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| Status |
Public on Mar 12, 2019 |
| Title |
Whole transcriptome targeted gene quantification provides new insights on pulmonary sarcomatoid carcinomas |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Pulmonary sarcomatoid carcinomas (PSCs) are rare and aggressive histological types of non-small cell lung cancer (NSCLC) with a median overall survival of about 9-12 months. In detail, PSCs comprise five different histological subtypes: pleomorphic carcinoma (PLC), giant cell carcinoma (GCC), spindle cell carcinoma (SCC), carcinosarcoma (CS) and pulmonary blastoma (PB). Preoperative pathological diagnosis may fail to identify these tumors and therapeutic options are still limited. PSCs have been scarcely characterized from a molecular point of view because of their rarity, and to date no specific markers have been found for PSCs in comparison with other NSCLC types. In this study a highly sensitive amplicon based whole transcriptome quantification analysis was performed, using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Life Technologies) on a selected series of 14 PSCs (1 PB, 4 CS, 2 SCC, 2 GCC, 5 PLC) and 3 samples of normal lung parenchyma. PSCs expression data were then compared with transcriptome data of lung adenocarcinoma and squamous cell carcinoma available on The Cancer Genome Atlas database. Thirty-eight genes specifically deregulated in PSC samples were identified. Among these, IGJ and SLMAP were validated by immunohistochemistry on an independent cohort (30 PSCs, 31 lung adenocarcinoma and 31 squamous cell carcinoma cases). Furthermore, a pathway enrichment analysis, performed on differentially expressed genes, revealed that FOXO signalling and Fanconi Anemia pathways, playing a pivotal role in cancer development and progression, are enriched in PSC tumors. The description of peculiar molecular profiles besides increasing our knowledge on PSCs biology may suggest new diagnostic and therapeutic strategies.
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| Overall design |
Whole transcriptome targeted gene quantification analysis was perfomed on a selected series of 14 pulmonary sarcomatoid carcinomas (1 pulmonary blastoma, 4 carcinosarcomas, 2 spindle cell carcinomas, 2 giant cell carcinomas, 5 pleomorphic carcinomas) and 3 samples of normal lung parenchyma, using the Ion AmpliSeq Transcriptome Human Gene Expression Kit ( Life Technologies).
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| Contributor(s) |
Alì G, Bruno R, Poma AM, Affinito O, Monticelli A, Piaggi P, Ricciardi S, Lucchi M, Melfi F, Cocozza S, Fontanini G |
| Citation(s) |
30837581 |
| Submission date |
Feb 06, 2018 |
| Last update date |
Mar 12, 2019 |
| Contact name |
Gabriella Fontanini |
| E-mail(s) |
gabriella.fontanini@med.unipi.it
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| Phone |
+39 050-993260
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| Organization name |
University of Pisa
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| Department |
Department of Surgical, Medical, Molecular Pathology and Critical Area
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| Street address |
Via Roma 57
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| City |
Pisa |
| State/province |
Italy |
| ZIP/Postal code |
56126 |
| Country |
Italy |
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| Platforms (1) |
| GPL17303 |
Ion Torrent Proton (Homo sapiens) |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA433178 |
| SRA |
SRP132285 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE110205_normalized_data.rpm.bcmatrix.txt.gz |
961.7 Kb |
(ftp)(http) |
TXT |
| GSE110205_raw_counts.bcmatrix.txt.gz |
601.8 Kb |
(ftp)(http) |
TXT |
| GSE110205_samples.bc_summary.txt.gz |
427 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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