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Expression profiling of papillary carcinoma of the breast

ABSTRACT: Expression profiling of papillary carcinoma of the breast and grade- and ER-matched cases of invasive ductal breast cancer To identify differential expression between papillary carcinomas of the breast and grade- and ER-matched invasive ductal breast cancers, we performed expression profiling of 16 cases of papillary carcinomas of the breast and 16 cases of grade- and ER-matched invasive ducatal carcinoma of no special subtype. We further reviewed the papillary carcinomas of the breast and classified them into 3 subtypes, namely, invasive papillary carcinoma, encapsulated papillary carcinoma and solid papillary carcinoma. We also performed a hypothesis-generating comparison of differential expression between the 3 subtypes of papillary carcinoma of the breast. Expression profiling of 16 cases of papillary carcinioma of the brest and 16 cases of invasive ducal carcinomas using the Illumina HT-12 v4 arrays

ORGANISM(S): Homo sapiens

SUBMITTER: Ng Charlotte

PROVIDER: S-ECPF-GEOD-55639 | biostudies-other |

REPOSITORIES: biostudies-other

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Expression profiling of papillary carcinoma of the breast

Project description:Expression profiling of papillary carcinoma of the breast and grade- and ER-matched cases of invasive ductal breast cancer To identify differential expression between papillary carcinomas of the breast and grade- and ER-matched invasive ductal breast cancers, we performed expression profiling of 16 cases of papillary carcinomas of the breast and 16 cases of grade- and ER-matched invasive ducatal carcinoma of no special subtype. We further reviewed the papillary carcinomas of the breast and classified them into 3 subtypes, namely, invasive papillary carcinoma, encapsulated papillary carcinoma and solid papillary carcinoma. We also performed a hypothesis-generating comparison of differential expression between the 3 subtypes of papillary carcinoma of the breast.

2014-06-20 | GSE55639 | GEO

SNP6 and expression profiling of papillary carcinoma of the breast

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Clear cell papillary renal cell carcinoma: micro-RNA expression profiling and comparison with clear cell renal cell carcinoma and papillary renal cell carcinoma.

Project description:Clear cell papillary renal cell carcinoma (CCPRCC) is a low-grade renal neoplasm with morphological characteristics mimicking both clear cell renal cell carcinoma (CCRCC) and papillary renal cell carcinoma (PRCC). However, despite some overlapping features, their morphological, immunohistochemical, and molecular profiles are distinct. Micro-RNAs (miRNAs) are small noncoding RNAs that play a crucial role in regulating gene expression and are involved in various biological processes, including cancer development. To better understand the biology of this tumor, we aimed to analyze the miRNA expression profile of a set of CCPRCC using microarray and quantitative reverse transcription-polymerase chain reaction. A total of 15 cases diagnosed as CCPRCC were used in this study. Among the most differentially expressed miRNA in CCPRCC, we found miR-210, miR-122, miR-34a, miR-21, miR-34b*, and miR-489 to be up-regulated, whereas miR-4284, miR-1202, miR-135a, miR-1973, and miR-204 were down-regulated compared with normal renal parenchyma. To identify consensus of differentially regulated miRNA between CCPRCC, CCRCC, and PRCC, we additionally determined differential miRNA expression using 2 publically available microarray data sets from the NCBI Gene Expression Omnibus database (GSE41282 and GSE3798). This comparison revealed that the miRNA expression profile of CCPRCC shows some overlapping characteristics between CCRCC and PRCC. Moreover, CCPRCC lacks dysregulation of important miRNAs typically associated with aggressive behavior. In summary, we describe the miRNA expression profile of a relatively infrequent type of renal cancer. Our results may help in understanding the molecular underpinning of this newly recognized entity.

| S-EPMC4332813 | biostudies-literature

Expression profiling of papillary carcinoma of the breast

2014-06-20 | E-GEOD-55639 | biostudies-arrayexpress

SNP6 profiling of papillary carcinoma of the breast

Project description:SNP6 profiling of papillary carcinoma of the breast

2014-06-20 | GSE55638 | GEO

SNP6 and expression profiling of papillary carcinoma of the breast

Project description:SNP6 and expression profiling of papillary carcinoma of the breast

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SNP6 and expression profiling of papillary carcinoma of the breast

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-06-20 | E-GEOD-55640 | biostudies-arrayexpress

SNP6 profiling of papillary carcinoma of the breast

Project description:SNP6 profiling of papillary carcinoma of the breast Affymetrix SNP6 arrays were performed according ro manufacturer's directions on DNA extracted from 16 papillary carcinomas of the breast.

