Craig et al. Mol Cytogenet (2020) 13:40 https://doi.org/10.1186/s13039-020-00506-1 CASE REPORT Open Access Diagnosis of FOXG1 syndrome caused by recurrent balanced chromosomal rearrangements: case study and literature review Connor P. Craig1,2, Emily Calamaro3, Chin‑To Fong3, Anwar M. Iqbal1, Alexander R. Paciorkowski3,4,5,6 and Bin Zhang1,3* Abstract Background: The FOXG1 gene plays a vital role in mammalian brain diferentiation and development. Intra‑ and intergenic mutations resulting in loss of function or altered expression of the FOXG1 gene cause FOXG1 syndrome. The hallmarks of this syndrome are severe developmental delay with absent verbal language, post‑natal growth restric‑ tion, post‑natal microcephaly, and a recognizable movement disorder characterized by chorea and dystonia. Case presentation: Here we describe a case of a 7‑year‑old male patient found to have a de novo balanced translo‑ cation between chromosome 3 at band 3q14.1 and chromosome 14 at band 14q12 via G‑banding chromosome and Fluorescence In Situ Hybridization (FISH) analyses. This rearrangement disrupts the proximity of FOXG1 to a previously described smallest region of deletion overlap (SRO), likely resulting in haploinsufciency. Conclusions: This case adds to the growing body of literature implicating chromosomal structural variants in the manifestation of this disorder and highlights the vital role of cis‑acting regulatory elements in the normal expression of this gene. Finally, we propose a protocol for refex FISH analysis to improve diagnostic efciency for patients with suspected FOXG1 syndrome. Keywords: FOXG1, Haploinsufciency, Postnatal microcephaly, FISH, Enhancer, Chromosomal rearrangement, Diagnosis Introduction brain development, with high levels of expression in the Te Forkhead Box G1 (FOXG1) gene [OMIM: 164874], developing fetal telencephalon [1–4]. Specifcally, it is located on chromosome 14q12, encodes the protein expressed in the rostral forebrain prior to diferentia- forkhead box protein G1 (FOXG1). It belongs to a class tion into the telencephalon and diencephalon, indicating of winged-helix transcriptional regulators and contains its role in early diferentiation between these structures a highly conserved fork head DNA-binding domain. [5]. It exerts its efects via DNA binding-dependent and Tis protein plays an important role in mammalian -independent mechanisms to encourage neocortical pro- genitor proliferation and prevent precocious diferentia- tion [6]. In addition to regulating neocortical progenitor *Correspondence: [email protected] 1 Department of Pathology and Laboratory Medicine, University cell populations, it also plays an important role in con- of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY trolling post-mitotic pyramidal cortical neuron migration 14642, USA and post-migration dorsal–ventral patterning to establish Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. 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Mol Cytogenet (2020) 13:40 Page 2 of 7 normal cortical laminar structure and the corpus callo- the neonatal intensive care unit for poor weight gain and sum [7]. jaundice requiring phototherapy and discharged after Both intra- or inter-genic mutations resulting in altered 8 days. FOXG1 expression or protein function causes FOXG1 At approximately 4 months of age the patient’s par- syndrome. Te syndrome is characterized by post-natal ents noted developmental motor delays with an inabil- growth defciency, postnatal microcephaly, intellectual ity to raise his head, push himself up, and limited overall disability, restricted language development, autism-like movement as well as microcephaly. An initial work-up social defcits, stereotypies and dyskinesias, epilepsy, at the time was notable for: metabolic screening showed poor sleep, irritability, excessive crying episodes, recur- non-specifc elevations in glutamate and mild abnor- rent aspiration, and gastroesophageal refux [8]. Charac- malities in excretion of 4-hydroxyphenylacetate, mildly teristic fndings on imaging include: frontal predominant elevated NH3, and elevated lactate at two to three times simplifed gyral patterning, reduced white matter vol- the upper reference limit. Magnetic resonance