Germline variants in pheochromocytomas, paragangliomas and pituitary adenomas: Expanding the genetic landscape to DNA repair and telomere maintenance genes

Technical Summary: Germline Variants in Pheochromocytomas, Paragangliomas, and Pituitary Adenomas

Problem Statement
Pheochromocytomas and paragangliomas (PPGL) and pituitary adenomas (PA) are neuroendocrine tumors with established hereditary components. While up to 40% of PPGL cases and approximately 5% of PA cases are estimated to have a genetic origin, the current genetic landscape is largely defined by a specific set of neuroendocrine-associated genes (e.g., VHL, SDHx, RET, MEN1, AIP). However, the genetic etiology remains unexplained in a significant portion of patients. Furthermore, the potential contribution of genes involved in DNA repair (e.g., ATM, CHEK2, MUTYH) and telomere maintenance (e.g., TERT, POT1) to the predisposition of these specific endocrine tumors has not been thoroughly investigated. This study addresses the need to expand the genetic screening panel beyond traditional neuroendocrine genes to evaluate the prevalence of pathogenic germline variants in DNA repair and telomere maintenance genes within PPGL and PA cohorts.

Methodology
The study analyzed two independent, non-related cohorts comprising a total of 101 patients:

1. PPGL Cohort: 77 patients (median age 59; 52% female) diagnosed with pheochromocytoma, paraganglioma, or related syndromes (e.g., Reed's syndrome).
2. PA Cohort: 24 patients (median age 44.5; 62.5% female) diagnosed with various pituitary adenoma subtypes, including non-functioning macroadenomas, acromegaly, and prolactinomas.

Genetic Analysis:

• Sequencing: Germline DNA was extracted from peripheral blood and analyzed using Next-Generation Sequencing (NGS) via the Illumina TruSight™ Hereditary Cancer Panel on the MiSeq system.
• Gene Panels:
  • PPGL Cohort: Included standard neuroendocrine genes (FH, MAX, MEN1, RET, SDHA/B/C/D/AF2, TMEM127, VHL) plus DNA repair genes (BRCA1/2, PALB2, MLH1, MSH2/6, MUTYH, ATM, CHEK2) and telomere maintenance genes (ACD, POT1, TERT, TERF2IP).
  • PA Cohort: Included standard PA-associated genes (AIP, CaSR, CDC73, CDKN1B, PRKAR1A, MEN1, RET, SDHx) plus the same DNA repair and telomere maintenance gene sets.
• Variant Classification: Detected variants were manually reviewed using Integrated Genomics Viewer (IGV) and classified according to American College of Medical Genetics and Genomics (ACMG) guidelines, utilizing ClinVar and HGMD databases.

Key Results

• PPGL Cohort Findings:

  • Traditional Genes: 12 patients (21%) harbored pathogenic or likely pathogenic variants in established neuroendocrine genes. SDHB showed the highest prevalence (4 cases), followed by RET (3 cases), SDHD (2 cases), and single cases in SDHA, SDHC, and FH.
  • Expanded Genes: Eight variants of uncertain significance (VUS) or likely pathogenic variants were identified in DNA repair and telomere genes:
    • ATM: 3 VUS variants.
    • MUTYH: 2 likely pathogenic variants (c.1103G>A).
    • TERT: 3 variants (1 likely pathogenic, 2 VUS), including a novel TERT variant (c.164T>C, p.Leu55Pro).
  • No pathogenic variants were found in BRCA1/2, PALB2, MLH1, MSH2/6, CHEK2, ACD, POT1, or TERF2IP.

• PA Cohort Findings:

  • Traditional Genes: Only 2 patients (8.3%) presented VUS in SDHA and MEN1. No pathogenic variants were found in the standard PA gene panel.
  • Expanded Genes: Three variants were detected:
    • ATM: 2 VUS variants.
    • MUTYH: 1 likely pathogenic variant (c.1227_1228dup).
  • No variants were detected in BRCA1/2, PALB2, CHEK2, MLH1, MSH2/6, ACD, TERF2IP, POT1, or TERT.

Significance and Claims
The authors describe this as the first study to suggest a potential association between pathogenic variants in TERT and genetic predisposition to PPGL. Specifically, the novel TERT p.Leu55Pro variant is highlighted as likely pathogenic due to its location in a conserved N-terminal RNA-interacting domain and structural disruption.

Additionally, the study identifies a potential role for the ATM gene in both PPGL and PA endocrine tumors. The frequency of ATM variants in the cohorts (3.8% in PPGL and 8.3% in PA) exceeds the expected population carrier frequency (0.5–1%), suggesting a possible, though currently unproven, link to tumorigenesis in these specific tissues.

Regarding MUTYH, the observed frequency (2.5% in PPGL and 4.1% in PA) aligns with general population allele frequencies, leading the authors to conclude that their data does not support an overrepresentation of MUTYH variants as a specific susceptibility factor for these tumors. Conversely, the study found no evidence to support associations with CHEK2 or the other tested DNA repair/telomere genes (BRCA1/2, PALB2, MLH1, MSH2/6, ACD, POT1, TERF2IP).

Conclusion
The paper concludes that while the prevalence of pathogenic variants in traditional neuroendocrine genes was lower than some literature reports (likely due to the sporadic nature of the cohort), expanding genetic testing to include DNA repair and telomere maintenance genes reveals novel candidate variants. The authors emphasize the importance of reanalyzing negative cases and broadening genetic panels, while acknowledging the descriptive nature of the study and the need for further investigation in larger cohorts to confirm the roles of TERT and ATM.