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We report two novel cases of Xp11 translocation renal cell carcinomas with the MED15::TFE3 gene fusion in adult females aged 40 and 74 years. Both cases were extensively cystic and contained only minimal clear cells lining cysts and within septal walls, raising the differential diagnosis of multilocular cystic renal neoplasm of low malignant potential. By immunohistochemistry, both neoplasms labeled for PAX8, TFE3, cathepsin K and Melan A but not for HMB45. On review of the published literature and the two cases reported herein, over 90% of MED15::TFE3 renal cell carcinomas (RCCs) have been described as cystic. The correlation of the MED15::TFE3 fusion with extensively cystic morphology represents the strongest association of TFE3 fusion partner with clinicopathological features among TFE3-rearranged RCC reported to date.

Identical TFE3-related gene fusions may be found in renal cell carcinoma and mesenchymal neoplasms such as alveolar soft part sarcoma and TFE3-rearranged perivascular epithelioid cell tumor (PEComa). Among mesenchymal neoplasms, the ASPSCR1-TFE3 gene fusion has previously been described only in alveolar soft part sarcoma. We report 3 unusual mesenchymal neoplasms harboring the ASPSCR1-TFE3 gene fusion, the morphologic phenotype of which more closely matches PEComa rather than alveolar soft part sarcoma. All 3 neoplasms occurred in females ranging in age from 18 to 34 years and were located in the viscera (kidney, bladder, and uterus). All 3 contained nests of epithelioid cells bounded by fibrovascular septa. However, all were associated with hyalinized stroma, tight nested architecture, mixed spindle cell and epithelioid pattern, clear cytoplasm, and lacked significant discohesion. Overall, morphologic features closely resembled PEComa, being distinct from the typical alveolar soft part sarcoma phenotype. While none of the neoplasms labeled for HMB45, cytokeratin, or PAX8 all showed positivity for TFE3 and cathepsin K, and all except 1 were positive for smooth muscle actin. One patient developed a liver metastasis 7 years after nephrectomy. These cases bridge the gap between 2 TFE3-rearranged neoplasms, specifically alveolar soft part sarcoma and Xp11 translocation PEComa, highlighting the relatedness and overlap among Xp11 translocation neoplasms. While most TFE3-rearranged neoplasms can be confidently placed into a specific diagnostic category such as alveolar soft part sarcoma, PEComa, or Xp11 translocation renal cell carcinoma, occasional cases have overlapping features, highlighting the potential role that the cell of origin and the specific gene fusion play in the phenotype of these neoplasms.

The genetics of nephroblastoma (Wilms tumor) occurring in adults is largely unknown, as studies have largely been limited to isolated case reports. We, therefore, studied 14 adult Wilms tumors for genetic alterations, using expanded targeted sequencing on 11 cases. The patients ranged from 17 to 46 years of age (mean and median, 31 y), and there were 8 males and 6 females. Five Wilms tumors harbored BRAF V600E mutations. All of these had better-differentiated areas identical to metanephric adenoma, as has previously been described. In 3 such cases, microdissection studies revealed that the BRAF V600E mutation was present in both the metanephric adenoma and Wilms tumor areas; however, additional genetic alterations (including TERT promoter mutations in 2 cases, ASLX1/ATR mutations in 1 other case) were limited to the Wilms tumor component. These findings suggest that the Wilms tumor developed from the metanephric adenoma. Other adult Wilms tumors harbored genetic alterations previously reported in the more common pediatric Wilms tumors, including WT1 mutations (2 cases), ASLX1 mutations (3 additional cases), NSD2 mutation (1 additional case), and 11p loss (3 cases). In summary, a significant subset of adult Wilms tumors (specifically those of epithelial type with differentiated areas) harbor targetable BRAF V600E mutations and appear to arise from metanephric adenomas as a consequence of additional acquired genetic alterations. Other adult Wilms tumors often harbor genetic alterations found in their more common pediatric counterparts, suggesting at least some similarities in their pathogenesis.

