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Slightly Deleterious Genomic Variants and Transcriptome Perturbations in Down Syndrome Embryonic Selection

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Slightly Deleterious Genomic Variants and Transcriptome Perturbations in Down Syndrome Embryonic Selection Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Research Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection Konstantin Popadin,1,2,3,4 Stephan Peischl,4,5 Marco Garieri,1 M. Reza Sailani,6 Audrey Letourneau,1 Federico Santoni,1 Samuel W. Lukowski,7 Georgii A. Bazykin,8,9 Sergey Nikolaev,1 Diogo Meyer,10 Laurent Excoffier,4,11 Alexandre Reymond,2,12 and Stylianos E. Antonarakis1,12 1Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; 2Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland; 3Immanuel Kant Baltic Federal University, Kaliningrad, 236041, Russia; 4Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; 5Interfaculty Bioinformatics Unit, University of Bern, 3012 Bern, Switzerland; 6Stanford School of Medicine, Stanford University, Stanford, California 94305, USA; 7Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia; 8Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, 127051, Russia; 9Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, 143026, Russia; 10Department of Genetics and Evolutionary Biology, University of Sao Paulo, 05508-090, Sao Paulo, Brazil; 11Institute for Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland The majority of aneuploid fetuses are spontaneously miscarried. Nevertheless, some aneuploid individuals survive despite the strong genetic insult. Here, we investigate if the survival probability of aneuploid fetuses is affected by the genome-wide burden of slightly deleterious variants. We analyzed two cohorts of live-born Down syndrome individuals (388 genotyped samples and 16 fibroblast transcriptomes) and observed a deficit of slightly deleterious variants on Chromosome 21 and de- creased transcriptome-wide variation in the expression level of highly constrained genes. We interpret these results as sig- natures of embryonic selection, and propose a genetic handicap model whereby an individual bearing an extremely severe deleterious variant (such as aneuploidy) could escape embryonic lethality if the genome-wide burden of slightly deleterious variants is sufficiently low. This approach can be used to study the composition and effect of the numerous slightly dele- terious variants in humans and model organisms. [Supplemental material is available for this article.] The majority of miscarriages are selective, i.e., contain chromo- 2004), which may indicate strong embryonic selection. We hy- somal abnormalities or other severe mutations (Forbes 1997; pothesize that as a result of this selection, live-born T21 individu- Larsen et al. 2013). However, little is known about why fetuses als possess a reduced burden of SDVs compared to live-born, with the same severe de novo variant can be either viable (at euploid control individuals. We hypothesized that a substantial term) or not (miscarried). We hypothesize that the outcome is in- fraction of the SDVs interacts with trisomy, so that their preva- fluenced by the burden of slightly deleterious variants (SDVs). lence differs between T21 and euploid individuals. Although the Every human genome carries at least 1000 SDVs, including several SDVs on Chromosome 21 may directly affect the genes mapping loss-of-function variants (Kaiser et al. 2015), dozens of exon-inter- on this chromosome, interactions may also involve genes else- secting copy number variants (Sudmant et al. 2015), hundreds of where in the genome. We provisionally categorized SDVs into single-nucleotide missense coding substitutions (Xue et al. 2012; directly and indirectly interacting with trisomy on the basis of Henn et al. 2016), and thousands of single-nucleotide regulatory their genomic location: We assumed that Chromosome 21 SDVs variants (Gulko et al. 2015). Numerous studies have demonstrated are directly interacting, whereas the SDVs on all other autosomes that this burden of SDVs is under purifying selection in the human may only be indirectly interacting. population (Männik et al. 2015; Sulem et al. 2015; Narasimhan In this study, we observed several lines of evidence, which is et al. 2016; Sohail et al. 2017) and thus might affect fetal viability. in line with embryonic selection of T21 individuals acting against In this study, we focus on trisomy 21 (T21). T21 fetuses have a burden of SDVs. Based on our findings, we formulated the genet- extremely high (up to 80%) miscarriage rates (Nussbaum et al. ic handicap model, stating that an individual bearing an extremely © 2018 Popadin et al. This article is distributed exclusively by Cold Spring 12These authors contributed equally to this work. Harbor Laboratory Press for the first six months after the full-issue publication Corresponding authors: [email protected], stylianos. date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it [email protected] is available under a Creative Commons License (Attribution-NonCommercial Article published online before print. Article, supplemental material, and publi- 4.0 International), as described at http://creativecommons.org/licenses/by- cation date are at http://www.genome.org/cgi/doi/10.1101/gr.228411.117. nc/4.0/. 