Looking closely at overgrowth: Constitutional mosaicism in PTEN hamartoma tumor syndrome

Phosphatase and tensin homolog (PTEN) is a tumor suppressor gene on chromosome 10q23.31, and is a member of the PI3K/AKT/mTOR signaling cascade influencing cell growth and survival,¹ metabolic regulation,² and maintenance of genomic integrity.³ Germline variants in the PTEN gene lead to an overgrowth phenotype and a spectrum of cancer predisposition syndromes collectively referred to as PTEN hamartoma tumor syndrome (PHTS).⁴ Phenotypic manifestations of these syndromes include macrocephaly, developmental delay, autism spectrum disorder, hamartomas, vascular malformations, gastrointestinal polyps, and thyroid nodules.⁵ Alterations in PTEN may place individuals at increased risk for developing thyroid cancer (in childhood or adulthood), as well as breast, endometrial, colorectal, kidney, and skin cancer later in life.⁶

PHTS is classically considered an autosomal dominant condition. Here we describe a child with PTEN constitutional mosaicism identified by deep sequencing and a woman with PTEN mosaicism whose pathogenic variant was discovered with close analysis of next generation sequencing (NGS). Table 1 summarizes these cases and seven cases previously reported.

TABLE 1.

Patient characteristics in PTEN mosaicism

PMID	CHOP case 1	UPenn case 2	Gammon et al. 23240978	Pritchard et al. 23619277	Salo-Mullen et al. 24609522	Golas et al. 31062505	Golas et al. 31062505	Goldenberg et al. 31796102	Rofes et al. 35102303
PTEN variant	c.1003C>T, p.R335*	c.697C>T, p.R233*	c.966_967delinsG, p.Asn323Metfs*21	c.767_768del, p.Glu256Valfs*41	Partial deletion (exons 6-9)	10q23.1q23.3 del (6 Mb)	10q23.1q23.3 del (4.4 Mb)	c.970dup, p.(Asp324Glyfs*3)	c.331T>C, p.(Trp111Arg)
Blood VAF	20%	5.6%	<10%	1.7%	~47%	Not reported	<10%	3.5%	22.5%
Tumor VAF	49%	45%	N/A	~50% (dysplastic gangliocytoma)				30% (glioneuronal hamartoma)	N/A *sperm 5.7%
Age at evaluation (years)	3	41	20	40	43	16	15	11	53
Family history		Son with known PHTS	Daughter: CS, thyroid goiter Mother: endometrial cancer Father: melanoma	No	Nephew: macrocephaly, speech delay Aunt: breast cancer	Mother: colorectal polyps Paternal grandfather: colorectal polyps	Paternal grandmother: breast cancer Paternal grandfather: pancreatic cancer Maternal grandmother: thyroid cancer	None	None
Major criteria
Adult lhermitteduclos disease (cerebellar dysplastic gangliocytoma)				x
Macrocephaly (≥97 percentile)	x	x	x	x	x	x	x		x
Macular pigmentation of glans penis							x		x
Multiple mucocutaneous lesions (trichilemmomas (≥3), acral keratoses (≥3), mucocutaneous neuromas (≥3), oral papillomas)				x	x				x
Breast cancer		x			x (DCIS)
Endometrial cancer (epithelial)
Thyroid cancer (follicular)
Gastrointestinal hamartomas				x	x	x	x
Minor criteria
Autism spectrum disorder	x							x
Intellectual disability (IQ ≤75)
Colon cancer
Esophageal glycogenic acanthosis (≥3)
Lipomas	x			x
Fibromas	x				x
Renal cell carcinoma
Testicular lipomatosis
Thyroid structural lesions (e.g., adenoma, goiter)				x			x
Vascular anomalies					x
Other			Hashimoto's thyroiditis		Neuroendocrine pancreatic tumor, later developed metastatic breast cancer	Mild intellectual disability		Central and peripheral nervous system hamartomas
Met clinical criteria for testing	x			x	x	x	x		x

CASE 1

A 3-year-old boy was referred to oncology for lipofibromatosis. A lipofibroma of the right neck was resected at age 15 months. At age 3 he developed a mass on his thigh, which was resected and had similar pathology. Somatic and germline genetic testing was performed. NGS revealed the pathogenic variant PTEN (c.1003C>T, p.Arg335*) with variant allele fraction (VAF) of 20% in the normal specimen and 49% in tumor. His history was also notable for autism and macrocephaly.

CASE 2

A 41-year-old woman with macrocephaly and history of breast cancer was referred for genetic evaluation given PHTS diagnosed in her son with a pathogenic nonsense variant in PTEN (c.697C>T, p.Arg233*). Her genetic testing, including targeted Sanger sequencing of exon 7 of the PTEN gene, was negative.

She first had a NGS hereditary cancer panel sent with a diagnosis of invasive ductal carcinoma at age 38. Two years later she was re-referred to genetics due to oligometastasis. The commercial genetics laboratory reviewed her original NGS and confirmed that the familial PTEN variant was present at a 5.6% allelic frequency in over 2500 reads in the patient's germline testing (reportable cutoff of 10%). Somatic testing of the patient's breast cancer detected the pathogenic PTEN variant at a VAF of 45%.

DISCUSSION

Constitutional mosaicism is caused by postzygotic variant changes during embryonic development; thus, only a fraction of cells in an individual are affected. Reliable detection requires high analytic sensitivity and reporting of variants at low allelic frequency. Even with deep sequencing, reassessing reporting cutoffs may be indicated. PTEN mosaicism has been previously reported in seven patients, four of whom met criteria for testing based on the Tan et al.⁷ guidelines, and two demonstrated full penetrance (Table 1).⁸

These cases highlight the need for clinical judgment and sensitive testing when faced with a high index of suspicion for a PHTS-like phenotype in both the pediatric and adult population. Close attention must be paid to somatic testing results that may suggest underlying mosaicism.

DATA AVAILABILITY STATEMENT

The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.