Perturbations of genes essential for Müllerian duct and Wölffian duct development in Mayer-Rokitansky-Küster-Hauser syndrome

Abstract

Mayer-Rokitansky-Ku ¨ster-Hauser syndrome (MRKHS) is associated with congenital absence of the uterus, cervix, and the upper part of the vagina; it is a sex-limited trait. Disrupted development of the Mu ¨llerian ducts (MD)/Wo ¨lffian ducts (WD) through multifactorial mechanisms has been proposed to underlie MRKHS. In this study, exome sequencing (ES) was performed on a Chinese discovery cohort (442 affected subjects and 941 female control subjects) and a replication MRKHS cohort (150 affected subjects of mixed ethnicity from North America, South America, and Europe). Phenotypic follow-up of the female reproductive system was performed on an additional cohort of PAX8-associated congenital hypothyroidism (CH) (n ¼ 5, Chinese). By analyzing 19 candidate genes essential for MD/WD development, we identified 12 likely gene-disrupting (LGD) variants in 7 genes:, and WNT9B (n ¼ 1), while LGD variants in these genes were not detected in control samples (p ¼ 1.27EÀ06). Interestingly, a sex-limited penetrance with paternal inheritance was observed in multiple families. One additional PAX8 LGD variant from the replication cohort and two missense variants from both cohorts were revealed to cause loss-of-function of the protein. From the PAX8-associated CH cohort, we identified one individual presenting a syndromic condition characterized by CH and MRKHS (CH-MRKHS). Our study demonstrates the comprehensive utilization of knowledge from developmental biology toward elucidating genetic perturbations, i.e., rare pathogenic alleles involving the same loci, contributing to human birth defects.Mayer-Rokitansky-Ku ¨ster-Hauser syndrome (MRKHS [MIM: 277000]), also referred to as Mu ¨llerian aplasia, is characterized by congenital absence of the uterus, cervix, and upper part of the vagina in females with a normal karyotype (46, XX). 1 With an incidence of 1 in 4,500-5,000 newborn females, MRKHS is the second most common cause of primary amenorrhea after gonadal dysgenesis. 2 MRKHS is further divided into MRKHS type I (isolated) and MRKHS type II (syndromic) according to the presence of multi-organ involvement. 3 Formation and morphogenesis of the Mu ¨llerian ducts take place during weeks 5-6 of human embryogenesis

Homozygous WNT9B variants in two families with bilateral renal agenesis/hypoplasia/dysplasia

“…The difference between the null mouse Müllerian phenotypes and our patient phenotypes could be explained by a difference in WNT9B's role in the urogenital system development between humans and mice, domain specific mutations, or the effect of a variable degree of loss of WNT9B function, although the variant in Family 2 is presumably a null variant. As prior reports have suggested WNT9B as a candidate gene for human Müllerian agenesis (Chen et al, 2021;Wang et al, 2014;Waschk et al, 2016), we looked further at the reported variants in these papers (Table 1). The five heterozygous candidate variants for Müllerian agenesis reported by Waschk et al (2016), have allele counts of 1, 348, 55, 0, and 12 in gnomAD v2.1.1 (Karczewski et al, 2020), suggesting that at least three of them are too common to cause this rare anomaly on their own.…”

“…One variant was rare but in the 3′ untranslated region and not predicted to impact splicing based on SpliceAI score (Jaganathan et al, 2019), and the other was a missense variant that is now known to have 8 allele counts in gnomAD v2.1.1 (Karczewski et al, 2020), making these unlikely to cause this rare phenotype. Moreover, the heterozygous nonsense variant recently reported by Chen et al is not expressed in WNT9B 's canonical transcript (NM_003396.2) and is in the last exon of the NM_001320458.2 transcript, removing only four amino acids from the WNT9B protein and not predicted to result in nonsense‐mediated mRNA decay (Chen et al, 2021). This variant has two allele counts in gnomAD v2.1.1 (Karczewski et al, 2020) and was not segregated in family members.…”

“…Two heterozygous variants in WNT9B of unknown phase were reported in a woman with isolated Müllerian agenesis (Wang et al, 2014) and Waschk et al (2016) reported five candidate heterozygous variants in WNT9B in five additional women with isolated Müllerian agenesis (Table 1). Chen et al (2021) also recently reported a heterozygous candidate variant in WNT9B in a woman with isolated Müllerian agenesis (Table 1). No functional assays were performed in either of these reports to determine if these candidate variants impaired WNT9B function.…”

Novel FGFR1 Variants Are Associated with Congenital Scoliosis

“…WES data processing was performed using the Peking Union Medical college hospital Pipeline (PUMP) [13,14] developed in-house. Computational prediction tools (Genomic Evolutionary Rate Profiling [GERP] [15], Combined Annotation Dependent Depletion [CADD PHRED-score, GRCh37-v1.6] [16], Sorting Intolerant Form Tolerant [SIFT] [17], Polyphen-2 [18], and MutationTaster [19]) were used to predict the conservation and pathogenicity of candidate variants.…”

Disruptive NADSYN1 Variants Implicated in Congenital Vertebral Malformations

“…Congenital vertebral malformation (CVM) refers to abnormal development of the spine structure presenting as congenital scoliosis, kyphosis, or other congenital vertebral defects and may occur simultaneously with other birth defects or as part of an underlying genetic syndrome [1,2]. In human embryogenesis, the vertebral column develops at 4-6 weeks of gestation from the paraxial mesoderm (PSM) and is closely related to the spinal cord and other organs originating from mesoderm [3][4][5]. Multiple organ defects, most frequently involving the cardiac system, urogenital system, limbs, and spinal cord, have a higher occurrence in CVM than in the general population [3].…”