28:1–10 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/18; www.genome.org Genome Research 1 www.genome.org Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Popadin et al. severe deleterious variant (i.e., genetic handicap) might escape and annotated derived alleles as GOE and LOE cis-eQTLs (Fig. embryonic lethality if the genome-wide burden of SDVs is suffi- 1C, upper). We assumed that the direction of the derived allele ciently low. in trisomic cases is the same as in disomic, i.e., if D is annotated in the GenCord collection as GOE, the expression levels would Results be ordered as AAA < AAD < ADD < DDD (Fig. 1C, lower). We only used concordant (i.e., with the same direction) cis-eQTLs detected Genomic and transcription variation of genes encoded in more than one cell type. on Chromosome 21 in T21 individuals We then analyzed the genotype frequencies of the annotated cis-eQTLs in a population of unrelated live-born T21 individuals Functionally constrained Chromosome 21 genes demonstrate <1.5-fold (N = 338). For the 63 annotated cis-eQTLs on Chromosome 21 increased expression in T21 individuals (32 GOE and 31 LOE), we compared the observed and predicted (Methods) frequencies of the DDD genotypes. Due to the small T21 fetuses with a relatively reduced expression of Chromosome sample size, we did not split the cis-eQTLs according to the proper- 21 genes (<1.5-fold increase) might be favored by embryonic selec- ties (functionally constrained and functionally nonconstrained) tion and thus have a higher probability of being live-born (Fig. 1A; of associated genes. Our null expectation is that excess and deficit Antonarakis et al. 2004; Aït Yahya-Graison et al. 2007; Prandini of different genotypes is independent of the effect of regulatory al- et al. 2007; Biancotti et al. 2010). We tested this by analyzing fibro- leles (Fig. 1D, dotted line). However, we observed that the majority blast transcriptomes of 16 T21 and 11 control live-born individu- of LOE DDD genotypes (22 of 32) have a higher frequency than ex- als. We used a set of Chromosome 21 genes (N = 233) that were pected, whereas the majority of GOE DDD genotypes (19 of 31) expressed in all 27 samples. For each gene, we estimated the have a lower frequency than expected (N = 63, Fisher’s odds ratio mean expression level in T21 and controls and computed a ratio = 3.41, P = 0.023) (Fig. 1D). Interestingly, if we further restrict our of these values (Fig. 1B). The median of the ratios was 1.473, which analysis only to those cis-eQTLs that were concordant in all three does not significantly differ from the expected 1.5 (P-value = 0.78, cell types of the GenCord collection, the signal becomes stronger, one-sample Wilcoxon signed rank test with μ = 1.5). However, although less significant due to the small sample size (N = 16, when we focused on a subset of functionally constrained genes Fisher’s odds ratio = 7.63, P = 0.118). We conclude that the distri- (highly expressed and essential, N = 23) (Methods), the median bution of LOE and GOE cis-eQTLs (Fig. 1D) in live-born T21 indi- of the ratios was significantly lower as compared to the whole set viduals is compatible with embryonic selection favoring decreased of Chromosome 21 genes (1.379 versus 1.473, P-value = 0.035, gene expression level of trisomic genes. Mann-Whitney U test) (Fig. 1B), and the deviation from the ex- pected 1.5 was also significant (P-value = 0.020, one-sample Wilcoxon signed rank test with μ = 1.5) (Fig. 1B). Deviation of Chromosome 21 alleles from the Hardy–Weinberg Equilibrium The <1.5-fold increase in the expression of functionally con- uncovers signatures of selection strained genes is compatible with two explanations: (1) It might be We next aimed to estimate the effect of all potentially deleterious the effect of embryonic selection against T21 fetuses with high variants on Chromosome 21. Rare derived alleles are enriched in overexpression of these genes; or (2) it might reflect a buffering deleterious variants (MacArthur et al. 2012; Fu et al. 2013), allow-
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