Kabuki syndrome and rare tumors in a young girl carrying a frameshift KMT2D mutation

INTRODUCTION

Kabuki syndrome (KS, OMIM ID: 147920; http://www.omim.org) is a congenital disorder characterized by atypical facies resembling Japanese traditional Kabuki actors. It is associated with mild-to-moderate cognitive disability, immunodeficiency, seizures, and internal malformations involving the heart, kidneys, eyes, skeleton, and gastrointestinal system.

Two genes are involved in KS: KMT2D (lysine methyltransferase 2D; NM_003482.3; formerly MLL2) at 12q13.12 (KS subtype-1; OMIM ID: 147920) and KDM6A (lysine (K)-specific demethylase 6A; NM_021140.2) at Xp11.3 (X-linked KS subtype-2; OMIM ID: 300867)^[1,2]. Most patients (> 80%) with a clinical diagnosis of KS harbor pathogenic variants in KMT2D, whereas a smaller number (6%-10%) have KDM6A. Other genes in KS-like phenotypes include RAP1A/RAP1B, HNRNPK, and ZMZ1. Other genes associated may exist^[3]. More than 650 genetic variants of the KMT2D gene have been described, including missense deletions, indels, duplications, frameshifts, and splice site variants; most of these variants lead to truncated protein synthesis^[4] [Table 1].

Both genes affect chromatin opening and promote gene expression. Most pathogenic variants in KMT2D and KDM6A are associated with loss-of-function (resulting in haploinsufficiency) or missense variants^[3]. Individuals with pathogenic missense variants of KMT2D involving exons 38 or 39 may have features atypical for KS. Patients may have choanal atresia, hypoplastic or absent nipples, external and internal ear anomalies with hearing loss, brachial sinus abnormalities, interstitial lung disease, hypothyroidism, hypoparathyroidism, variable developmental delay, and dysmorphic features. A possible gain-of-function mechanism has also been hypothesized. KMT2D variants may also be associated with isolated alobar holoprosencephaly^[1,3]. No other phenotypes have been associated with germline pathogenic variants in KDM6A^[1].

The clinical variability of KS may be attributable to differences in genotypes and unknown genetic and epigenetic factors^[3]. Outcomes vary based on systemic involvement. Early recognition of eventual complications is essential to improving outcomes, mainly because the treatments for non-KS and KS patients are identical.

Interestingly, although the concurrence of neoplastic lesions in the context of KS has been limited to isolated and sporadic case reports, reports in the last ten years have allowed the drawing of associations between tumors and KS^[6,7]. Only 18 cases of KS with malignancies have been reported, including cases of Wilms tumor^[8], hepatoblastoma and neuroblastoma, pilomatrixoma^[9], spinal ependymoma^[10,11], Burkitt’s lymphoma^[12], and embryonal rhabdomyosarcoma^[13] [Table 2]. Here, we describe a girl with KS who carries a KMT2D frameshift variant; she developed rare neoplasms in childhood, an insulinoma, liver metastasis, a benign phyllodes tumor of the breast, a pilomatrixoma, and an atypical melanocytic nevus.

CASE REPORT

Our patient is a 13-year-old girl born from a normal, full-term pregnancy from unrelated parents. At around three years old, she was diagnosed with KS due to the delay in psychomotor development, typical facial dysmorphisms, and other typical features, including tetralogy of Fallot, cleft lip and palate, congenital hip dysplasia, epilepsy, and immunodeficiency.

During school age, she presented sporadic focal seizures, which were well controlled by therapy with valproic acid.

During a recurrence of seizures at 13 years, a reduced blood glucose level [35 mg/dL (1.9 mmol/L)] was observed. In the subsequent six months, she was admitted to the hospital because of several episodes of transient confusion,NArrowing of consciousness, sialorrhea, and myoclonic seizures, occasionally prolonged with at least two episodes of status epilepticus requiring anesthesia support. Her adherence to therapy was good.

While hospitalized, an electroencephalogram revealed focal electrical anomalies in the right hemisphere in a poorly modulated tracing with an excess of rapid activity. Cerebral magnetic resonance imaging showed specific anomalies and a supra-vermian arachnoid cyst. Due to recurrent daily seizures, treatment with valproic acid was started with topiramate but was later replaced with perampanel, followed by symptomatic improvement.

