Birt-Hogg-Dubé renal tumors are genetically distinct from other renal neoplasias and are associated with up-regulation of mitochondrial gene expression
- Jeff A Klomp1,
- David Petillo2,
- Natalie M Niemi3,
- Karl J Dykema1,
- Jindong Chen2,
- Ximing J Yang4,
- Annika Sääf5,
- Peter Zickert6,
- Markus Aly7,
- Ulf Bergerheim8,
- Magnus Nordenskjöld5,
- Sophie Gad9,
- Sophie Giraud10, 11,
- Yves Denoux12,
- Laurent Yonneau13,
- Arnaud Méjean11, 14,
- Viorel Vasiliu11, 15,
- Stéphane Richard9,
- Jeffrey P MacKeigan3,
- Bin T Teh2, 16 and
- Kyle A Furge1, 2Email author
© Klomp et al; licensee BioMed Central Ltd. 2010
Received: 20 May 2010
Accepted: 16 December 2010
Published: 16 December 2010
Germline mutations in the folliculin (FLCN) gene are associated with the development of Birt-Hogg-Dubé syndrome (BHDS), a disease characterized by papular skin lesions, a high occurrence of spontaneous pneumothorax, and the development of renal neoplasias. The majority of renal tumors that arise in BHDS-affected individuals are histologically similar to sporadic chromophobe renal cell carcinoma (RCC) and sporadic renal oncocytoma. However, most sporadic tumors lack FLCN mutations and the extent to which the BHDS-derived renal tumors share genetic defects associated with the sporadic tumors has not been well studied.
BHDS individuals were identified symptomatically and FLCN mutations were confirmed by DNA sequencing. Comparative gene expression profiling analyses were carried out on renal tumors isolated from individuals afflicted with BHDS and a panel of sporadic renal tumors of different subtypes using discriminate and clustering approaches. qRT-PCR was used to confirm selected results of the gene expression analyses. We further analyzed differentially expressed genes using gene set enrichment analysis and pathway analysis approaches. Pathway analysis results were confirmed by generation of independent pathway signatures and application to additional datasets.
Renal tumors isolated from individuals with BHDS showed distinct gene expression and cytogenetic characteristics from sporadic renal oncocytoma and chromophobe RCC. The most prominent molecular feature of BHDS-derived kidney tumors was high expression of mitochondria-and oxidative phosphorylation (OXPHOS)-associated genes. This mitochondria expression phenotype was associated with deregulation of the PGC-1α-TFAM signaling axis. Loss of FLCN expression across various tumor types is also associated with increased nuclear mitochondrial gene expression.
Our results support a genetic distinction between BHDS-associated tumors and other renal neoplasias. In addition, deregulation of the PGC-1α-TFAM signaling axis is most pronounced in renal tumors that harbor FLCN mutations and in tumors from other organs that have relatively low expression of FLCN. These results are consistent with the recently discovered interaction between FLCN and AMPK and support a model in which FLCN is a regulator of mitochondrial function.
Renal cell carcinomas (RCC) represent the most common type of tumors that arise within the adult kidney. They can be divided into several subtypes - clear cell, papillary, chromophobe, and collecting duct - based on differences in cellular morphology, gene expression, and cytogenetic and genetic abnormalities that are found within the tumor cells [1–4]. The two most common types of RCC are clear cell and papillary, which together account for approximately 85-90% of RCCs. Chromophobe RCC accounts for an additional 5% of renal tumors, and a histologically similar subtype, renal oncocytoma, represents another 5% (see [5, 6] for recent reviews). Although the neoplastic cells of chromophobe RCC and renal oncocytoma share morphological features, renal oncocytomas are generally asymptomatic and nearly always present as localized lesions with low metastatic potential .
