Biology subjects

Borel, C.

Publications and source records attributed to Borel, C..

5 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

Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results

The independent reproduction of research results is a cornerstone of experimental research, yet it is beset by numerous challenges, including the quality and veracity of reagents and materials. Much of life science research depends on life materials, including human tissue culture cells. In this study we aimed at determining the degree of variability in the molecular makeup and the ensuing phenotypic consequences in commonly used human tissue culture cells. We collected 14 stock HeLa aliquots from 13 different laboratories across the globe, cultured them in uniform conditions and profiled the genome-wide copy numbers, mRNAs, proteins and protein turnover rates via genomic techniques and SWATH mass spectrometry, respectively. We also phenotyped each cell line with respect to the ability of transfected Let7 mimics to modulate Salmonella infection.\n\nWe discovered significant heterogeneity between HeLa variants, especially between lines of the CCL2 and Kyoto variety. We also observed progressive divergence within a specific cell line over 50 successive passages. From the aggregate multi-omic datasets we quantified the response of the cells to genomic variability across the transcriptome and proteome. We discovered organelle-specific proteome remodeling and buffering of protein abundance by protein complex stoichiometry, mediated by the adaptation of protein turnover rates. By associating quantitative proteotype and phenotype measurements we identified protein patterns that explained the varying response of the different cell lines to Salmonella infection.\n\nAltogether the results indicate a striking degree of genomic variability, the rapid evolution of genomic variability in culture and its complex translation into distinctive expressed molecular and phenotypic patterns. The results have broad implications for the interpretation and reproducibility of research results obtained from HeLa cells and provide important basis for a general discussion of the value and requirements for communicating research results obtained from human tissue culture cells.

systems biology↗

bioRxiv2017

Deciphering cell lineage specification during male sex determination with single-cell RNA sequencing

The gonad is a unique biological system for studying cell fate decisions. However, major questions remain regarding the identity of somatic progenitor cells and the transcriptional events driving cell differentiation. Using time course single cell RNA sequencing on XY mouse gonads during sex determination, we identified a single population of somatic progenitor cells prior sex determination. A subset of these progenitors differentiate into Sertoli cells, a process characterized by a highly dynamic genetic program consisting of sequential waves of gene expression. Another subset of multipotent cells maintains their progenitor state but undergo significant transcriptional changes that restrict their competence towards a steroidogenic fate required for the differentiation of fetal Leydig cells. These results question the dogma of the existence of two distinct somatic cell lineages at the onset of sex determination and propose a new model of lineage specification from a unique progenitor cell population.

developmental biology↗

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↗