Purpose: To evaluate the expression of cathepsin K (CTSK) and CXCL14 in stromal and epithelial cells in human breast tumor progression.Experimental Design: We did immunohistochemical analyses of CTSK and CXCL14 expression in normal breast tissue, biopsy sites, benign lesions, ductal carcinoma in situ, and invasive breast tumors of different stages. Expression patterns were related to histopathologic characteristics of the tumors and clinical outcome. The effect of CTSK+ breast stromal fibroblasts on CTSK- breast cancer cells was assessed in coculture.Results: Epithelial expression of CTSK was rarely detected in any of the tissue samples analyzed, whereas CXCL14-positive epithelial cells were found in all tissue types. The expression of CXCL14 was not associated with any tumor or patient characteristics analyzed. Stromal CTSK expression was significantly higher in invasive compared with in situ carcinomas, and in one of the two data sets analyzed, it correlated with higher tumor stage. Among all samples examined, the highest stromal CTSK levels were detected in biopsy sites. Neither epithelial nor stromal expression of CTSK was significantly associated with recurrence-free or overall survival. Coculture of CTSK+ fibroblasts enhanced the invasion of CTSK- breast tumor epithelial cells and this was blocked by CTSK inhibitors.Conclusions: CTSK may function as a paracrine factor in breast tumorigenesis. CTSK+ fibroblasts may play a role in tumor progression by promoting the invasiveness of tumor epithelial cells. The possibility that CTSK inhibitors may have a clinical role in decreasing the risk of tumor progression merits further investigation.

PDF file - 159K, Supplementary Figure 3. BMTP78 kills breast cell lines in a GRP78-dependent manner.

Supplementary Table 1 from Pharmacologic Unmasking of Epigenetically Silenced Genes in Breast Cancer

Supplementary Data from Heterogeneity of Breast Cancer Metastases: Comparison of Therapeutic Target Expression and Promoter Methylation Between Primary Tumors and Their Multifocal Metastases

Supplementary Table 2 from Pharmacologic Unmasking of Epigenetically Silenced Genes in Breast Cancer

Purpose: A comprehensive comparison of biomarker expression between patients' primary breast carcinoma (PBC) and their metastatic breast carcinomas (MBC) has not been done.Experimental Design: We did rapid autopsies (postmortem intervals, 1-4 hours) on 10 consenting patients who died of MBC. We constructed single-patient tissue microarrays from the patients' archived PBC and multiple different MBCs harvested at autopsy, which were immunohistochemically labeled for multiple biomarkers. Methylation of multiple gene promoters was assessed quantitatively on dissected PBC and MBC samples.Results: Extensive heterogeneity was observed between PBC and their paired MBC, as well as among multiple MBC from the same patient. Estrogen and progesterone receptors tended to be uniformly down-regulated in metastases. E-cadherin was down-regulated in a subset of the MBC of one case. Variable overexpression in MBC compared with the PBC was observed for cyclooxygenase-2 (five cases), epidermal growth factor receptor (EGFR; four cases), MET (four cases), and mesothelin (four cases). No case strongly overexpressed HER-2/neu by immunohistochemistry, but eight cases showed variable protein expression ranging from negative to equivocal (2+) in different MBC. In one case, variable low-level HER-2/neu gene amplification was found. EGFR and MET overexpression were restricted to the four basal-type cancers. EGFR protein overexpression did not correlate with EGFR gene amplification. Multigene promoter hypermethylation of RASSF1a, HIN1, cyclin D2, Twist, estrogen receptor α, APC1, and RARβ was overall very similar in the PBC and all MBCs in all cases.Conclusions: Therapeutic targets identified in the PBC or even some MBC may not reflect targets present in all metastatic sites.

PDF file - 151K, Supplementary Figure 4. Effect of cell growth in different concentrations of oxygen on the extent of surface GRP78 in normal and transformed human and mouse cells.

