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| Status |
Public on Mar 09, 2019 |
| Title |
Gene Expression In Blood From an Individual With β-Thalassemia: an RNA Sequence Analysis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Background: The thalassemias are highly diverse at both the molecular and clinical levels. Many of the HBB mutations that result in β-thalassemia are missense mutations in the coding region of the β-globin gene, but a few cause alternative splicing, and interfere with normal processing of the β-globin transcripts. Transcriptome profiling in individuals affected with β-thalassemia, especially in individuals who carry novel mutations in the HBB, may improve our understanding of the heterogeneity and molecular mechanisms of the disease. Methods: Members of a family with a daughter affected with thalassemia intermedia, although her mother was not clinically affected, were examined for physical characteristics, hematological parameters and β-globin gene sequences. We also characterized genome-wide gene expression in the family using RT-qPCR and high-throughput RNA-sequencing mRNA expression profiling of blood. Results: Clinical findings, hematological indices, DNA and RNA sequence analysis of individuals with β-thalassemia, including the description of a novel mutation in the β-globin gene, which introduces a cryptic donor splice site. More than 300 genes are differentially expressed in β-thalassemic blood with many of the DEGs involved in pathways relevant to the clinical management of β-thalassemia. β-thalassemia shows important similarities and differences with sickle cell disease at the transcriptome level. Conclusions: We described the down-regulation of the β-globin gene in β-thalassemia by RNA-sequencing analysis using a sample from an affected individual and her mother, who have a novel mutation in the HBB that creates a cryptic donor splice site. The daughter has a typical β-thalassemia allele as well, and an unexpectedly severe phenotype. The DEGs are enriched in pathways that are directly or indirectly related to β-thalassemia such as hemopoiesis, heme biosynthesis, response to oxidative stress, inflammatory responses, immune responses, control of circadian rhythm, apoptosis, and other cellular activities. We compare our findings with published results of RNA-Sequencing analysis of sickle cell disease (SCD) and erythroblasts from a KLF1-null neonate with hydrops fetalis, and recognize similarities and differences in their transcriptional expression patterns.
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| Overall design |
Total RNA was isolated from blood using EDTA as an anticoagulant and Trizol reagent (Sigma-Aldrich, Germany). 500ng of the total RNA from each of the daughter (sample D), mother (sample M), and a control individual with normal hematological indices (sample N) was used for RNA-Sequencing library preparation, and the quality of RNA was determined with Bioanalyzer 2100. Libraries for RNA-sequencing were prepared with a KAPA Stranded RNA-sequencing Kit (Illumina), following the manufacture’s instructions. Sequencing was performed on an Illumina HiSeq 2500 system for pair-ended reads with a length of 100 bp (2x100 bp). Pre-processing and data quality control were performed using Illumina proprietary software.
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| Contributor(s) |
Taghavifar F, Hamid M, Shariati G, Metzenberg S, Metzenberg A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Aida Metzenberg |
| E-mail(s) |
aida.metzenberg@csun.edu
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| Phone |
8186773355
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| Organization name |
California State University, Northridge
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| Department |
Biology
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| Lab |
Molecular Genetics Laboratory
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| Street address |
18111 Nordhoff Street
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| City |
Northridge |
| State/province |
CA |
| ZIP/Postal code |
91330-8303 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (3) |
| GSM2531494 |
Daughter (compound heterozygote for two HBB mutations) |
| GSM2531495 |
Mother (Heterozygote for a novel HBB mutation) |
| GSM2531496 |
Normal (an individual with wildtype HBB alleles and normal hematological indices) |
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| Relations |
| BioProject |
PRJNA378716 |
| SRA |
SRP101697 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE96060_S1_file.Expression.txt.gz |
240.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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