Lurie, E. | Search bioRxiv

bioRxiv2019

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software

Cell-type heterogeneity of tumors is a key factor in tumor progression and response to chemotherapy. Tumor cell-type heterogeneity, defined as the proportion of the various cell-types in a tumor, can be inferred from DNA methylation of surgical specimens. However, confounding factors known to associate with methylation values, such as age and sex, complicate accurate inference of cell-type proportions. While reference-free algorithms have been developed to infer cell-type proportions from DNA methylation, a comparative evaluation of the performance of these methods is still lacking.\n\nHere we use simulations to evaluate several computational pipelines based on the software packages MeDeCom, EDec, and RefFreeEWAS. We identify that accounting for confounders, feature selection, and the choice of the number of estimated cell types are critical steps for inferring cell-type proportions. We find that removal of methylation probes which are correlated with confounder variables reduces the error of inference by 30-35%, and that selection of cell-type informative probes has similar effect. We show that Cattells rule based on the scree plot is a powerful tool to determine the number of cell-types. Once the pre-treatment steps are achieved, the three deconvolution methods provide comparable results. We observe that all the algorithms performance improves when inter-sample variation of cell-type proportions is large or when the number of available samples is large. We find that under specific circumstances the methods are sensitive to the initialization method, suggesting that averaging different solutions or optimizing initialization is an avenue for future research. Based on the lessons learned, to facilitate pipeline validation and catalyze further pipeline improvement by the community, we develop a benchmark pipeline for inference of cell-type proportions and implement it in the R package medepir.

bioinformatics↗

bioRxiv2017

Compositional shifts in the root microbiota track the life-cycle of field-grown rice plants

Bacterial communities associated with roots impact the health and nutrition of the host plant. While a multitude of static factors are known to influence the composition of the root-associated microbiota, the dynamics of these microbial assemblies over the plant life cycle are poorly understood. Here, we use dense temporal sampling of spatial compartments to characterize the root-associated microbiota of field grown rice (Oryza sativa) over the course of three consecutive growing seasons and two sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth, then stabilizes compositionally for the remainder of the life cycle. Bacterial taxa conserved between field sites can be used as predictive features of rice plant age by modeling using a random forests approach. The age-prediction models were used to reveal that drought stressed plants have developmentally delayed microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle.

plant biology↗