Though most renal tumors occur sporadically (~95%), several hereditary syndromes are associated with a high risk of renal tumor development. These syndromes include von Hippel-Lindau disease, hereditary papillary RCC, hereditary leiomyomatosis and renal cancer, and Birt-Hogg-Dubé syndrome (BHDS) . In von Hippel-Lindau disease, a rare germline mutation in the VHL gene is associated with development of the disease (reviewed in ). Individuals with von Hippel-Lindau disease are predisposed to the development of renal tumors of the clear cell histology. In addition, somatic mutations in the VHL gene are also found in the majority of the sporadic cases of clear cell RCC . Birt-Hogg-Dubé syndrome is an extremely rare syndrome-approximately 200 families have been described as having BHDS worldwide [11, 12]. Germline inheritance of a mutated allele of the folliculin (FLCN) gene, located at chromosome location 17p11.2, is strongly associated with individuals that develop BHDS . In individuals afflicted with BHDS, the majority (~85%) of renal tumors that develop are histologically similar to chromophobe RCC or described as oncocytic hybrid tumors, with portions appearing as both renal oncocytoma and chromophobe RCC [14, 15]. Unlike VHL, somatic mutations in the FLCN gene are not strongly associated with the development of sporadic renal oncocytoma and chromophobe RCC [16, 17]. As such, the role that FLCN plays in the development of sporadic renal oncocytoma, chromophobe RCC, and other sporadic tumors remains unclear.
The folliculin gene encodes a highly conserved, 64kD protein with no known functional domains. Recent reports support its role as a tumor suppressor [18, 19] and in energy-related signaling, involving the mTOR and AMPK pathways [20–22]. FLCN has been shown to interact with AMPK through the binding of two intermediary proteins, folliculin interacting protein 1 and folliculin interacting protein 2 (FNIP1/2) and the activity of FLCN may be altered by its subsequent phosphorylation by AMPK or localization to the cytoplasm with its binding partners, or a combination of these two mechanism [20, 23, 24]. As indicated previously, while germline mutations in FLCN cause BHDS, these mutations are not strongly associated with either sporadic chromophobe RCC or renal oncocytoma . The most well characterized somatic mutations found in these two sporadic tumor subtypes are mutations within the mitochondrial genome [25–29]. Renal oncocytoma, in particular, is characterized by the accumulation of somatic mutations in mtDNA that inactivate subunits of mitochondrial complex I and other members of the electron transport chain, severely limiting ATP production[26, 27]. In addition, both sporadic renal oncocytoma and chromophobe RCC possess mitochondria-dense cytoplasm and aberrant expression of genes associated with oxidative phosphorylation (OXPHOS) [25, 27, 30]. However, the mechanism by which these mitochondrial defects contribute to tumor development remains unclear and the gene expression and cellular phenotypes observed are thought to represent feedback mechanisms to compensate for mitochondrial impairment.
While expression of some key markers of renal tumors have been examined in a single BHDS-derived tumor , we conducted gene expression profiling of multiple renal tumors that arose in individuals with BHDS along with sporadic renal oncocytoma and chromophobe RCC to develop a better understanding of the underlying molecular genetics of these tumors. We found that tumors that arose in individuals with BHDS were genetically distinct from sporadic tumors, showing distinct gene expression and cytogenetic characteristics. However, similar to sporadic renal oncocytoma and chromophobe RCC, BHDS-derived renal tumors displayed high expression of mitochondria and OXPHOS-associated genes. Indeed, the expression of mitochondria and OXPHOS-associated genes was even more pronounced in the BHDS-derived tumors than the other sporadic tumors and was correlated to increased expression of key mitochondria transcriptional regulators. We have also noted an inverse correlation between FLCN expression and mitochondria- and OXPHOS-associated genes across a variety of tumor types, most evident in tumors that possessed relatively low levels of FLCN and enrichment in mitochondria- and OXPHOS-associated gene expression. Taken together, our data suggest that FLCN has an important role in the regulation of genes associated with mitochondria and OXPHOS in BHDS-derived tumors and possibly others.
