Summary
This study profiles ARID1B haploinsufficiency in six patients presenting with a spectrum of clinical features such as intellectual disability, distinct facial dysmorphism, plantar fat pads, and speech impairments. Heterozygous deletions, including a ~1.2 Mb deletion at 6q25.3 (encompassing ARID1B), and frameshift as well as nonsense mutations like NM_020732.3(ARID1B):c.3208_3209delAA and NM_020732.3(ARID1B):c.2941C>T were identified across patients, often originating de novo. Inheritance was tested and confirmed de novo status in five instances; however, inheritance information was not available for the initial patient discussed. Functional analyses supported haploinsufficiency as a significant disease mechanism, demonstrating reduced cell cycle re-entry in patient-derived fibroblasts upon serum starvation, significantly reduced ARID1B transcription levels, and perturbed cell cycle regulation. Collectively, these results underscore the critical role of ARID1B function in neurodevelopmental disorders and affirm the genetic evidence for ARID1B haploinsufficiency in pathogenesis.
Evidence of Haploinsufficiency
Patient Identifier: the patient
Mutation Type: heterozygous deletion
Mutation Details: a heterozygous deletion at 6q25.3 including ARID1B
Clinical Phenotype: intellectual disability, plantar fat pads, facial dysmorphism
Inheritance Tested: No
Effect on Gene Function: ARID1B haploinsufficiency
Direct Quote: "High density microarray analysis of the patient demonstrated a heterozygous deletion at 6q25.3, which resulted in the loss of four genes including ARID1B. Subsequent quantitative real-time PCR analysis revealed ARID1B haploinsufficiency in the patient."
Location in Paper: Methods/results
Patient Identifier: patient 1
Mutation Type: heterozygous deletion
Mutation Details: a heterozygous deletion of ~1.2 Mb at 6q25.3 resulting in single allele loss of ARID1B
Clinical Phenotype: moderate intellectual disability, absent speech, dysmorphic features, fetal finger and toe pads, plantar lipomas
Inheritance Tested: Yes
Effect on Gene Function: significant reduction in ARID1B transcription level
Direct Quote: "a heterozyous deletion of ~1.2 Mb was identified on 6q25.3 that resulted in single allele loss of ARID1B. Real-time PCR analysis revealed that the transcription level of ARID1B in patient 1 was significantly reduced."
Location in Paper: Results; ARID1B haploinsufficiency in patient 1
Patient Identifier: Patient 2
Mutation Type: frameshift
Mutation Details: NM_020732.3(ARID1B):c.3208_3209delAA (p.(Lys1070Alafs*47))
Clinical Phenotype: Intellectual disability, absent speech, facial dysmorphism, plantar fat pads, fetal finger/toe pads
Inheritance Tested: Yes
Effect on Gene Function: predicts a loss of function
Direct Quote: "Direct sequencing of genomic DNA revealed that three additional patients encoded de novo single allelic ARID1B mutations; NM_020732.3(ARID1B):c.3208_3209delAA in patient 2 predicts a loss of function."
Location in Paper: Results
Patient Identifier: patient 3
Mutation Type: frameshift
Mutation Details: NM_020732.3(ARID1B):c.2306_2308delCCGinsTCCGCAGCCACTCC (p.(Pro769Leufs*17))
Clinical Phenotype: phenotype consistent with Pierpont syndrome
Inheritance Tested: Yes
Effect on Gene Function: Predicted to be truncating
Direct Quote: "Direct sequencing of genomic DNA revealed that patient 3 encoded a de novo single allelic ARID1B frameshift mutation predicted to be truncating."
Location in Paper: Text before Table 1
Patient Identifier: patient 4
Mutation Type: frameshift
Mutation Details: NM_020732.3(ARID1B):c.4273dupT (p.(Tyr1425Leufs*34))
Clinical Phenotype: intellectual disability, speech impairment, facial dysmorphism, plantar fat pads, fetal finger/toe pads
Inheritance Tested: Yes
Effect on Gene Function: predicts a loss of function
Direct Quote: "Direct sequencing of genomic DNA revealed that patient 4 encoded a de novo single allelic ARID1B frameshift mutation predicted to be truncating."