2014-06-20 | E-GEOD-55638 | biostudies-arrayexpress

Hobnail variant of papillary thyroid carcinoma: molecular profiling and comparison to classical papillary thyroid carcinoma, poorly differentiated thyroid carcinoma and anaplastic thyroid carcinoma.

Project description:BackgroundAs a rare but aggressive papillary thyroid carcinoma (PTC) variant, the genetic changes of hobnail variant of PTC (HVPTC) are still unclear.ResultsThe prevalence of HVPTC was 1.69% (18/1062) of all PTC diagnosed in our cohort. 73 samples from 55 patients (17 HVPTC, 26 CPTC, 7 PDTC and 5 ATC) were successfully analyzed using targeted NGS with an 18-gene panel. Thirty-seven mutation variant types were identified among 11 genes. BRAF V600E mutation was the most common mutation, which is present in almost all HVPTC samples (16/17, 94%), most CPTC samples (20/26, 77%), and none of the ATC and PDTC samples. TERT promoter mutation (C228T) was identified in 2 ATC and one HVPTC patient. RAS and TP53 mutation are almost exclusively present among ATC and PDTC samples although TP53 mutation was also observed in 3 HVPTC patients. Six different GNAS mutations were identified among 8 CPTC patients (31%) and none of the HVPTC patients. The only patient who died of disease progression harbored concomitant TERT C228T mutation, BRAF V600E mutation and TP53 mutation.MethodsHVPTC cases were identified from a group of 1062 consecutive surgical specimens diagnosed as PTC between 2000 and 2010. Targeted next-generation sequencing (NGS) was applied to investigate the mutation spectrum of HVPTC, compared to classical PTC (CPTC), poorly differentiated thyroid carcinoma (PDTC) and anaplastic thyroid carcinoma (ATC).ConclusionAs an aggressive variant of PTC, HVPTC has relatively specific molecular features, which is somewhat different from both CPTC and ATC/PDTC and may underlie its relatively aggressive behavior.

| S-EPMC5400643 | biostudies-literature

Microarray profiling of circular RNAs in human papillary thyroid carcinoma.

Project description:BackgroundNon-coding circular RNAs (circRNAs) have displayed dysregulated expression in several human cancers. Here, we profiled the circRNA expression of papillary thyroid carcinoma (PTC) tumors to improve our understanding of PTC pathogenesis.MethodsMicroarray profiling was performed on 18 thyroid samples, consisting of six PTC tumors, six matching contralateral normal samples, and six benign thyroid lesions. After low-intensity filtering, hierarchical clustering revealed the circRNA expression patterns. Statistical analysis followed by qRT-PCR validation identified the differential circRNAs. MicroRNA (miRNA) target prediction software identified putative miRNA response elements (MREs), which were used to construct a network map of circRNA-miRNA interactions for the differential circRNAs. Bioinformatics platforms predicted cancer-related circRNA-miRNA associations and putative downstream target genes, respectively.ResultsA total of 88 circRNAs and 10 circRNAs were significantly upregulated and downregulated, respectively, in PTC tumors relative to normal thyroid tissue, while 129 circRNAs and 226 circRNAs were significantly upregulated and downregulated, respectively, in PTC tumors relative to benign thyroid lesions. A total of 12 upregulated and four downregulated circRNAs were overlapping between the foregoing comparisons. One downregulated circRNA (hsa_circRNA_100395) showed interactive potential with two cancer-related miRNAs (miR-141-3p and miR-200a-3p). From this analysis, we identified several promising cancer-related genes that may be targets of the dysregulated hsa_circRNA_100395/miR-141-3p/miR-200a-3p axis in PTC tumors.ConclusionscircRNA dysregulation may play a role in PTC pathogenesis, and several key circRNAs show promise as candidate biomarkers for PTC. The hsa_circRNA_100395/miR-141-3p/ miR-200a-3p axis may be involved in the pathogenesis of PTC.

| S-EPMC5347999 | biostudies-literature

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