Gene sequencing was performed based on the clinical picture. Genetic analysis revealed a heterozygous c.446_449del variant in the KMT2D gene, confirming the diagnosis of KS-1. Continuous glucose monitoring (CGM; Ipro2, Medtronic, Milan, Italy) revealed several prolonged episodes of low blood glucose at night, early morning, and lunchtime. Blood insulin levels during two hypoglycemic episodes on two consecutive days were low (18.5 µU/mL and 20.3 µU/mL). She started diazoxide (10 mg/kg/day divided into three doses per day) but discontinued it due to the lack of benefit and the development of adverse effects (hypotension, tachycardia, and cold sweats). Ultrasound of the abdomen revealed no abnormalities; contrast-enhanced computer tomography revealed a 2.4 × 2.0 cm lesion at the head of the pancreas without local invasion and two small hepatic lesions.

Laboratory data were notable for increased circulating chromogranin A (29 U/L, n.v. 2-18 U/L), normal gastrin (50 pg/mL, n.v 6-108 pg/mL), neuron-specific enolase (NSE; 14.8 ng/mL, n.v. < 16.3 ng/mL), vasoactive intestinal peptide (33 ng/mL, n.v. < 200 ng/mL), and glucagon (30 pg/mL, n.v. 25-250 pg/mL).

The patient underwent pylorus-preserving pancreatoduodenectomy, partial hepatectomy, and microwave ablation of the remaining hepatic lesions. Histological examination of the pancreatic lesion confirmed the presence of a well-differentiated neuroendocrine tumor of intermediate grade, expressing insulin, chromogranin, CD56, and synaptophysin [Figure 1A-D]. One of the two hepatic lesions was a neuroendocrine tumor metastasis (3 mm) with a solid immunoreactivity for chromogranin with mitosis count (seven per ten high-power fields). The remaining metastasis-free liver tissue of the specimen showed some degree of fibrosis, diffuse neogenesis of intrahepatic bile ductules, and diffuse dilation and congestion of the portal veins [Figure 1E and F]. The other hepatic lesion was a ciliated hepatic foregut cyst (CHFC) [Figure 1G]. After surgery, her blood glucose levels returned to the normal range.

Figure 1. (A) Hematoxylin-eosin (H&E) stained section of the pancreatic endocrine neoplasm. Immunostaining revealed a strong expression of insulin; (B) chromogranin (C) and CD56 (D). The section was also strongly positive for Ki-67 and synaptophysin staining (not shown). The morphology indicates a well-differentiated neuroendocrine tumor and a mitotic count of 20 per 10 high-power fields and a Ki-67 index (%) of 20 % indicates a tumor of intermediate-grade (G2). (A, H&E, original magnification × 200; B-D, immunohistochemistry, original magnification × 200); (E) H&E stained section of the metastasis-free liver tissue showing fibrous bands encircling small islets of hepatic tissue; (F) Numerous small bile ducts were scattered in the fibrous tissue well evidenced by cytokeratin 7 immunostaining. We also observed a diffuse, pronounced, dilation and congestion of the portal veins (E, H&E, original magnification ×100; F, immunohistochemistry, original magnification × 100); (G) Liver tissue with a cyst entirely lined with ciliated columnar epithelium, showing pseudo-stratification, surrounded by smooth muscle (G, H&E, original magnification ×400); (H) H&E x25 Leaf-like processes with a moderately cellular stroma phyllodes tumour; (I) H&E x200 cellular spindle cell stroma. No evidence of mitoses or necrosis in low-grade phyllodes tumor.

Two months later, during a physical examination, we perceived two small nodules in the left breast. Ultrasound examination confirmed the presence of two rounded masses of 50 mm and 16 mm (without malignant appearance). Because of the growth pattern over the subsequent 12 months, the nodules were removed. Histological examination showed they were benign phyllodes tumors, a rare fibroepithelial breast tumor at a young age [Figure 1H and I]. Follow-up revealed another neoplasm in the right shoulder, diagnosed as a pilomatrixoma and a junctional melanocytic nevus with cytological atypia, which was completely excised.

At the six-year follow-up, the girl showed no neoplasms and presented reasonable control of epileptic seizures. The Array-CGH was negative, and no other variants associated with predisposition to cancer were detected. However, whole exome sequencing was not performed.

DISCUSSION

The genetic analysis in our patient revealed a heterozygous c.446_449del frameshift variant in the KMT2D gene, predicted to generate the p.(Val149Glyfs*58) protein. Frameshift variants are the most common mechanisms of gene loss-of-function, reported in 36.67% of cases^[14].

The c.446_449del variant of the KMT2D gene has been described only in one previous KS case; however, the precise clinical description is lacking^[5]. Our KS patient is notable because she developed very rare tumors. Insulinoma, phyllodes tumor of the breast, CHFC, and melanocytic nevus with cytological atypia have never been described in patients with KS.

Benign tumors, especially pilomatrixoma, have rarely been described in patients with KS^[9]. Associations between KS and other tumors are uncommon; however, there have been significant reports in the last ten years.

