Prenatal diagnosis and molecular cytogenetic analysis of pure chromosome 10p15.3 microdeletion using chromosomal microarray analysis

Abstract

Background

The literature contains exceedingly limited reports on chromosome 10p15.3 microdeletions. In the present study, two cases of fetuses with pure terminal 10p15.3 microdeletion syndrome in a Chinese population were examined, with the objective of enhancing understanding of the genotype-phenotype correlation associated with 10p15.3 microdeletions.

Methods

Two fetuses with chromosome 10p15.3 microdeletion were identified from a cohort of 5,258 cases undergoing amniocentesis. Karyotyping and chromosomal microarray analysis (CMA) was conducted to assess chromosomal abnormalities and detect copy number variations (CNVs) within the families, respectively.

Results

In Family 1, the fetus exhibited a 556.2-Kb deletion in the 10p15.3 region, encompassing OMIM genes such as DIP2C and ZMYND11, and presented with increased nuchal translucency on prenatal ultrasound examination. Parental CMA analysis revealed that the 10p15.3 microdeletion was inherited from the father, who displayed mild language impairment. In Family 2, a comparable 10p15.3 microdeletion was identified in a fetus presenting with asymmetric butterfly vertebrae at T10 and T12, along with mild scoliosis of the spine. Family 1 elected to terminate the pregnancy, while Family 2 chose to continue. At a follow-up conducted at one year and eight months, the child demonstrated delays in both speech and motor development.

Conclusion

The present study is the first to report two cases of pure terminal chromosome 10p15.3 microdeletion syndrome in fetuses, offering valuable insights for the prenatal diagnosis of 10p15.3 microdeletion syndrome. Further, it is the first to describe mild clinical features, specifically limited to language impairment, in a patient with 10p15.3 microdeletion syndrome.

Introduction

Partial chromosome 10p deletion represents a rare chromosomal abnormality characterized by three distinct contiguous gene deletion syndromes. Hypoparathyroidism, sensorineural deafness, and renal dysplasia syndrome (HDRS), also referred to as Barakat syndrome, is attributed to haploinsufficiency of the GATA3 gene (131320) on chromosome 10p14, with variable clinical features including hypogonadotrophic hypogonadism, polycystic ovaries, congenital heart disease, retinitis pigmentosa, and cognitive disability [1]. Haploinsufficiency of a more proximal region, located on 10p13-10p14, designated as DiGeorge critical region 2 (DGCR2) syndrome is associated with congenital heart defects and thymus hypoplasia/aplasia or T cell defect [2]. In addition, a novel microdeletion syndrome involving a small terminal deletion at 10p15.3 was first described by DeScipio et al. in 2012 [3].

Terminal 10p15.3 deletion is a clinically recognizable syndrome consistently associated with neurodevelopmental disorders. It is characterized by variable cognitive impairment or developmental delay, speech delay, and abnormalities in speech development. Additionally, affected individuals may exhibit uncharacterized dysmorphic features [3]. The minimal critical region of the overlap in the deletions identified two genes, ZMYND11 and DIP2C, as candidate genes for 10p15.3 microdeletion syndrome. These genes are proposed to be responsible for the associated developmental delay and language impairment observed in affected individuals [4, 5]. A previous study conducted by Coe et al. [6], which involved a large-scale analysis of copy number variants (CNVs) in neurodevelopmental disorders and dosage-sensitive genes, identified six truncating mutations in ZMYND11 across seven individuals with autosomal dominant intellectual developmental disorder-30 (MRD30). These individuals exhibited speech delay and behavioral abnormalities. Furthermore, ZMYND11 haploinsufficiency was confirmed as a primary contributor to the pathogenesis of 10p15.3 microdeletion syndrome [4, 7].

The aim of the study was to describe the prenatal and postnatal clinical features of two fetuses with pure terminal 10p15.3 microdeletion, encompassing the DIP2C and ZMYND11 genes. Notably, the present study is the first to report an individual with a 10p15.3 microdeletion who exhibited only mild clinical features.