Supplementary Table 3 from Pharmacologic Unmasking of Epigenetically Silenced Genes in Breast Cancer

Purpose: The major cause of morbidity in breast cancer is development of metastatic disease, for which few effective therapies exist. Because tumor cell dissemination is often an early event in breast cancer progression and can occur before diagnosis, new therapies need to focus on targeting established metastatic disease in secondary organs. We report an effective therapy based on targeting cell surface–localized glucose-regulated protein 78 (GRP78). GRP78 is expressed normally in the endoplasmic reticulum, but many tumors and disseminated tumor cells are subjected to environmental stresses and exhibit elevated levels of GRP78, some of which are localized at the plasma membrane.Experimental Design and Results: Here, we show that matched primary tumors and metastases from patients who died from advanced breast cancer also express high levels of GRP78. We used a peptidomimetic targeting strategy that uses a known GRP78-binding peptide fused to a proapoptotic moiety [designated bone metastasis targeting peptide 78 (BMTP78)] and show that it can selectively kill breast cancer cells that express surface-localized GRP78. Furthermore, in preclinical metastasis models, we show that administration of BMTP78 can inhibit primary tumor growth as well as prolong overall survival by reducing the extent of outgrowth of established lung and bone micrometastases.Conclusions: The data presented here provide strong evidence that it is possible to induce cell death in established micrometastases by peptide-mediated targeting of cell surface–localized GRP in advanced breast cancers. The significance to patients with advanced breast cancer of a therapy that can reduce established metastatic disease should not be underestimated. Clin Cancer Res; 19(8); 2107–16. ©2013 AACR.

Background: Gallbladder cancer (GBC) is an uncommon neoplasm in the United States, but one with high mortality rates. This malignancy remains largely understudied at the molecular level such that few targeted therapies or predictive biomarkers exist.Experimental Design: We built the first series of serial analysis of gene expression (SAGE) libraries from GBC and nonneoplastic gallbladder mucosa, composed of 21-bp long-SAGE tags. SAGE libraries were generated from three stage-matched GBC patients (representing Hispanic/Latino, Native American, and Caucasian ethnicities, respectively) and one histologically alithiasic gallbladder. Real-time quantitative PCR was done on microdissected epithelium from five matched GBC and corresponding nonneoplastic gallbladder mucosa. Immunohistochemical analysis was done on a panel of 182 archival GBC in high-throughput tissue microarray format.Results: SAGE tags corresponding to connective tissue growth factor (CTGF) transcripts were identified as differentially overexpressed in all pairwise comparisons of GBC (P < 0.001). Real-time quantitative PCR confirmed significant overexpression of CTGF transcripts in microdissected primary GBC (P < 0.05), but not in metastatic GBC, compared with nonneoplastic gallbladder epithelium. By immunohistochemistry, 66 of 182 (36%) GBC had high CTGF antigen labeling, which was significantly associated with better survival on univariate analysis (P = 0.0069, log-rank test).Conclusions: An unbiased analysis of the GBC transcriptome by SAGE has identified CTGF expression as a predictive biomarker of favorable prognosis in this malignancy. The SAGE libraries from GBC and nonneoplastic gallbladder mucosa are publicly available at the Cancer Genome Anatomy Project web site and should facilitate much needed research into this lethal neoplasm.

Purpose: Aberrant promoter hypermethylation of several known or putative tumor suppressor genes occurs frequently during the pathogenesis of various cancers including breast cancer. Many epigenetically inactivated genes involved in breast cancer development remain to be identified. Therefore, in this study we used a pharmacologic unmasking approach in breast cancer cell lines with 5-aza-2′-deoxycytidine (5-aza-dC) followed by microarray expression analysis to identify epigenetically inactivated genes in breast cancer.Experimental Design: Breast cancer cell lines were treated with 5-aza-dC followed by microarray analysis to identify epigenetically inactivated genes in breast cancer. We then used bisulfite DNA sequencing, conventional methylation-specific PCR, and quantitative fluorogenic real-time methylation-specific PCR to confirm cancer-specific methylation in novel genes.Results: Forty-nine genes were up-regulated in breast cancer cells lines after 5-aza-dC treatment, as determined by microarray analysis. Five genes (MAL, FKBP4, VGF, OGDHL, and KIF1A) showed cancer-specific methylation in breast tissues. Methylation of at least two was found at high frequency only in breast cancers (40 of 40) as compared with normal breast tissue (0 of 10; P < 0.0001, Fisher's exact test).Conclusions: This study identified new cancer-specific methylated genes to help elucidate the biology of breast cancer and as candidate diagnostic markers for the disease.