Tissue sample collection and DNA sequencing
Internal review board approval was obtained from each participating institution for the renal neoplasms under study. Samples isolated from individuals afflicted with BHDS were flash-frozen in liquid nitrogen and stored at -80°C following excision from patients as previously described . FLCN mutation status was confirmed through DNA extraction from tumor samples and sequencing, as described previously , using primer sequences from Nickerson et al. . The histological classification and FLCN mutation information for the BHDS-derived renal tumor samples are given in Additional file 1 Table S1.
Gene expression profiling datasets
RNA was isolated and expression profiles generated from BHDS-derived tumor samples using the Affymetrix HG-U133 Plus 2.0™chipset as previously described . These data are available at the Gene Expression Omnibus (GEO, GSE21816). Expression profiles for the remaining RCC subtypes and non-RCC tumors used in the analysis are publicly available from the GEO database (GSE8271, GSE11024, GSE11016, GSE7023, and GSE2109). All data analysis was performed using software available from the BioConductor Project (version 2.5) and the R statistical environment v. 2.10.1 [34, 35]. Prior to analysis, the robust multi-chip average (RMA), as implemented in the Affy package (1.24.2), was used for background correction and normalization of raw expression image intensities using updated probeset mapping  and data were normalized to corresponding normal tissue type. The technical replicate expression datasets from the DT017 sample of patient BHD1 were averaged prior to discriminate gene and gene set analyses.
Validation of gene expression microarray data by qRT-PCR
Single-step, quantitative reverse transcription-PCR (qRT-PCR) was performed to validate expression levels for the following genes: PVALB, CDH19, RGS20, and LRRTM4, with the GAPDH gene as a control. To perform the single-step qRT-PCR, we used the Power SYBR® Green PCR Master Mix with Taqman® Gold RT-PCR enzymes (Applied Biosystems, Foster City, CA). We also conducted qRT-PCR using Taqman® assays (Applied Biosystems) using the manufacturer's protocol for the following genes: FLCN, FNIP2, PPARGC1A, PVALB, RGS20, TFAM, and TSC1. The reactions were run on an ABI 7500 Fast Real-Time PCR system using a dissociation curve analysis for the SYBR Green assays to confirm primer specificity. We used the PerlPrimer software  to design PCR primers within the exons that were interrogated by the Affymetrix expression chips. Primer sequences and assay ids have been made available in Additional file 1 Table S4.
Clustering and differential gene expression
Prior to clustering of all RCC samples, the 1000 most variable genes were isolated using an interquartile range filter of greater than 1.54. Clustering was performed using Euclidean distance with complete linkage. For the clustering of sporadic chromophobe RCC, sporadic oncocytoma, and BHDS-derived renal tumor samples, the 1500 most variable genes were isolated, corresponding to an interquartile range filter of greater than 0.79. Euclidean distance with average linkage was used, followed by resampling for node support. Bootstrap resampling for 10,000 replications and a relative sample size of 1 was used to generate the bootstrap probability values, as implemented in the pvclust package v.1.2-1 .
Discriminatory genes were identified using a moderated t-statistic as implemented in the limma package. Significance values were adjusted to correct for multiple testing using the Benjamini and Hochberg method . Genes with false discovery rate (FDR) values less than 0.01 were reported as significant. Given that the sample size of BHDS-derived tumors was disproportionate to the number of either sporadic oncocytoma or chromophobe RCC tumors, we conducted a permutation test to decide whether the distinctiveness of BHDS-derived tumors was a result of bias from a sample size effect. The test was conducted using 1000 iterations comparing the entire data set from the six BHDS-derived tumors to five randomly selected oncocytoma data sets (without replacement). The number of significantly differentially expressed genes from this BHD-oncocytoma comparison was greater than the number derived from a similar discriminate analysis of five randomly selected oncocytoma data sets with the remaining six oncocytoma data sets in all of 1000 permutations. Likewise, a similar permutation test using the six BHD and six randomly selected chromophobe RCC datasets was found to contain a greater number of differentially expressed genes than a comparison of six randomly chosen chromophobe with the remaining six chromophobe datasets in all of 1000 permutations.
