PRDM10 RCC: A Birt-Hogg-Dubé-like Syndrome Associated With Lipoma and Highly Penetrant, Aggressive Renal Tumors Morphologically Resembling Type 2 Papillary Renal Cell Carcinoma

Abstract

Objective: To characterize the clinical manifestations and genetic basis of a familial cancer syndrome in patients with lipomas and Birt-Hogg-Dubé-like clinical manifestations including fibrofolliculomas and trichodiscomas and kidney cancer.

Methods: Genomic analysis of blood and renal tumor DNA was performed. Inheritance pattern, phenotypic manifestations, and clinical and surgical management were documented. Cutaneous, subcutaneous, and renal tumor pathologic features were characterized.

Results: Affected individuals were found to be at risk for a highly penetrant and lethal form of bilateral, multifocal papillary renal cell carcinoma. Whole genome sequencing identified a germline pathogenic variant in PRDM10 (c.2029 T>C, p.Cys677Arg), which cosegregated with disease. PRDM10 loss of heterozygosity was identified in kidney tumors. PRDM10 was predicted to abrogate expression of FLCN, a transcriptional target of PRDM10, which was confirmed by tumor expression of GPNMB, a TFE3/TFEB target and downstream biomarker of FLCN loss. In addition, a sporadic papillary RCC from the TCGA cohort was identified with a somatic PRDM10 mutation.

Conclusion: We identified a germline PRDM10 pathogenic variant in association with a highly penetrant, aggressive form of familial papillary RCC, lipomas, and fibrofolliculomas/trichodiscomas. PRDM10 loss of heterozygosity and elevated GPNMB expression in renal tumors indicate that PRDM10 alteration leads to reduced FLCN expression, driving TFE3-induced tumor formation. These findings suggest that individuals with Birt-Hogg-Dubé-like manifestations and subcutaneous lipomas, but without a germline pathogenic FLCN variant, should be screened for germline PRDM10 variants. Importantly, kidney tumors identified in patients with a pathogenic PRDM10 variant should be managed with surgical resection instead of active surveillance.

Figure 1:. Family 171 pedigree

This family pedigree demonstrates the co-segregation of the p.Cys677Arg variant with clinical features. The presence of clinical features is shown by quadrants representing renal cell carcinoma (red), fibrofolliculoma or trichodiscoma (blue), lipoma (yellow), and presence of lung cysts or spontaneous pneumothorax (green). Two patients each presented with a single, unilateral lung cyst (III:5, III:7) and one patient (II:1) had a history of pneumothorax.

Figure 2:. Imaging, histopathology, and immunohistochemistry of Family 171 renal tumors

Axial imaging of patients from Family 171 showing both primary RCC (patients III:8, III:7, and III:5) and metastatic RCC (III:2) is matched to the histopathology of the excised tumors and immunohistochemistry for TFE3 and GPNMB. Histopathology, TFE3 and GPNMB staining are shown for 4 additional primary tumors for patients III:2, II:4, and II:1. These tumors demonstrate papillary histologies with clear cell and/or eosinophilic features, reminiscent of TFE3 and TFEB kidney cancer. All tumors demonstrated nuclear localization of TFE3, clearly visible by 4x magnification (TFE3 Inset) and positive GPNMB staining. pRCC – papillary renal cell carcinoma

Figure 3:. Tumor growth rate and PRDM10 sequence analysis in patient III:8

A) Patient III:8 had clinical imaging on 4 occasions before the excision of their 2.3 cm left pRCC with clear cell features. Measurements from these four events were used to calculate the overall growth rate for the tumor over the last four and a half years and demonstrated the increased growth rate that occurred in the last few years prior to surgery. B) Post-surgical surveillance imaging, including fluorodeoxyglucose (FDG)-positron emission tomography (PET), demonstrated the rapid development of multiple ipsilateral retroperitoneal metastases less than 10 months after the excision of the 2.3 cm left pRCC with clear cell features. C) Sanger sequencing demonstrates the germline nucleotide variant c.2029 T>C in PRDM10 that results in the p.Cys677Arg substitution in the PRDM10 protein in patient III:8. Tumor DNA analysis demonstrates somatic loss of heterozygosity (LOH) in both the 2.3 cm left pRCC with clear cell features and an example of the retroperitoneal metastases.

Figure 4:. Proposed schematic of PRDM10 loss resulting in FLCN suppression and GPNMB expression

A) In normal cells, PRDM10 transcriptionally activates FLCN expression. The FLCN protein, in the presence of sufficient amino acids, is a GTPase activating protein (GAP) that targets RagC/D and regulates mTORC1 phosphorylation of TFE3 and TFEB resulting in their cytoplasmic sequestration. Alteration of PRDM10 in renal tumors has been shown to result in loss of FLCN expression, mimicking FLCN inactivation as seen in BHD syndrome. Loss of FLCN results in the inability of the mTORC1 complex to phosphorylate TFE3 and TFEB and their subsequent translocation to the nucleus to activate expression of the CLEAR (Coordinated Lysosomal Expression and Regulation) pathway genes. The known CLEAR genes, GPNMB, NPC1, SQSTM1, can be used as specific markers of CLEAR pathway activation. Overexpression of another CLEAR gene, RRAGC, results in increased levels of RagC protein, proposed to hyperactive the mTORC1 complex in BHD tumors resulting in a powerful growth signal via phosphorylation of S6K and 4EBP1. B) Tumor cDNA was available for patients III:2 (red) and III: 8 (crimson) and this was compared to cDNA derived from the adjacent normal kidney tissue from patient III:8 (dark green ) and 4 unrelated normal kidney tissue samples (light green). Dot plots demonstrate statically significant decrease in FLCN expression and increase in RRAGC and GPNMB expression in the tumors. Mann Whitney test, ** < 0.01.