Location in Paper: Figure 4
Patient Identifier: patient 5
Mutation Type: nonsense
Mutation Details: NM_020732.3(ARID1B):c.2941C > T (p.(Gln981*))
Clinical Phenotype: phenotype consistent with Pierpont syndrome
Inheritance Tested: Yes
Effect on Gene Function: predicts a loss of function
Direct Quote: "Whole exome sequencing of patient 5 identified a de novo heterozygous ARID1B nonsense mutation predicted to be truncating."
Location in Paper: Text before Table 1
Clinical Features
Feature: intellectual disability
Frequency: Commonly observed in all patients described
Direct Quote: "ARID1B mutations have been identified as the predominant cause of Coffin-Siris syndrome and have also been shown to be a frequent cause of nonsyndromic intellectual disability."
Location in Paper: AbstractBackground
Feature: plantar fat pads
Frequency: Observed in the patient and is part of the distinctive phenotype in four additional patients
Direct Quote: "Here, we investigate the molecular basis of a patient with an overlapping but distinctive phenotype of intellectual disability, plantar fat pads and facial dysmorphism."
Location in Paper: AbstractBackground
Feature: facial dysmorphism
Frequency: Observed in multiple patients
Direct Quote: "Facial dysmorphism is a common feature in patients with ARID1B haploinsufficiency."
Location in Paper: AbstractBackground
Feature: absent speech
Frequency: Observed in the five patients described
Direct Quote: "absent speech"
Location in Paper: Introduction
Feature: dysmorphic features with narrow palpebral fissures, long eyelashes, a thin upper lip and full lower lip
Frequency: Observed in the five patients described
Direct Quote: "Dysmorphic features with narrow palpebral fissures, long eyelashes, a thin upper lip and full lower lip"
Location in Paper: Introduction
Feature: fetal finger and toe pads
Frequency: Observed in the five patients described
Direct Quote: "Fetal finger and toe pads"
Location in Paper: Results
Feature: speech impairment
Frequency: Present in our cohort
Direct Quote: "The phenotypes associated with ARID1B haploinsufficiency are variable but common features of the syndromic and nonsyndromic cases include intellectual disability and speech impairment."
Location in Paper: Discussion
Functional Studies
Study Type: cell cycle analysis
Methodology: Patient-derived and ARID1B knockdown fibroblasts were analyzed after serum starvation to assess cell cycle re-entry
Conclusions: Alterations in cell cycle contribute to the underlying pathogenesis of syndromes associated with ARID1B haploinsufficiency.
Direct Quote: "Analysis of both patient-derived and ARID1B knockdown fibroblasts after serum starvation demonstrated delayed cell cycle re-entry associated with reduced cell number in the S1 phase."
Location in Paper: Methods/results
Study Type: transcription level analysis
Methodology: Real-time PCR analysis was used to measure ARID1B transcription level in patient-derived primary fibroblasts
Conclusions: Significant reduction in ARID1B transcription level confirms the deletion's effect on gene function.
Direct Quote: "Real-time PCR analysis revealed that the transcription level of ARID1B in patient 1 was significantly reduced."
Location in Paper: ARID1B haploinsufficiency in patient 1
Study Type: Real Time Quantitative PCR analysis
Methodology: Quantitative PCR was used to compare ARID1B expression levels between patients and control fibroblasts.
Conclusions: Reduced ARID1B expression is associated with perturbed cell cycle regulation.
Direct Quote: "Collectively these observations suggested that reduced ARID1B was associated with perturbed cell cycle regulation."
Location in Paper: Results
Study Type: Mutation analysis
Methodology: Direct sequencing, whole exome sequencing, and Sanger sequencing were utilized to identify mutations in patients.
Conclusions: Patients possess de novo mutations consistent with haploinsufficiency of the ARID1B gene.
Direct Quote: "Direct sequencing of genomic DNA revealed that patients encoded de novo single allelic ARID1B mutations."
Location in Paper: Text before Table 1
Study Type: Animal model study
Methodology: Observations from homozygous knockout of arid1b in mouse embryonic stem (ES) cells.
Conclusions: ARID1B knockout in mice is embryonic lethal, highlighting the gene's critical role in development.
Direct Quote: "Homozygous knockout of arid1b in mouse is embryonic lethal but the ES cells demonstrated a reduced proliferation rate and perturbation of differentiation and cell cycle."
Location in Paper: Discussion