Gene set enrichment analyses
Parametric gene set enrichment was used to identify chromosomal expression abnormalities using gene sets corresponding to chromosomal arms as implemented in the reb package . For pathway analysis 1892 gene sets were obtained from the Molecular Signatures Database v2.5 (MsigDB, http://www.broadinstitute.org/gsea/msigdb/). These gene sets were curated from multiple sources including online pathway databases, biomedical literature, and mammalian microarray studies. Parametric gene set enrichment analysis method as implemented in the PGSEA package was used generate enrichment scores for each pathway within each tumor sample using corresponding non-diseased kidney tissue as a reference. A moderated t-statistic as implemented in the limma package  was used to identify gene set enrichment scores that could discriminate between subtypes. In order to visualize the fraction of genes that overlapped between deregulated gene sets, we calculated pair-wise dissimilarity (D) scores using the formula: , where N A∩B is the number of genes in common between gene sets A and B and N A and N B are the numbers of genes making up gene sets A and B. The dissimilarity score was used to compute a hierarchical clustering dendrogram using Euclidean distance with average linkage.
PGC-1α signature generation
We produced a gene overexpression signature of PGC-1α using gene expression data obtained from the comparison of PGC-1α transfected HepG2 cells to mock transfected cells (GSE5968). A moderated t-statistic was used to identify genes with expression differences that were both significant (FDR < 0.00001) and had a greater than two-fold change in expression (N = 374).
BHDS tumors have distinct gene expression patterns
In the initial gene expression analysis the BHDS-derived tumors formed a distinct branch in the clustering diagram (Figures 1A, B). These gene expression differences were not due to a sample batch effect since these renal tumors were collected at multiple institutions and the gene expression profiles were generated at various times between 2004 through 2009 using multiple chip lots (Additional file 1, Table S1 and data not shown). A more focused examination of the DCT-derived tumors confirmed those from patients with BHDS possess distinct expression characteristics with strong node support as inferred by gene resampling (Figure 1B). Several genes were differentially expressed between BHDS-derived tumors and renal oncocytoma (n = 401) and BHDS-derived tumors and chromophobe RCC (n = 2922; FDR < 0.01; Additional file 1, Table S2). For comparison, we found 1050 differentially expressed genes between sporadic oncocytoma and chromophobe RCC. Moreover, we saw few, if any, gene differences when we performed resampling with the discriminate analysis within either the sporadic renal oncocytoma or sporadic chromophobe samples, indicating the high numbers of differentially expressed genes between tumor subtypes were not due to differences in sample size between the tumor subtypes (p < 0.001, see Methods). The molecular distinction between BHDS-derived tumors, sporadic renal oncocytoma, and sporadic chromophobe RCC is in contrast to the similarities of VHL disease-associated tumors with sporadic clear cell RCC. In those studies, no significant differences in gene expression were identified between the two entities . Together, the gene expression analyses indicate that distinctions exist between BHDS-derived renal tumors and other RCC subtypes similar in magnitude to those between the other recognized subtypes of RCC, such as oncocytoma and chromophobe RCC. Notable genes that are more highly expressed in BHDS-derived tumors when compared to sporadic renal oncocytoma and chromophobe RCC include CDH19, RSG20, DAPL1, LRRTM4, and HHATL (Figure 1EAdditional file 2, Figure S2, and Additional file 1, Table S2). We validated the expression levels of PVALB and three of the most significantly over-expressed genes, CDH19 (cadherin 19, type 2), RGS20 (regulator of G-protein signaling 20), and LRRTM4 (leucine rich repeat transmembrane neuronal 4) using qRT-PCR (Figure 1DAdditional file 2, Figures S1B-C, and data not shown). We chose to validate these particular genes for their consistently high expression in BHD-derived tumor samples, their low expression in the other RCC subtypes examined.
