Single cell transcriptome in aneuploidies reveals mechanisms of gene dosage imbalance

Georgios Stamoulis,Periklis Makrythanasis,Frédérique Sloan-Béna,Nikolaos Panousis,Michel Guipponi,Audrey Letourneau,Marco Garieri,Pascale Ribaux,Christelle Borel,Stylianos E Antonarakis,Federico Santoni,Emilie Falconnet

doi:10.1038/s41467-019-12273-8

Abstract

Aneuploidy is a major source of gene dosage imbalance due to copy number alterations (CNA), and viable human trisomies are model disorders of altered gene expression. We study gene and allele-specific expression (ASE) of 9668 single-cell fibroblasts from trisomy 21 (T21) discordant twins and from mosaic T21, T18, T13 and T8. We examine 928 single cells with deep scRNAseq. Expected and observed overexpression of trisomic genes in trisomic vs. diploid bulk RNAseq is not detectable in trisomic vs. diploid single cells. Instead, for trisomic genes with low-to-average expression, their altered gene dosage is mainly due to the higher fraction of trisomic cells simultaneously expressing these genes, in agreement with a stochastic 2-state burst-like model of transcription. These results, confirmed in a further analysis of 8740 single fibroblasts with shallow scRNAseq, suggest that the specific transcriptional profile of each gene contributes to the phenotypic variability of trisomies. We propose an improved model to understand the effects of CNA and, generally, of gene regulation on gene dosage imbalance.

Highlights

Aneuploidy is a major source of gene dosage imbalance due to copy number alterations (CNA), and viable human trisomies are model disorders of altered gene expression
We used six different cell lines of skin fibroblasts from six individuals: two samples are from a pair of monozygotic twins discordant for T2125; four were from individuals mosaics for trisomy 21 (T21): CM05287, T13: GM00503, T18: AG13074, T8: GM02596 (Supplementary Fig. 1 and Supplementary Table 1)
In order to classify trisomic and diploid cells in a mosaic trisomy cell population we developed an iterative clustering method based on k-means (k = 2) using two metrics: the average cellular gene expression and allele-specific expression (ASE) at heterozygous sites, both measured from the genes located on the supernumerary chromosome

Summary

Introduction

Aneuploidy is a major source of gene dosage imbalance due to copy number alterations (CNA), and viable human trisomies are model disorders of altered gene expression. For trisomic genes with low-to-average expression, their altered gene dosage is mainly due to the higher fraction of trisomic cells simultaneously expressing these genes, in agreement with a stochastic 2-state burst-like model of transcription These results, confirmed in a further analysis of 8740 single fibroblasts with shallow scRNAseq, suggest that the specific transcriptional profile of each gene contributes to the phenotypic variability of trisomies. Single-cell RNA-seq (scRNAseq) studies have revealed pervasive genome-wide skewed monoallelic gene expression in diploid cells[17], and variability and gradation of gene expression for different genomic phenomena/ processes, such as imprinting[18] and X-inactivation[19] These phenomena are likely the outcomes of the discrete and stochastic nature of RNA transcription with each gene bearing his own specific regulation[20,21]. In agreement with the 2-state burst-like model, we provide evidence that, in trisomic cells, the additional allele is independently transcribed, leading to an increased monoallelic expression with respect to the diploid cells, and a significant fraction of trisomic cells simultaneously activating gene expression as compared to diploid controls

Methods

Results

Conclusion