Biology subjects

Ribaux, P.

Publications and source records attributed to Ribaux, P..

4 recordsLinked to original sources

bioRxiv2018

Time and space dimensions of gene dosage imbalance of aneuploidies revealed by single cell transcriptomes.

The mechanisms underlying cellular and organismal phenotypes due to copy number alterations (CNA) are not fully understood. Aneuploidy is a major source of gene dosage imbalance due to CNA and viable human trisomies are model disorders of altered gene expression. To understand the cellular impact of gene dosage imbalance, we studied gene and allele specific expression (ASE) of 9668 single-cell fibroblasts in trisomies T21, T18, T13 and T8. To limit the bias of interindividual noise, all comparisons between euploid and trisomic single-cells were performed on an isogenic setting for all trisomies studied. Initially we examined 928 single cells with deep RNA-Seq. For T21 we used fibroblasts from one pair of monozygotic twins discordant for T21 and from mosaic T21. For T18, T13 and T8 we analyzed single cells from mosaic individuals. Single-cell analyses revealed inconsistencies concerning the overexpression of some genes observed in differential trisomic vs euploid bulk RNAseq while this imbalance was not detectable in trisomic vs. euploid single cells. Moreover, ASE profiling of all single cells uncovered a substantial monoallelic pattern of expression in the trisomic fraction of the genome. By classifying genes according to the level of mono and bi-allelic transcription, we have observed that, for genes with monoallelic and low-to-average expression, the altered gene dosage is mainly due to the higher fraction of cells simultaneously expressing these genes in the trisomic samples. These results were confirmed in a further experiment of 8740 single fibroblasts from the monozygotic twins discordant for T21 samples. We conclude that gene dosage imbalance is of bidimensional nature: over time (simultaneous expression of all alleles resulting in increased accumulation of RNA of copy altered genes in each single cell) as previously stated, and over space (increased fraction of cells simultaneously expressing copy altered genes). These results strongly suggest that each class of genes contributes to the phenotypic variability of trisomies according to its temporal and spatial behavior and propose an improved model to understand the effects of copy number alterations.

genomics↗

bioRxiv2018

Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts.

In eutherian mammals, X chromosome inactivation (XCI) provides a dosage compensation mechanism where in each female cell one of the two X chromosomes is randomly silenced. However, some genes on the inactive X chromosome and outside the pseudoautosomal regions escape from XCI and are expressed from both alleles (escapees). Given the relevance of the escapees in biology and medicine, we investigated XCI at an unprecedented single-cell resolution. We combined deep single-cell RNA sequencing with whole genome sequencing to examine allelic specific expression (ASE) in 935 primary fibroblast and 48 lymphoblastoid single cells from five female individuals. In this framework we integrated an original method to identify and exclude doublets of cells. We have identified 55 genes as escapees including 5 novel escapee genes. Moreover, we observed that all genes exhibit a variable propensity to escape XCI in each cell and cell type, and that each cell displays a distinct expression profile of the escapee genes. We devised a novel metric, the Inactivation Score (IS), defined as the mean of the allelic expression profiles of the escapees per cell, and discovered a heterogeneous and continuous degree of cellular XCI with extremes represented by \"inactive\" cells, i.e., exclusively expressing the escaping genes from the active X chromosome, and \"escaping\" cells, expressing the escapees from both alleles. Intriguingly we found that XIST is the major genetic determinant of IS, and that XIST expression, higher in G0 phase, is negatively correlated with the expression of escapees, inactivated and pseudoautosomal genes. In this study we use single-cell allele specific expression to identify novel escapees in different tissues and provide evidence of an unexpected cellular heterogeneity of XCI driven by a possible regulatory activity of XIST.

genetics↗

bioRxiv2017

Intra- and inter-chromosomal chromatin interactions mediate genetic effects on regulatory networks

Genome-wide studies on the genetic basis of gene expression and the structural properties of chromatin have considerably advanced our understanding of the function of the human genome. However, it remains unclear how structure relates to function and, in this work, we aim at bridging both by assembling a dataset that combines the activity of regulatory elements (e.g. enhancers and promoters), expression of genes and genetic variations of 317 individuals and across two cell types. We show that the regulatory activity is structured within 12,583 Cis Regulatory Domains (CRDs) that are cell type specific and highly reflective of the local (i.e. Topologically Associating Domains) and global (i.e. A/B nuclear compartments) nuclear organization of the chromatin. These CRDs essentially delimit the sets of active regulatory elements involved in the transcription of most genes, thereby capturing complex regulatory networks in which the effects of regulatory variants are propagated and combined to finally mediate expression Quantitative Trait Loci. Overall, our analysis reveals the complexity and specificity of cis and trans regulatory networks and their perturbation by genetic variation.

genomics↗

bioRxiv2017

Improving Leukemic CD34+/CD38- Blasts Characterization With Single-Cell Transcriptome Sequencing

SUMMARY / ABSTRACTAcute myeloid leukemia (AML) is a particularly aggressive blood cancer that is difficult to treat because of the incomplete eradication of rare blast cells that possess self-renewal and leukemia-initiating properties. To characterize resistant blasts, we analyzed for the first time the transcriptomes of individual CD34+/CD38- blasts by single-cell mRNA sequencing of 359 CD33+/CD34+/CD38-/+ sorted cells from two patients with AML and four unaffected individuals. We demonstrated that the captured blasts possess the transcriptomic hallmarks of self-renewal and leukemia-initiating ability. The effects of somatic mutations on the cancer cells are visible at the transcriptional level, and the cellular signaling pathway activity of the blasts is altered, revealing disease-associated gene networks. We also identified a core set of transcription factors that were co-activated in blasts, which suggests a joint transcription program among blasts. Finally, we revealed that leukemogenesis and putative prognostic gene-expression signatures are present at diagnosis in leukemic CD33+/CD34+/CD38- cells and can be detected using a single-cell RNA sequencing approach.

cancer biology↗