BHDS-derived tumors lack evidence of cytogenetic features present in sporadic oncocytoma and chromophobe RCC tumors
A mitochondrial gene expression phenotype is a prominent feature of BHDS-derived tumors
An expression phenotype involving the PGC-1α-TFAM signaling axis is unique to BHDS-derived tumors
We also examined transcription levels of genes associated with AMPK signaling, as this was a likely candidate for signaling based on our observation of mitochondrial gene set enrichment and the recently discovered indirect interaction between FLCN and AMPK. AMPK is a key molecule for energy sensing and a regulator of the PGC-1α transcription factor, a potent inducer of mitochondrial biogenesis (Figure 4A). We noted that two transcription factors, PGC-1α and TFAM (transcription factor A, mitochondrial), were also up-regulated in the BHDS-derived tumors (Figure 4E and Additional file 2, Figure S1G). Both transcription of mitochondrial genes and replication of the mitochondrial genome depend on TFAM function and the TFAM gene is uniquely over-expressed in the BHDS-derived tumors (for a review of transcriptional regulators of mitochondria, see [56–58]). PGC-1α (PPARGC1A) was also highly expressed in the BHDS-derived tumors as measured by gene expression profiling. However, the levels of PGC-1α as measured by qRT-PCR in BHDS tumors were sensitive to the probe/primer sets used, suggesting that BHDS tumors may have a difference in the abundance of a particular PGC-1α isoform (Additional file 2, Figure S1G). The PGC-1α binding partner, nuclear receptor peroxisome proliferator-activated receptor gamma (PPARG) was highly expressed in BHDS-derived tumors as compared to non-diseased tissue, sporadic oncocytoma, and chromophobe RCC (Additional file 2, Figure S1F) while the peroxisome proliferator-activated receptor alpha (PPARA) was higher in BHDS-derived tumors versus sporadic oncocytoma and chromophobe (data not shown). Moreover, we found a set of PGC-1α regulated genes, entitled "PGC," was highly up-regulated in BHDS-derived samples (Figure 3D). To confirm this "PGC" gene set from MsigDB was representative of PGC-1α activation, we generated an independent gene expression signature from HepG2 cells that were adenovirally infected with PGC-1α versus control (Figure 4C, performed by Gaillard et al.) . Although there was only 11.8 percent similarity between these two independently generated PGC-1α gene sets, both gene sets were significantly up-regulated in BHDS-derived patient tumors (Figure 4D). We did not see expression changes associated with genes encoding the mitochondria-associated transcription factors NRF-1 and NRF-2. Taken together, these results indicate that deregulation of FLCN function by point mutation is associated with FNIP2 deregulation and perturbation of the PGC-1α-TFAM signaling axis.
FLCN expression inversely correlates with PGC-1αactivation
To establish the molecular characteristics of tumors that arise in individuals afflicted with BHDS, we compared gene expression data from renal tumors of BHDS patients with expression data from sporadic renal tumors. Although previous gene expression profiling studies indicated that renal tumors isolated from individuals afflicted with von Hippel-Lindau disease are indistinguishable from sporadic clear cell RCC, we show that kidney tumors from patients with BHDS also have unique genetic and cytogenetic characteristics from sporadic renal oncocytoma and chromophobe RCC. In particular, cytogenetic defects that are typical of sporadic oncocytoma and chromophobe RCC, including defects of chromosome 19, loss of chromosome 1, and translocations involving chromosome 11, were largely absent from BHDS-derived tumors. Interestingly, we did not find differences in FLCN expression by either our gene expression arrays nor by qRT-PCR, suggesting that the FLCN mRNA transcript may not be subject to nonsense-mediated mRNA decay. However, several individual genes are differentially expressed between BHDS-derived tumors and the sporadic tumors. One gene in particular, DAPL1 (death-associated protein-like 1), is expressed at a high level in BHDS-derived tumors. Although the function of DAPL1 is not known, it was originally termed early epithelial differentiation associated (EEDA) for its expression in stratified squamous epithelium, specifically in a population of cells of the hair follicle . High expression of this gene in BHDS-derived tumors is a potentially interesting finding given the clinical presentation of fibrofolliculomas that arise in BHDS-afflicted individuals.