Supplementary Data from Epithelial and Stromal Cathepsin K and CXCL14 Expression in Breast Tumor Progression

PDF file - 425K, Supplementary Figure 5. Body weights of mice bearing 4T1.2 mammary tumors during treatment with BMTP78 or control peptide or saline.

PDF file - 395KB, Figure S1. Pre-surgery plasma ddPCR analysis for PIK3CA mutations. Figure S2. Positive and negative controls for droplet thresholds and counts. Figure S3. Lower Limit of Detection for PIK3CA Exon 9. Supplementary Table S1: Primers used to amplify and sequence FFPE specimens. Supplementary Table S2: Primers and probes used for ddPCR on FFPE samples. Supplementary Table S3: Primers and probes for ddPCR of plasma DNA. Supplementary Table S4: Fractional abundance and 95% confidence intervals of positive ptDNA samples.

Purpose: Detecting circulating plasma tumor DNA (ptDNA) in patients with early-stage cancer has the potential to change how oncologists recommend systemic therapies for solid tumors after surgery. Droplet digital polymerase chain reaction (ddPCR) is a novel sensitive and specific platform for mutation detection.Experimental Design: In this prospective study, primary breast tumors and matched pre- and postsurgery blood samples were collected from patients with early-stage breast cancer (n = 29). Tumors (n = 30) were analyzed by Sanger sequencing for common PIK3CA mutations, and DNA from these tumors and matched plasma were then analyzed for PIK3CA mutations using ddPCR.Results: Sequencing of tumors identified seven PIK3CA exon 20 mutations (H1047R) and three exon 9 mutations (E545K). Analysis of tumors by ddPCR confirmed these mutations and identified five additional mutations. Presurgery plasma samples (n = 29) were then analyzed for PIK3CA mutations using ddPCR. Of the 15 PIK3CA mutations detected in tumors by ddPCR, 14 of the corresponding mutations were detected in presurgical ptDNA, whereas no mutations were found in plasma from patients with PIK3CA wild-type tumors (sensitivity 93.3%, specificity 100%). Ten patients with mutation-positive ptDNA presurgery had ddPCR analysis of postsurgery plasma, with five patients having detectable ptDNA postsurgery.Conclusions: This prospective study demonstrates accurate mutation detection in tumor tissues using ddPCR, and that ptDNA can be detected in blood before and after surgery in patients with early-stage breast cancer. Future studies can now address whether ptDNA detected after surgery identifies patients at risk for recurrence, which could guide chemotherapy decisions for individual patients. Clin Cancer Res; 20(10); 2643–50. ©2014 AACR.

PDF file - 735K, Supplementary Figure 1. Details of the analysis of cell surface GRP78 levels using flow cytometry.

PDF file - 1974K, Supplementary Figure 2. Antibody against GRP78 protects 4T1.2 cells from BMTP78 but alone has no effect on viability.

Supplementary Data from Serial Analysis of Gene Expression Identifies Connective Tissue Growth Factor Expression as a Prognostic Biomarker in Gallbladder Cancer

XLSX file - 32K, Shannon and Simpson's index for each tumor and each probe based on BAC, CEP, BAC/CEP and unique counts.