Materials and methods

Subjects

In the present study, two unrelated fetuses with pure chromosome 10p15.3 microdeletion were identified from a total of 5,258 cases undergoing CMA in the Quanzhou region of China between July 2017 and April 2023. Both families reported no consanguinity or history of inherited diseases. Written informed consent was obtained from all families prior to participation. Karyotyping and CMA were performed on the individuals. The study was approved by the Institutional Ethics Committee of Quanzhou Women’s and Children’s Hospital (2020No.31).

Karyotype analysis

Approximately 30 ml amniotic fluid was obtained from each pregnant woman for fetal chromosome karyotype analysis and chromosomal microarray analysis. Of this, 20 ml amniotic fluid was used for karyotype analysis. Cultured amniotic fluid cells and peripheral blood lymphocytes were harvested using a SinochromeChromprepII automatic chromosome harvesting system according to the standard protocol (Shanghai Lechen Biotechnology Co., Ltd.), which was previously described by the present authors [8]. Nomenclature of chromosomal karyotype was conducted according to ISCN 2020 [9].

DNA extraction

Approximately 10 mL of amniotic fluid was obtained via amniocentesis for fetal chromosomal microarray analysis (CMA). Genomic DNA was extracted from peripheral blood using the QIAamp DNA Blood Kit (QIAGEN, Germany) following the manufacturer’s protocol (www.qiagen.com).

Chromosomal microarray analysis

CMA was conducted using the Affymetrix Cytoscan 750 K chip (Life Technologies, American) following the protocol previously described by the present authors [8]. The Genotyping Console and Chromosome Analysis Suite software were utilized for the analysis of single-nucleotide polymorphism and copy number variants (CNVs). The Database of Genomic Variants (DGV) (http://dgv.tcag.ca/dgv), Online Mendelian Inheritance in Man (OMIM) (https://omim.org/), DECIPHER (https://decipher.sanger.ac.uk/) and PubMed (https://www.ncbi.nlm.nih.gov/pubmed/), as well as other databases, were used as reference resources. CNV pathogenicity was interpreted following the American College of Medical Genetics (ACMG) standards and guidelines [10], with classification into five categories: pathogenic, likely pathogenic, variants of unknown significance (VUS), likely benign, and benign.

Results

Subjects information

Proband 1

The proband in Family 1 was a fetus, the first pregnancy for this couple. Both parents were 28 years old and reported no consanguineous marriage. The pregnant woman exhibited normal clinical features, whereas the husband presented with mild language impairment. He measured 165 cm in height (10th percentile) and weighed 63 kg, placing him at the borderline for short stature, but he showed no other significant clinical abnormalities. Unfortunately, detailed information regarding the husband’s developmental milestones was unavailable.

During the pregnancy, a nuchal translucency (NT) screening conducted at 12 weeks of gestation revealed an increased NT measurement of 3.3 mm in the fetus. At 17^+ 2 weeks of gestation, placental thickening was also observed (Fig. 1). Following comprehensive clinical counseling, amniocentesis was performed at 18^+ 2 weeks of gestation.

Fig. 1

Ultrasound findings in the enrolled fetuses with pure 10p15.3 microdeletion. A, B: An increased NT and placental thickening was observed in fetus of family 1. C, D: Prenatal ultrasound examination indicated a scoliosis and asymmetric butterfly vertebrae of the 10th and 12th vertebrae in the fetus of family 2

Proband 2

The proband in Family 2 was also a fetus and the first child of the family. The pregnant woman was 37 years old, and the couple denied consanguinity or any history of inherited family diseases. At 11 weeks of gestation, a normal NT screening result was reported. Subsequent NIPT results indicated a low risk for trisomy 21, 18, and 13 but identified a high risk for chromosome 10 duplication. Amniocentesis was performed at 18^+ 1 weeks of gestation. At 19^+ 1 weeks of gestation, ultrasound examination revealed scoliosis and asymmetric butterfly vertebrae involving the 10th and 12th vertebrae (Fig. 1).

Karyotype analysis results

Conventional chromosome analysis revealed no obvious chromosomal abnormalities in both fetuses. In addition, both parents in each family were found to have normal karyotype results as determined by Giemsa banding analysis.