Somatic variants of KMT2D, particularly loss-of-function, have been reported in gastric cancer, lymphoma, and medulloblastoma; somatic variants of KDM6A have recently been described in some malignancies (most commonly in urothelial carcinoma, T-cell acute lymphoblastic leukemia, and breast cancer)^[1]. KMT2D encodes a lysine-specific methyltransferase, responsible for post-translational histone 3 lysine 4 (H3K4) mono-, di- and tri-methylation, which is exclusively associated with actively transcribed genes^[3,6]. KDM6A encodes an X-linked H3K27 demethylase that removes repressive epigenetic marks and interacts with KMT2D in regulating gene expression in the activating signal integrator-2-containing complex^[3]. Defective demethylation dysregulates gene expression with the proliferation of neoplastic cells. However, the significance of germline (i.e., present in all tissues) pathogenic variants in neoplasms of KS patients is yet to be determined^[6,11].

Insulinoma, the most common functioning neoplasm of the endocrine pancreas, is infrequent in childhood (about 30 cases have been reported) and usually affects individuals in their late 50 s and early 60 s. The clinical presentation is characterized by neuroglycopenic symptoms due to severe hypoglycemia, i.e., irrational behavior, somnolence, impaired school performance, and refractory seizures. Hyperinsulinemic hypoglycemia should be considered in cases of unexplained psychiatric and neurologic disorders or worsening neurologic conditions (e.g., increased seizures or seizures becoming refractory to treatment, as in our case). Diazoxide (5-20 mg/kg/day given orally) may reduce the frequency and severity of hypoglycemic events, although tumor resection is the gold standard.

Phyllodes tumors are rare fibroepithelial tumors of the breast, representing only 0.3%-0.9% of all breast tumors and 2%-3% of fibroepithelial neoplasms in adults. The tumor usually occurs in women aged 35-55; only 35 cases have been reported in girls under 20. Phyllodes tumors are often benign but may be borderline and malignant. Although it presents as a well-delimited, rapidly growing, painless, and mobile mass with an overall good outcome, it often recurs^[15], and surgery is the standard treatment^[16].

Congenital hepatic malformations have been rarely described in patients with KS^[17]. Our patient showed the presence of a CHFC and some degree of hepatic fibrosis. CHFCs are rare cystic lesions of embryological origin. Because metaplastic and malignant epithelial lining has been described in CHFC, complete surgical excision is recommended, given the potential for metaplastic or malignant squamous carcinoma^[18]. While CHFC has not been reported in KS, hepatic fibrosis has been described, supporting that hepatic abnormalities may be common in KS^[1]. KMT2D is mutated in hepatocellular carcinoma cases, with earlier disease recurrence, more significant microvascular invasion, and a more aggressive phenotype. Therefore, the potential development of malignant liver cancer must be considered in KS patients^[11].

Pilomatricoma is a cystic follicular lesion that commonly arises on the head and neck in children. This lesion has been linked to various syndromes (Turner, Gardner, RubinsteinTaybi, Sotos, Trisomy 9, myotonic dystrophy, spina bifida, sarcoidosis, and gliomatosis cerebri); however, only three cases of pilomatrixoma associated with KS have been reported^[8]. All three cases had common facial and syndromic features; they were referred to dermatology for lesions described as cutaneous skin-colored papulonodular lesions, which were subsequently diagnosed as pilomatrixoma following biopsy. A somatic variant in CTNNB1 causes the only known mutation confirmed in pilomatrixoma. Predisposition to pilomatrixoma in KS may not be coincidental because CTNNB1 plays a pivotal role in the Wnt pathway, encoding b-catenin, which may recruit KMT2D to regulate Wnt pathway target genes involved in morphogenesis and tumorigenesis^[11]. The case of the junctional melanocytic nevus with cytological atypia is the first described in the literature associated with KS. The only previous association was a Becker nevus.

In our patient, the aCGH was negative; no other searches for cancer susceptibility genes were performed; further investigations will be needed to clarify the relationship between KS variants and neoplastic lesion development.

CONCLUSION

Our case broadens the phenotypic spectrum of KS, especially the neoplasms associated with this syndrome. This case agrees with the most recent literature showing a significant association between KS and tumors, even if the molecular basis of this relationship is not well understood.

A large case series with an accurate description of the neoplastic phenotypes and precise genetic characterization of the patients are needed to clarify the relationship between KMT2D gene variants, KS, susceptibility to neoplastic lesions, and eventual specific tumor phenotypes associated with KS. To date, there are no indications for oncologic screening in KS patients. Studies are needed in this regard. Finally, although a second genetic syndrome in the patient is unlikely, we cannot rule out a tumor predisposition syndrome.