The ability to consistently detect cell-free tumor-specific DNA in peripheral blood of patients with metastatic breast cancer provides the opportunity to detect changes in tumor burden and to monitor response to treatment. We developed cMethDNA, a quantitative multiplexed methylation-specific PCR assay for a panel of ten genes, consisting of novel and known breast cancer hypermethylated markers identified by mining our previously reported study of DNA methylation patterns in breast tissue (103 cancer, 21 normal on the Illumina HumanMethylation27 Beadchip) and then validating the 10-gene panel in The Cancer Genome Atlas project breast cancer methylome database. For cMethDNA, a fixed physiologic level (50 copies) of artificially constructed, standard nonhuman reference DNA specific for each gene is introduced in a constant volume of serum (300 μL) before purification of the DNA, facilitating a sensitive, specific, robust, and quantitative assay of tumor DNA, with broad dynamic range. Cancer-specific methylated DNA was detected in training (28 normal, 24 cancer) and test (27 normal, 33 cancer) sets of recurrent stage IV patient sera with a sensitivity of 91% and a specificity of 96% in the test set. In a pilot study, cMethDNA assay faithfully reflected patient response to chemotherapy (N = 29). A core methylation signature present in the primary breast cancer was retained in serum and metastatic tissues collected at autopsy two to 11 years after diagnosis of the disease. Together, our data suggest that the cMethDNA assay can detect advanced breast cancer, and monitor tumor burden and treatment response in women with metastatic breast cancer. Cancer Res; 74(8); 2160–70. ©2014 AACR.

Supplementary Figure Legends. Legend for Supplementary Figures S1-S10.

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Supplementary Table 1 and Figures 1-4 from TFE3 Fusions Activate MET Signaling by Transcriptional Up-regulation, Defining Another Class of Tumors as Candidates for Therapeutic MET Inhibition

Supplementary Table 1, Figure 1 from Epigenetic Inactivation of the Potential Tumor Suppressor Gene FOXF1 in Breast Cancer

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Supplementary Methods and Figure Legends 1-4 from TFE3 Fusions Activate MET Signaling by Transcriptional Up-regulation, Defining Another Class of Tumors as Candidates for Therapeutic MET Inhibition

The expression of several members of the FOX gene family is known to be altered in a variety of cancers. We show that in breast cancer, FOXF1 gene is a target of epigenetic inactivation and that its gene product exhibits tumor-suppressive properties. Loss or downregulation of FOXF1 expression is associated with FOXF1 promoter hypermethylation in breast cancer cell lines and in invasive ductal carcinomas. Methylation of FOXF1 in invasive ductal carcinoma (37.6% of 117 cases) correlated with high tumor grade. Pharmacologic unmasking of epigenetic silencing in breast cancer cells restored FOXF1 expression. Re-expression of FOXF1 in breast cancer cells with epigenetically silenced FOXF1 genes led to G1 arrest concurrent with or without apoptosis to suppress both in vitro cell growth and in vivo tumor formation. FOXF1-induced G1 arrest resulted from a blockage at G1-S transition of the cell cycle through inhibition of the CDK2-RB-E2F cascade. Small interfering RNA–mediated depletion of FOXF1 in breast cancer cells led to increased DNA re-replication, suggesting that FOXF1 is required for maintaining the stringency of DNA replication and genomic stability. Furthermore, expression profiling of cell cycle regulatory genes showed that abrogation of FOXF1 function resulted in increased expression of E2F-induced genes involved in promoting the progression of S and G2 phases. Therefore, our studies have identified FOXF1 as a potential tumor suppressor gene that is epigenetically silenced in breast cancer, which plays an essential role in regulating cell cycle progression to maintain genomic stability. Cancer Res; 70(14); 6047–58. ©2010 AACR.

