EP159: A TOPBP1 variant associated With BAFopathy methylation pattern

Abstract

DNA Topoisomerase II Binding Protein 1 (TOPBP1) is a topoisomerase involved in maintaining genomic integrity via numerous functions including the regulation of DNA replication and replication stress response. A number of studies have shown that TOPBP1 also interacts with the BAF complex. The BAF complex is a group of ATP-dependent chromatin remodeling enzymes, including 10-12 proteins that regulate the nucleosomal structure by altering histone-DNA interactions. For example, the BRCT motif of TOPBP1 interacts with E2F1, a transcription factor, by recruiting BRG1/BRM, a core member of the BAF complex, to prevent apoptosis. In addition, TOPBP1 directly associates with BRG1(SMARCA4) and BAF250a (ARID1A) in the BAF complex to prevent DNA entanglement during mitosis. While TOPBP1 is not currently associated with a genetic syndrome, the BAF complex proteins with which it interacts are associated with BAFopathies such as Coffin Siris Syndrome (CSS) and Nicolaides-Baraitser Syndrome (NCBRS). For example, the gene encoding BRG1 (SMARCA4) is mutated in 11% of individuals affected by CSS, and the gene encoding BRM (SMARCA2) is mutated in almost all NCBRS patients. The gene encoding BAF250a (ARID1A) is also associated with CSS. We have previously demonstrated overlapping DNA methylation episignatures in individuals with CSS and NCBRS, consistent with a common functional basis of these disorders. A 15-month-old boy, born to first cousin Syrian parents, presented with respiratory distress, recurrent aspiration pneumonia, failure to thrive, seizure disorder, cortical blindness, microcephaly, and severe developmental delay. He was born at term weighing 2.2 kg and started having seizures at 4 months. At 8 months, after his first aspiration pneumonia, he stopped sucking and swallowing. At 15 months, he was very small with weight, length, and head circumference at a 4 to 8 month level. He made few attempts to move spontaneously and had no head control. He did not fix or follow, showed no blinking response to threat, and had disconjugate and roving eye movements. There was no response to sounds. He had a right plagiocephaly, deficiency of the lateral eyebrows, high arched palate, and long ears. No organomegaly was noted. He had significant central hypotonia with head lag. There was spasticity with flexion contractures in the upper extremities. Lower extremities had normal tone with hyperreflexia. He had intermittent spontaneous hip flexion. Family history was positive for a sister who developed seizures at 8 months, had poor vision and developmental delay, and died at 7 years. A brother has mild to moderate intellectual delay with no history of seizures or poor vision. MRI of the head showed severe cerebral atrophy with nonobstructive hydrocephalus ex-vacuo. An echocardiogram showed moderate aortic root dilatation. Metabolic testing was negative. Chromosome microarray was normal. Exome sequencing with trio analysis showed a de novo variant of uncertain significance in a candidate gene, NM_007027.3(TOPBP1):c.2396C>T, p.(Ala799Val). He was also hemizygous for a maternally inherited VUS in MAP7D2 and heterozygous for a paternally inherited VUS in TGFBR3. DNA from peripheral blood was analyzed by EpiSign version 3 which includes an episignature for BAFopathies based on pathogenic variants in ARID1A, ARID1B, SMARCB1, SMARCA4, and SMARCA2. Results showed a methylation pattern which was inconclusive with mild methylation differences overlapping the episignature for CSS and NCBRS. There is an overlap between this patient’s phenotype and the features of CSS and NCBRS. For example, CSS and NCBRS can present with variable degrees of developmental delay, seizures, feeding difficulties, hypotonia, visual deficits, slow growth, and microcephaly. NCBRS can also present with regression or lack of developmental progress, especially at the onset of seizures, and CSS is associated with frequent upper respiratory tract infections. In this patient with a VUS in TOPBP1, the overlap of methylation profile with CSS and NCBRS is intriguing, given the known interaction of TOPBP1 with the BAF complex. We propose that the child’s clinical features and methylation findings may be due to a disruption of the TOPBP1-BAF interaction and that the TOPBP1 variant is actually pathogenic. Since there is currently no known association between TOPBP1 and any genetic syndrome, we suggest that any cases with TOPBP1 variants identified through exome sequencing be assessed for the episignature associated with the BAFopathies.