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Series GSE65823

Query DataSets for GSE65823

Status

Public on Oct 22, 2015

Title

Identification of a new subclass of ALK negative ALCL expressing aberrant levels of ERBB4 transcripts

Organism

Homo sapiens

Experiment type

Expression profiling by array

Summary

Anaplastic Large Cell Lymphoma (ALCL) is a clinical and biological heterogeneous disease including ALK positive and ALK negative systemic forms. To discover biomarkers and/or genes involved in ALK negative ALCL pathogenesis, we applied the Cancer Outlier Profile Analysis (COPA) algorithm to a gene expression profiling data set including 249 cases of T-NHLs and normal T-cells. Ectopic co-expression of ERBB4 and COL29A1 genes was detected in 24% of ALK negative ALCL patients. RNA sequencing and 5'RNA Ligase Mediated Rapid Amplification of cDNA Ends (RLM-RACE) identified two novel ERBB4 truncated transcripts, displaying intronic Transcription Starting Sites. ERBB4 expression was confirmed at protein level by western blotting and immunohistochemistry. Moreover, by luciferase assays we defined that the expression of ERBB4 aberrant transcripts is promoted by endogenous intronic Long Terminal Repeats (LTRs). In conclusion, we identified a new subclass of ALK negative ALCL characterized by aberrant expression of ERBB4 truncated transcripts carrying intronic 5'UTRs.

Overall design

To discover genes putatively involved in the pathogenesis of ALK negative ALCL patients, we applied the Cancer Outlier Profile Analysis (COPA) algorithm10 to a large gene expression profiling (GEP) data set including 249 cases of T-NHLs and normal T-cells, obtained as previously described (PMID: 22740451 http://www.ncbi.nlm.nih.gov/pubmed/22740451).

Contributor(s)

Scarfò I, Pellegrino E, Kwee I, Agnelli L, Mereu E, Bergaggio E, Abate F, Caputo M, Novero D, Rinaldi A, Tiacci E, Serra S, Deaglio S, Neri A, Falini B, Rabadan R, Bertoni F, Inghirami G, Piva R

Citation(s)

26463425

Submission date

Feb 10, 2015

Last update date

Mar 25, 2019

Contact name

Luca Agnelli

E-mail(s)

luca.agnelli@istitutotumori.mi.it, luca.agnelli@gmail.com

Phone

+390223903581

Organization name

IRCCS Istituto Nazionale dei Tumori

Department

Department of Advanced Diagnostics

Street address

Venezian 1

City

MILAN

ZIP/Postal code

20133

Country

Italy

Platforms (1)

GPL570

[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array

Samples (31)

More...

GSM1607007	PTCL, nos - sample 1
GSM1607008	PTCL, nos - sample 2
GSM1607009	PTCL, nos - sample 3

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BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE65823_249_samples_RMA.txt.gz	73.6 Mb	(ftp)(http)	TXT
GSE65823_RAW.tar	145.6 Mb	(http)(custom)	TAR (of CEL)
Processed data included within Sample table
Processed data are available on Series record