML. We confirmed the prognostic value of our integrative gene network approach using two independent datasets, as well as through comparison with European LeukemiaNet and LSC17 criteria. Our approach could be useful in the prognostication of a subset of borderline AML cases. These cases would not be classified into appropriate risk groups by other approaches that use gene expression, but not DNA methylation data. Our findings highlight the significance of epigenomic data, and they indicate integrating DNA methylation data with gene coexpression networks can have a synergistic effect.

Regulation of correlative inhibition of axillary bud outgrowth by basal branches varies with growth stage in Trifolium repens.

In Trifolium repens the decline in bud outgrowth that occurs with distance from basal root systems is due to correlative inhibition by the first-formed basal branches. The apical and axillary buds on these basal branches are the source of the inhibitory effect, but their mode of action is unclear. Inhibition might occur via basal branches being a sink for xylem-transported branching stimulants or alternatively by providing a source of inhibitory signals, or by both mechanisms. To distinguish between these mechanisms, four experiments were conducted on plants varying in initial growth stage from 10 to 19 nodes along their main stems to determine any variation in the relative importance of the operative mechanisms of correlative inhibition. Inhibitory signal exported into the main stem, detected as a branching response to girdling of basal branches, was relatively more significant in smaller (initially with 10-15 nodes on the main stem) than in larger (>19 nodes on main stem) plants. This signal was shown not to involve auxin fluxes, and is unidentified. However, across all stages of growth, the predominant mechanism driving correlative inhibition was the action of axillary and apical buds of basal branches as sinks for the stimulatory signal. This study indicates that the relative importance of the mechanisms regulating bud outgrowth in T. repens varies with growth stage and that, during intermediate stages, regulation has some similarity to that in Pisum.

Shoot branching in response to nodal roots is mimicked by application of exogenous cytokinin in Trifolium repens.

In nodally-rooting prostrate herbs the outgrowth of shoot axillary buds is highly influenced by the supply of a branch-promoting signal exported from nodal roots to the shoot. The aim of this study was to establish whether cytokinin could be a candidate for the positive component within this net root stimulus (NRS). The approach taken was based on the notion that should cytokinin be the activating signal, then the effects on bud outgrowth induced by exogenous supply of cytokinin (6-benzylaminopurine (BAP)) to plants should largely mimic the responses observed when experimental manipulations alter intra-plant supply of NRS. In Trifolium repens experimental results consistently indicated that supply of BAP into the stem vasculature induced responses mimicking those induced by manipulation of NRS supply: it induced the outgrowth of a similar number of distal axillary buds, activated buds to a similar extent, had similar properties of transport along stems, induced a similar dose dependent response in distal buds and also had the ability to induce bud outgrowth in P-deficient plants. These findings indicate a requirement for further detailed hormonal analytical work to confirm this result and identify the nature of the cytokinin(s) involved in the NRS signalling pathway.

Shoot branching in nutrient-limited Trifolium repens is primarily restricted by shortage of root-derived promoter signals.

Two experiments were used to test the hypothesis that regulation of axillary bud outgrowth in nutrient-limited Trifolium repens L. (white clover) is primarily via variation in the net supply of root-derived promoter signal rather than via direct nutrient effects or inhibitory influences from apical or basal tissues. In the first experiment, foliar nutrient applications to a non-rooted portion of a nutrient-limited stem increased nutrient content, size of organs and rate of growth in the treated region but branch development remained suppressed, indicating that nutrient supply does not directly regulate branching. The second experiment, using decapitation and basal branch excision treatments, showed that excision of basal branches had a major stimulatory effect on bud outgrowth whereas decapitation of the primary stem had only a minor effect. This indicates dominant and minor roles in branching regulation for, respectively, root-derived promoter signal(s) and inhibitory apical influences (apical dominance), and that any possible influence of the inhibitory strigolactone pathway on bud outgrowth is captured within the net root-derived promoter influence. Thus, the proposed hypothesis was supported by our results. These findings may be relevant for all species within the group of prostrate nodally-rooting clonal herbs.