PDF file - 1480K, Figure S1. Double knock in clones have single mutant PIK3CA alleles and equivalent expression of mutant and wild type PIK3CA and form aberrant structures in 3D culture. Figure S2. DKI xenografts retain the same number of KRAS and PIK3CA alleles. Figure S3. Knock out of mutant PIK3CA affects tumorigenicity in nude mouse xenograft assays. Figure S4. DKI cell lines show phosphorylation of Akt and Erk in physiologic but not supra-physiologic concentrations of EGF. Figure S5. DKI cells have increased phosphorylation of S6 ribosomal protein but not 4E-BP1. Figure S6. DKI cells are sensitive to the MEK inhibitor U0126 but not to rapamycin and show differential effects on phosphorylation of Akt, Erk, p70S6K and p90RSK. Figure S7. Transgene expression of mutant PIK3CA cDNA with and without RBD mutations in MCF- 10A and KRAS G12V knock in cell lines. Figure S8. Pdk1 activity is increased in DKI cells.

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XLSX file - 32K, Shannon and Simpson's index for each tumor and each probe based on BAC, CEP, BAC/CEP and unique counts.

Supplementary Figure 2 from Epigenetic Inactivation of the Potential Tumor Suppressor Gene FOXF1 in Breast Cancer

Supplementary Methods. Description of additional methods and procedures used in the study.

Supplementary Table 3 from Cancer-Related Epigenome Changes Associated with Reprogramming to Induced Pluripotent Stem Cells

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XLS file - 32K

PDF file - 1559KB, This file contains detailed methods, tables of study samples and source, primer and probe sequences,and genes belonging to the panel. Supplementary Table 1. Patient sample sets used in this study. Supplementary Table 2. 10-gene marker panel and its performance. Supplementary Table 3A. cMethDNA and QM-MSP primer and probe sequences. Supplementary Table 3B. cMethDNA and QM-MSP primer and probe sequences. Supplementary Table 3C. cMethDNA and QM-MSP primer and probe sequences. Supplementary Table 4. Comparison and reproducibility of the cMethDFNA assay using three DNA purification methods. Supplementary Figure 1. Infinium Human Methylation27 tissue DNA methylation array profile of the 10-gene marker panel. Supplementary Figure 2. Illumina Infinium Human Methylation27 serum DNA array profile of the 10-gene marker panel. Supplementary Figure 3. cMethDNA assay using a 6-gene marker panel. Supplementary Figure 4. Scatter plot and data analysis of cumulative methylation of the 10-gene panel in normal serum DNA. Supplementary Figure 5. Monitoring of treatment response by the cMethDNA assay. Supplementary Figure 6. Methylation Profiles in serum, primary, and metastatic tumor DNA. Supplementary Figure 7. Methylation profiles of serum, primary tumor and/or metastasis in patients with Stage 4 breast cancer. Supplementary Figure 8A. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 8B. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 8C. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 8D. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 8E. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 8F. Performance of the 10-gene panel in arrays of a variety of tumor types. Supplementary Figure 9. Representative examples of amplification plots of cMethDNA real-time PCR.

Supplementary Methods from Epigenetic Inactivation of the Potential Tumor Suppressor Gene FOXF1 in Breast Cancer

Supplementary Figures S1-S10. Tests for specificity of the anti-HEYL antibody (S1); Notch pathway induces HEYL expression (S2); In vitro analysis of direct interaction of HEYL and Smad3 in Cos 1 cells (S3); Transcriptional control of TGF-ß responsive reporter consisting of tandem synthetic Smad-binding elements by luciferase assays (S4); Hematoxylin and eosin (H&E) staining of mammary glands of wild-type or transgenic HEYL+ virgin mice, 13 weeks of age (S5); Mammary gland H&E staining of wild-type or transgenic mice at day 10 of pregnancy (S6); Mammary gland hyperplasia was commonly observed in HEYL+ transgenic mice, Representative photomicrographs from mouse numbers, 1-4 are shown (S7); Expression of HeyL in mammary tumors from two HEYL+ transgenic mice measured by RT-PCR and IHC staining (S8); Expression of downstream effectors of TGFß, PAI-1 and P15 in HEYL+ transgenic mammary tumors in comparison to normal mammary glands of WT mice (S9); The antagonistic network between Notch and TGF-ß signaling through the interactions between HEY genes and Smads (S10).