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Series GSE138708 Query DataSets for GSE138708
Status Public on Oct 10, 2022
Title Typical Lung Carcinoids with Metastasis: Potential Role of MicroRNAs in the Regulation of Adaptive Immunity Associated with Disease: a Case Study
Organism Homo sapiens
Experiment type Expression profiling by RT-PCR
Summary Background/aims: Lung carcinoids are uncommon neuroendocrine tumours. Molecular features of lung carcinoids have been poorly defined. microRNAs (miRNAs) are potent gene expression regulators with important roles in cancer development and progression. However, little is known on the role of miRNAs in the pathogenesis of lung carcinoids. Our goals were to identify commonly deregulated miRNAs in a rare case of lung carcinoid of typical histology with metastasis, as well as map miRNA target genes in pathways potentially associated with disease development and progression.
Methods: miRNA expression profiles were assessed using the TaqMan Low Density Arrays, which is a platform including 384 miRNAs. miRNA profiles were generated in the tumor and its corresponding lymph node metastasis, compared to reference normal lung tissues. Furthermore, miRNA expression was validated in a separate, publicly available external dataset (n=19 typical lung carcinoids; 2/19 were metastatic tumors, compared to six normal lung tissues, GSE77380). Following this analysis, computational tools were applied for data interpretation. miRTarBase was used to determine miRNA-target genes, followed by ToppGene Suite analysis to identify pathways and biological functions. In addition, the expression of genes targeted by miRNAs was validated in a second, separate external dataset (n=13 tumour samples, GSE35679). GEO2R data analysis tool was used in both validation analyses (miRNAs and genes).
Results: We identified 15 commonly significantly downregulated miRNAs (fold change, FC≥2 and p<0.05) in the tumour and its paired metastasis, with further decreasing levels in the metastatic lesion. Downregulation of miR-126-3p and miR-146b-5p was validated in the external dataset GSE77380. In addition, SOX2 and TCF4 genes, targeted by miR-126-3p, were consistently overexpressed in a subset of six typical lung carcinoids from the external dataset GSE35679. Pathways analysis showed that miRNAs miR-126-3p and miR-146b-5p target genes with a role in the regulation of adaptive immune response.
Conclusion: Our results contribute to the identification of miRNA expression changes in a typical lung carcinoid and its corresponding lymph node metastasis. Down-regulated levels of miR-126-3p and miR-146b-5p and target gene over-expression could play a role in the progression of this case of primary typical lung carcinoid to regional metastasis. Identified miRNAs and target genes are potential candidates for validation in a larger number of cases.
 
Overall design miRNA expression profiles were assessed using TaqMan Low Density Arrays (384 miRNAs) in a rare case of typical lung carcinoid and its corresponding lymph node metastasis, compared to reference normal lung tissues (N=9 samples). Our results were validated in a separate, external dataset (N=19 typical carcinoids compared to 6 normal lung tissues, GSE77380). Furthermore, computational analyses were performed to determine validated miRNA target genes and miRNA-modulated pathways.
Web link https://www.cellphysiolbiochem.com/Articles/000320/
 
Contributor(s) Seneda AL, Lapa RM, Felix TF, Minutentag IW, Campos CF, de Oliveira RA, Oliveira CC, Hasimoto ÉN, Cataneo DC, Cataneo AJ, De Faveri J, Drigo SA, Mur LA, Reis PP
Citation(s) 33398982
Submission date Oct 10, 2019
Last update date Oct 10, 2022
Contact name Ana Laura Seneda
E-mail(s) anaseneda@gmail.com
Organization name São Paulo State University (UNESP), Faculty of Medicine
Department Surgery and Orthopedics
Street address Prof. Mário Rubens Guimarães Montenegro, Avenue - UNESP - Campus de Botucatu
City Botucatu
State/province São Paulo
ZIP/Postal code 18618687
Country Brazil
 
Platforms (1)
GPL18942 Applied Biosystems Taqman Low Density Array Human microRNA Card A+B Set v3.0
Samples (6)
GSM4116573 TUMOR 1A
GSM4116574 TUMOR 1B
GSM4116575 METASTASIS
Relations
BioProject PRJNA576877

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE138708_Non-normalized_data.txt.gz 7.1 Kb (ftp)(http) TXT
GSE138708_fold-change_data.txt.gz 3.0 Kb (ftp)(http) TXT
GSE138708_normalized_data.txt.gz 10.9 Kb (ftp)(http) TXT
Processed data are available on Series record

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