Chromosomal microarray analysis results

Chromosomal microarray analysis results demonstrated a 556.2-Kb deletion in 10p15.3 region in the fetus of Family 1 (arr[GRCh37] 10p15.3(100,047_656,286)x1), encompassing OMIM genes including DIP2C and ZMYND11 (Table 1; Fig. 2). Parental CMA verification results confirmed that the 10p15.3 microdeletion was inherited from the father, who exhibited abnormal clinical features limited to mild language impairment. According to the ClinGene database, the detected deletion corresponds to chromosome 10p15.3 microdeletion syndrome. Based on the ACMG guidelines, the 10p15.3 microdeletion was classified as pathogenic.

Table 1 Prenatal ultrasound examination and CMA results of the enrolled fetuses with pure 10p15.3 microdeletion

Fig. 2

Chromosomal microarray analysis results of the enrolled fetuses. A, B: Chromosomal microarray analysis results demonstrated a 556.2-Kb deletion in 10p15.3 region in the fetus of family 1 (arr[GRCh37] 10p15.3(100,047_656,286)x1), which encompasses OMIM genes including DIP2C and ZMYND11. C, D: A similar microdeletion was also identified in the fetus of family 2, in 10p15.3 region (arr[GRCh37]10p15.3(100,048_628,967)x1)

In the fetus of Family 2, chromosomal microarray analysis results showed similar microdeletion to fetus 1, with a 528.9 kb deletion in 10p15.3 region (arr[GRCh37]10p15.3(100,048_628,967)x1) (Table 1; Fig. 2). The deletion was classified as a pathogenic CNV according to the ACMG guidelines. However, parental CMA verification was not performed in this family.

Pregnancy outcome follow up results

The pregnant woman in Family 1 chose to terminate the pregnancy following genetic counseling, without undergoing a fetopathological examination. In contrast, the pregnant woman in Family 2 opted to continue her pregnancy. A female infant was delivered via cesarean section at 39 weeks of gestation, with no notable abnormalities at birth. However, at a postnatal follow-up at one year and eight months, the infant exhibited global developmental delay, was unable to stand independently, and could only vocalize “baba” and “mama,” indicating speech delay. Notably, no significant spinal deformities were observed after birth.

Relevant database information of 10p15.3 microdeletion

To better understand the results, the clinical findings and molecular analysis of pure terminal 10p15.3 microdeletion reported in other similar studies were reviewed. The studies are listed in Table 2. As shown, most of the 10p15.3 microdeletions were de novo, with only one case being inherited from an apparently affected mother.

Table 2 Summary of clinical findings in partial reported cases with pure 10p15.3 microdeletion

Discussion

Terminal 10p15.3 deletion represents a novel syndrome associated with neurodevelopmental disorders, including developmental delay and intellectual disability. Pure 10p15.3 microdeletion is an exceptionally rare condition, with fewer than 10 cases reported in the literature to date [3,4,5, 7, 11,12,13,14]. Prenatal diagnosis using CMA is an effective method for identifying rare syndromes such as terminal 10p15.3 microdeletion syndrome. In this study, we present the prenatal and postnatal clinical features of two new cases with pure terminal 10p15.3 microdeletion syndrome identified through CMA. Notably, parental CMA verification revealed that the 10p15.3 microdeletion in Family 1 was inherited from the father, who exhibited mild clinical features restricted to language impairment.

To date, no clinical or prenatal molecular cytogenetic characterization of pure 10p15.3 microdeletion syndrome has been reported in the literature. Furthermore, neurodevelopmental disorder, the primary manifestation of this syndrome, cannot be detected through prenatal ultrasound screening. Wei et al. [15] identified a partial trisomy of 13q21.33-qter and partial monosomy of 10p15.3-pter in a fetus with prenatal ultrasound findings of polydactyly and polyhydramnios. Additionally, in another prenatal diagnosis study [16], a deletion of 10p15.3 and a duplication of 10p15.3p12. were identified in a fetus with obvious facial dysmorphism after delivery. In the present study, for the first time, two fetuses with pure 10p15.3 microdeletion syndrome were reported. Proband 1 exhibited increased nuchal translucency, while Proband 2 presented with T10 and T12 asymmetric butterfly vertebrae and slight scoliosis of the spine. Notably, neither case displayed any characteristic prenatal ultrasonic features specific to the syndrome.