imag- ume, and callosal hypogenesis [8]. Te course of epilepsy ing (MRI, unavailable for review) was reportedly unre- in patients with FOXG1 syndrome varies based on the markable. Cytogenetic studies showed a balanced (3;14) underlying genetic mutation. Tose with deletions and translocation. intragenic mutations tend to have a wide variety of sei- Te patient had no speech development at 1 year zure types, ranging from complex partial to generalized of age. Seizures began at 18 months and were charac- tonic–clonic, while those with duplications frequently terized by staring episodes which would progress to exhibit infantile spasms [9]. Clinically, the developmental full-body limpness, stifening, followed by jerking move- encephalopathy index (DEI) has proven useful in delin- ments. Te patient had fve seizures prior to control with eating MECP2 and FOXG1 syndrome, showing that those levetiracetam. with FOXG1 syndrome had greater impairment overall, At 3 years of age the patient’s mother moved with with signifcantly worse function in the domains of fne him to the United States where evaluation showed a motor skills, receptive language, reciprocity and ability to severely underweight child (12.08 kg; 5th percentile; SD walk [10]. − 1.61) with microcephaly (head circumference 42.9 cm; Diferent mutation mechanisms, including intragenic SD − 4.0), congenital esotropia, reduced muscle bulk, point or indel (insertions and deletions) mutations, decreased axial and increased appendicular tone with microdeletions, or balanced chromosomal rearrange- antigravity strength throughout. Te patient remained ments can lead to FOXG1 haploinsufciency resulting non-verbal but exhibited social smiling, and the ability in FOXG1 syndrome. Tis makes efcient genetic diag- to track objects. Te patient had poor weight gain due nosis of the disease quite challenging [11–14]. Here we to severe oropharyngeal dysphagia with silent aspira- report a case of FOXG1 syndrome in a 7-year-old Puerto tion on pharyngogram, eventually necessitating G-tube Rican male patient found to have a de novo balanced placement. chromosomal rearrangement with the breakpoint in an EEG performed at 4 years of age showed a disordered intergenic region between FOXG1 and a nearby smallest background with slower than expected posterior domi- critical enhancer region (SRO). Tis report shows that nant rhythm consistent with a mild difuse encephalopa- chromosomal rearrangements disrupting a distant regu- thy. Tere were no focal or epileptiform changes noted. latory enhancer of FOXG1 is a recurrent event, and that a At present the patient continues to have severe global follow-up FISH analysis is important to reach a defnitive developmental delay, with no speech development, but genetic diagnosis for patients with balanced rearrange- he attempts to make sounds. He is able to roll over and ments involving 14q11-q13 with FOXG1 syndrome in the grab onto objects. He continues to exhibit upper and diferential diagnosis. lower extremity spasticity with grossly ataxic move- ments, and excessive purposeless arm movements. His Clinical report seizures continue to be well-controlled. He has recently Te patient is a 7-year-old male born in Puerto Rico at displayed episodes of inappropriate laughing and crying. 33-week gestation to an 18-year-old gravida 1 para 0 female of Puerto Rican descent. No prenatal complica- Methods tions or exposures are reported in the available medi- G‑banding chromosome and FISH analysis cal record. Birth weight was 1871 g (35th percentile; Peripheral blood samples were cultured using standard standard deviations (SD) − 0.38) and length was 48 cm cytogenetic methods for 72 h with phytohemaggluti- (93rd percentile; SD 1.82). Head circumference at birth nin (PHA) stimulation. Chromosomes were analyzed by is not available in the medical record. Newborn screen- G-banding using trypsin digestion and Wright’s staining ing was reportedly normal. Te patient was admitted to (GTW). Twenty metaphase spreads were analyzed. Te Craig et al. Mol Cytogenet (2020) 13:40 Page 3 of 7 karyotypes were described according to An International labeled with dyes Cyanine-5dUTP and Cyanine-3dUTP, System for Human Cytogenetic Nomenclature (ISCN respectively,