Gene expression of papillary renal neoplasm with reverse polarity (PRNRP) cases + PRCC cases
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PROVIDER: PRJNA1076203 | ENA |
REPOSITORIES: ENA
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Project description:Between 80% and 90% of renal carcinomas are either clear cell renal cell carcinoma or papillary RCC although there are at least 20 other distinct forms of RCC recognised by the World Health Organization (WHO). Emerging or provisional entities have been considered as variants of PRCC, including papillary renal neoplasm with reversed polarity (PRNRP). However, the molecular basis of PRNRP is unknown. We used microarray analysis to elucidate the gene profile of 10 PRNRP cases and an additional 7 PRCC cases. Cases were only considered for this study after fulfilment of strict inclusive histological and immunohistochemical criteria. We used Affymetrix Clariom D human arrays to elucidate the expression of these samples.
2024-02-18 | GSE255706 | GEO
Project description:Between 80% and 90% of renal carcinomas are either clear cell renal cell carcinoma or papillary RCC although there are at least 20 other distinct forms of RCC recognised by the World Health Organization (WHO). Emerging or provisional entities have been considered as variants of PRCC, including papillary renal neoplasm with reversed polarity (PRNRP). However, the molecular basis of PRNRP, and miRNA expression profile, is unknown. We used microarray analysis to elucidate the non-coding RNA (ncRNA) profiles of 10 PRNRP cases and compared them with other renal neoplasms. Cases were only considered for this study after fulfilment of strict inclusive histological and immunohistochemical criteria. We used Affymetrix miRNA v.4.0 arrays to elucidate the expression of these samples.
2024-02-18 | GSE255707 | GEO
Project description:miRNA expression of papillary renal neoplasm with reverse polarity (PRNRP) cases
| PRJNA1076204 | ENA
Project description:BACKGROUND: Despite the moderate incidence of papillary renal cell carcinoma; (PRCC), there is a disproportionately limited understanding of its underlying genetic programs. There is no effective therapy for metastatic PRCC, and patients are often excluded from kidney cancer trials. A morphological classification of PRCC into Type 1 and Type 2 tumors has been recently proposed, but its biological relevance remains uncertain. PATIENTS AND METHODS. We studied the gene expression profiles of 34 cases of PRCC using Affymetrix HGU133 Plus 2.0 arrays (54,675 probe sets) using both unsupervised and supervised analysis. Comparative genomic microarray analysis (CGMA) was used to infer cytogenetic aberrations, and pathways were ranked with a curated database. Expression of selected genes was validated by immunohistochemistry in 34 samples, with 15 independent tumors. RESULTS. We identified 2 highly distinct molecular PRCC subclasses with morphologic correlation. The first class, with excellent survival, corresponded to 3 histological subtypes: Type 1, low-grade Type 2 and mixed Type 1/low-grade Type 2 tumors. The second class, with poor survival, corresponded to high-grade Type 2 tumors (n=11). Dysregulation of G1/S and G2/M checkpoint genes were found in Class 1 and Class 2 tumors respectively, alongside characteristic chromosomal aberrations. We identified a 7-transcript predictor that classified samples on cross-validation with 97% accuracy. Immunohistochemistry confirmed high expression of cytokeratin 7 in Class 1 tumors, and of topoisomerase IIa in Class 2 tumors. CONCLUSIONS. We report 2 molecular subclasses of PRCC, which are biologically and clinically distinct, which may be readily distinguished in a clinical setting. Experiment Overall Design: 34 individual samples analyzed, no technical replicates. Based on histologic features and Fuhrman grading system, we designated four categories of tumors: type 1 (n = 14) characterized by small tumor cells of low Fuhrman grade (2); type 2A (n = 4) characterized by large eosinophilic tumor cells of low Fuhrman grade (2); combined type 1 and 2A (n = 5); and type 2B (n = 11) characterized by large eosinophilic tumor cells with Fuhrman grade.