The ZMYND11 and DIP2C genes are frequently implicated in patients with 10p15.3 microdeletion syndrome and are proposed as candidate genes responsible for its clinical manifestations. In addition, the phenotype of patients with ZMYND11 gene deficiency and 10p15.3 microdeletion is extremely similar [7]. Recently, ZMYND11 haploinsufficiency was confirmed as a major cause of 10p15.3 microdeletion syndrome [4, 7]. As is well known, ZMYND11 and DIP2C are expressed in various tissues, including the brain; however, their roles in 10p15.3 microdeletion syndrome remain to be clarified. According to the literature and databases, almost all patients with 10p15.3 microdeletion syndrome exhibit significant developmental delays and intellectual disabilities, which are believed to be associated with ZMYND11 haploinsufficiency. To the present knowledge, only one report described a mother with a 10p15.3 microdeletion who was characterized as a dissocial individual with severe alcohol abuse and minor cognitive disability; she may have passed the microdeletion to her child [11]. A previous study conducted by Oates et al. [17] indicated that reduced penetrance and variable expressivity were observed in patients with ZMYND11 putative pathogenic variants. In addition, a de novo 239 G > A variant in ZMYND11 gene was identified in a patient with autism spectrum disorder without intellectual disability [18]. In the present study, for the first time, a case was reported involving 10p15.3 microdeletion syndrome encompassing the ZMYND11 and DIP2C genes in the father of the proband, who exhibited mild clinical features restricted to language impairment without intellectual disability.

Despite ZMYND11 being indicated as a critical gene for 10p15.3 microdeletion syndrome, the molecular mechanism is still unclear. An increasing number of studies have found that neurodevelopmental disorders caused by epigenetic regulation disorders may be related to microdeletions and monogenic syndromes [19]. The ZMYND11 gene, acting as an unconventional transcriptional co-repressor of highly expressed genes, plays a significant role in epigenetic regulation and may participate in the global transcriptional repression of the genome [4]. A previous study indicated that ZMYND11 can specifically recognize H3 with trimethylated lysine-36 (H3K36me3) on H3.3 (H3.3K36me3) and regulate the extension of RNA polymerase II, which is associated with tumor inhibition [20]. In addition, a study by Oates et al. [17] suggested that the epileptogenic mechanism in patients with ZMYND11 variants may be related to its interaction with histone H3.3. However, the potential role of DIP2C in contributing to neurodevelopmental disorders in patients with 10p15.3 microdeletion syndrome cannot be excluded. DIP2C (disco-interacting protein 2 homolog C) is known to be expressed in all adult and fetal tissues, as well as in specific regions of the adult brain. Interestingly, one proband with a 10p15.3 deletion encompassing the ZMYND11 gene but not DIP2C, and another proband with a 10p15.3 deletion involving DIP2C but not ZMYND11, have been reported. These findings suggest that haploinsufficiency of ZMYND11 and/or DIP2C may contribute to the clinical features of 10p15.3 microdeletion syndrome [3]. In addition, a previous study identified an association between a DIP2C variant and focal infantile epilepsy [21]. Moreover, a recent study reported 23 individuals with heterozygous DIP2C variants, all of whom exhibited developmental delays primarily affecting expressive language and speech articulation. This finding strengthens the association between loss-of-function variants in DIP2C and a neurocognitive phenotype [22]. Therefore, the present authors propose that haploinsufficiency of ZMYND11 and/or DIP2C may underlie the neurodevelopmental disorders observed in patients with 10p15.3 microdeletion syndrome.

Nevertheless, further research is necessary to elucidate the pathogenesis of 10p15.3 microdeletion syndrome and to clarify the role of DIP2C in contributing to specific clinical features. The present study also has limitations, including the unavailability of parental CMA verification in Family 2. Additionally, a more extended postnatal follow-up would provide valuable clinical insights into the rare 10p15.3 microdeletion syndrome.

In conclusion, the present study is the first to describe two fetuses with pure chromosome 10p15.3 microdeletion syndrome in a Chinese population, offering valuable insights into the prenatal diagnosis of 10p15.3 microdeletion syndrome. Additionally, for the first time, the present findings highlight mild clinical features restricted to language impairment, without intellectual disability, in a patient with 10p15.3 microdeletion.