Complete lung agenesis caused by complex genomic rearrangements with neo-TAD formation at the SHH locus

Uirá Souto Melo,Francine Arbez-Gindre,Björn Fischer-Zirnsak,Robert Schöpflin,Virginie Rozé ,Martin A Mensah ,Manuel Holtgrewe,R Ramanah ,Dominique Gaillard,Malte Spielmann,Stefan Mundlos,A Martin ,Frederike L Harms,Emilie Landais,Marius-Konstantin Klever,Christelle Cabrol,Valérie Kremer ,Virginie Guigue,Juliette Piard,Uwe Kornak,Lionel Van Maldergem

doi:10.1007/s00439-021-02344-6

Abstract

During human organogenesis, lung development is a timely and tightly regulated developmental process under the control of a large number of signaling molecules. Understanding how genetic variants can disturb normal lung development causing different lung malformations is a major goal for dissecting molecular mechanisms during embryogenesis. Here, through exome sequencing (ES), array CGH, genome sequencing (GS) and Hi-C, we aimed at elucidating the molecular basis of bilateral isolated lung agenesis in three fetuses born to a non-consanguineous family. We detected a complex genomic rearrangement containing duplicated, triplicated and deleted fragments involving the SHH locus in fetuses presenting complete agenesis of both lungs and near-complete agenesis of the trachea, diagnosed by ultrasound screening and confirmed at autopsy following termination. The rearrangement did not include SHH itself, but several regulatory elements for lung development, such as MACS1, a major SHH lung enhancer, and the neighboring genes MNX1 and NOM1. The rearrangement incorporated parts of two topologically associating domains (TADs) including their boundaries. Hi-C of cells from one of the affected fetuses showed the formation of two novel TADs each containing SHH enhancers and the MNX1 and NOM1 genes. Hi-C together with GS indicate that the new 3D conformation is likely causative for this condition by an inappropriate activation of MNX1 included in the neo-TADs by MACS1 enhancer, further highlighting the importance of the 3D chromatin conformation in human disease.

Highlights

Complete absence of one or both lungs is an extremely rare malformation with an estimated birth prevalence below 1/107 if we estimate that only a dozen of reports have been published so far, mostly occurring unilaterally (Ostör et al 1978; Mardini et al 1985; Spear et al 1987; Engellenner et al 1989; Podlech et al 1995; Kayemba-Kay's et al 2014)
Complete absence of the lung is an ultra-rare malformation described in only few cases worldwide
After applying a combination of several genetic/genomic screening methodologies, we identified a complex genomic rearrangement (CGR) on 7q36.3 shared by all three affected fetuses, presenting duplicated, triplicated and deleted fragments

Summary

Introduction

Complete absence of one or both lungs is an extremely rare malformation with an estimated birth prevalence below 1/107 if we estimate that only a dozen of reports have been published so far, mostly occurring unilaterally (Ostör et al 1978; Mardini et al 1985; Spear et al 1987; Engellenner et al 1989; Podlech et al 1995; Kayemba-Kay's et al 2014) This extreme deleterious phenotype is caused by a failure in the proper formation of the lung buds derived from the foregut with no detectable respiratory tissue (lung agenesis). In the late 4th week after conception, the embryonic stage of lung development starts with the formation of two outpouchings in the ventral wall of the foregut termed lung buds, that start to proliferate in repetitive circles of growth and branching (Schittny 2017) While these buds, that form the later respiratory epithelium, are derived from the endoderm, they grow and branch inside of mesoderm derived tissues.

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