2007-10-20 | E-GEOD-2748 | biostudies-arrayexpress
Project description:to see if CCPRCC has a distinct miRNA profile from CCRCC and PRCC miRNA v.2.0 chips on two portions of five CCPRCC cases (total 10 samples), three portions of two CCRCC cases and a further three CCRCC cases (total 9 samples), and five type I PRCC samples; a total of 24 samples
2013-10-23 | E-GEOD-51554 | biostudies-arrayexpress
Project description:BackgroundPapillary renal neoplasm with reverse polarity (PRNRP) is a novel entity with unique clinicopathological characteristics, and only a small number of patients with PRNRP have been described.MethodsWe retrospectively analyzed the data for nine patients with PRNRP and evaluated differences in the clinical, histomorphological, immunohistochemical, and molecular features; prognosis; and differential diagnosis of PRNRP from other renal tumors with papillary structure.ResultsThere were six males and three females aged 36 to 74 years (mean: 62.33 years; median: 68 years). All the tumors were solitary and ranged from 1 to 3.7 cm (mean: 2.17 cm; median: 2 cm), with three and six tumors arose in the left and right renal tract, respectively. Pathologically, PRNRP is a small, well-circumscribed neoplasm with predominant papillary formations. The lining epithelium is composed of a monolayer of cuboidal to low-columnar cells with low-grade nuclei arranged against the apical pole of the tumor cells. Edema, mucinous degeneration, and hyaline degeneration are found in the fibrovascular cores. Foamy macrophages, psammoma bodies, hemosiderin deposition, and infiltrative tumor boundaries were present in some patients. Immunohistochemically, all tumors showed diffuse positive staining for GATA3. Sanger sequencing confirmed the presence of KRAS mutation in seven patients. All patients had a good prognosis after surgery and were relapse free. Positive staining for GATA3 and negative staining for vimentin were the most significant markers for differentiating PRNRP from other renal tumors with analogous structure.ConclusionsThese findings suggested that PRNRP is a distinctive subtype of renal tumor with specific pathological features and indolent behaviors that should be distinguished from other renal tumors, especially papillary renal cell carcinoma. A monolayer of tumor cells with an inverted nuclear pattern, positive staining for GATA3, and KRAS mutation are essential for pathological diagnosis. Owing to its satisfactory prognosis, the surveillance and follow-up of patients with PRNRP should be additionally formulated.
| S-EPMC10999029 | biostudies-literature
Project description:Renal cell carcinoma is the most common neoplasm of the adult kidney. A few subtypes of RCC include papillary RCC (pRCC), chromophobe RCC (chRCC) and the benign oncocytoma tumor. In some cases, distinguishing between the RCC subyptes is difficult. We performed a mircroRNA (miRNA) microarray to determine differential miRNA expression between pRCC, chRCC, and oncocytoma.
2012-08-14 | GSE39790 | GEO
Project description:Renal cell carcinoma is the most common neoplasm of the adult kidney. A few subtypes of RCC include papillary RCC (pRCC), chromophobe RCC (chRCC) and the benign oncocytoma tumor. In some cases, distinguishing between the RCC subyptes is difficult. We performed a mircroRNA (miRNA) microarray to determine differential miRNA expression between pRCC, chRCC, and oncocytoma. We performed a miRNA microarray on 10 tumor samples of each papillary renal cell carcinoma (pRCC), chromophobe renal cell carcinoma (chRCC), and oncocytoma.
2012-08-13 | E-GEOD-39790 | biostudies-arrayexpress
Project description:AimsThis study retrospectively investigated the morphological, immunohistochemical and molecular genetic features of papillary renal neoplasm with reverse polarity (PRNRP), a recently described renal tumor.Methods and resultsEleven cases of PRNRP were collected, and 16 cases of type I and 9 cases of type II papillary renal cell carcinoma were included as a control series. Pathological features were evaluated based on HE staining and immunohistochemistry. KRAS exon 2 and BRAF V600E mutations were detected by Real-time PCR and Sanger sequencing. Fluorescence in situ hybridization was conducted for identification of chromosomal abnormalities. Hemosiderin deposition was found in a small amount of tumor cells in 6 cases. Multifocal or patchy necrosis (5/11), small focal invasion of the pseudocapsules or renal parenchyma (6/11), and breakthrough of renal capsule with nerve invasion (1/11) were revealed, inconsistent with the previous view that the tumor lacks necrosis and intercellular hemosiderin. Immunohistochemical staining (diffusely positive for CK7 and GATA3, negative for CD117 and vimentin, and negative to weakly positive for P504S) and high frequency of KRAS mutations in exon 2 (9/10) supported the identification and inclusion of our cases. Chromosome 7 trisomy (1/7), chromosome 17 trisomy (0/7) and chromosome Y deletion (0/5 male patients) were seldom detected in this tumor. All patients were alive without metastasis or recurrence at the end of the follow-up.ConclusionOur findings may highlight the possibility of a low malignant potential of this emerging entity. We suggest that the tumor be classified as a novel renal cell tumor subtype independent of papillary renal cell carcinoma.
| S-EPMC9404576 | biostudies-literature
Project description:PRCC-TFE3 is an oncogenic chimeric transcription factor identified in human TFE3-rearranged renal cell carcinoma. To analyze gene expression changes driven by PRCC-TFE3, we generated and utilized an HA-tagged PRCC-TFE3-inducible HEK293 cell line, which expresses HA-tagged PRCC-TFE3 in a doxycycline-dependent manner. Cells were cultured with or without doxycycline, and comprehensive gene expression analysis was conducted using Affymetrix arrays .
2025-01-07 | GSE281146 | GEO