Several recent reports have implicated FLCN in the energy and nutrient signaling pathway through its interactions with FNIP1 and FNIP2 and its indirect interaction with AMPK (Figure 4A). These studies have also suggested that FLCN impacts the mammalian target of rapamycin (mTOR) related components of the PI3K-Akt signal transduction pathway . Consistent with the existence of a FLCN-mTOR relationship, treatment with the specific mTOR inhibitor, rapamycin, delays the death of mice that possess targeted deletion of FLCN in the kidney [61, 62]. We noted high expression of FNIP2 and TSC1 in BHDS-derived tumors, implicating a novel link between FLCN and both AMPK- and mTOR-mediated signaling and transcription. However, we did not see evidence of PI3K-Akt activation in BHDS-derived tumors using an expression signature that was a robust predictor of PI3K-Akt pathway activation in other renal tumors , nor did we see consistent enrichment of the three mTOR activation signatures from the MsigDB in the BHDS patient samples. It is possible that the up-regulation of TSC1 we have observed represents a feedback effect from the somatic mutation in FLCN. One potential rational for this observation is that is has recently been noted that activation of mTOR controls mitochondrial gene expression through signaling with PGC-1α . Moreover, mTOR-mediated control of mitochondrial gene expression is inhibited by application of rapamycin. Our results suggest that the effects of rapamycin noted in FLCN loss-of-function mice may be through the mitochondrial effects of mTOR activation as opposed to activation of PI3K-Akt.
Throughout our analysis, we observed that one sporadic renal oncocytoma co-clustered with the BHDS-derived tumors and showed strong PGC-1α-related gene expression (Figure 1B, F). This tumor sample also lacked the cytogenetic features typical of sporadic oncocytomas, such as loss of chromosome 1, deregulation of CCND1, and over-expression of chromosome 19 genes (Figure 2). Interestingly, this individual presented with renal oncocytoma at the age of 34 years old, while the median age of sporadic renal oncocytoma is between 65-70 [7, 64]. Given that early age at diagnosis (under age 50) is often a feature of hereditary disease, we sequenced the entire FLCN open reading frame from non-diseased kidney tissue of this patient and only identified a common single nucleotide polymorphism within the 5' UTR. Though somatic mutations in FLCN occur in approximately 10 percent of sporadic tumors, we lacked the tissue required to determine the FLCN status in the tumor itself. However, these results suggest that a separate BHDS-like group of sporadic renal oncocytomas could exist in the population, genetically distinct from other sporadic renal tumors.
Finally, although these DCT-derived tumors are genetically distinct, BHDS-derived tumors, sporadic renal oncocytoma, and chromophobe RCC share their histological and mitochondrial/OXHPOS gene expression characteristics. Development of oncocytomas in organ sites outside of the kidney are also associated with prominent mitochondrial DNA mutations, a high production of mitochondria, and deregulated OXPHOS gene expression [65, 66]. In renal oncocytoma and other mitochondrial myopathies, up-regulation of mitochondrial gene expression is thought to represent a feedback mechanism to compensate for mitochondrial damage [67, 68]. In this study, we show that the mitochondrial expression phenotype is even more pronounced in samples that harbor FLCN mutations. The enhanced mitochondrial gene expression in BHDS samples suggests that wild-type FLCN is important for efficient mitochondrial function and that lack of functional FLCN leads to a yet unknown mitochondrial dysfunction. Deregulation of mitochondrial proteins has recently been identified in sporadic oncocytoma and chromophobe RCC . Future studies will therefore help to clarify the role of FLCN in mitochondrial function.
Our results support a genetic distinction between BHDS-associated tumors and other sporadic renal neoplasias. In addition, we found that deregulation of the PGC-1α-TFAM signaling axis is most pronounced in renal tumors that harbor FLCN mutations and in tumors from other organs that have relatively low expression of FLCN. These results are consistent with the recently discovered interaction between FLCN and AMPK and support a model in which FLCN is a regulator of mitochondrial function.
This work was supported by the French NCI (Institut National du Cancer, PNES rein) and the Ligue Nationale contre le Cancer (Comités du Cher et de l'Indre).
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