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| Status |
Public on May 22, 2024 |
| Title |
MIR4435-2HG as a novel predictive biomarker of chemotherapy response and death in pediatric B-cell ALL [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
B-cell acute lymphoid leukemias (B-ALL) are the most common neoplastic diseases in children. Survival rates in Hispanics are lower than in non-Hispanic children. It is, therefore, necessary to find predictive and prognostic biomarkers of relapse and death in this population. Our aim was to identify biomarkers of treatment response, which may also predict relapse and death, through identifying differentially expressed and methylated genes between patients who responded or did not respond to induction treatment. DNA and RNA samples were extracted from 28 bone marrow samples from Hispanic children newly diagnosed with B-ALL. mRNA was sequenced using the NextSeq2000 Illumina platform. Bisulfite-treated DNA was annealed to Illumina Infinium EPIC Methylation chips. Gene expression and differential methylation were compared between responders and non-responders at day 15 and at the end of induction chemotherapy. DAPK1, CNKSR3, MIR4435-HG2, CTHRC1, NPDC1, SLC45A3, ITGA6, and ASCL2 were overexpressed and hypomethylated in non-responders. The overexpression of MIR4435-2HG, DAPK1, ASCL2, SCL45A3, CNKSR3, and NPDC1 can predict non-response at day 15 and refractoriness. Additionally, higher expression of MIR4435-2HG increases the probability of non-response, death, and the risk of death. DAPK1, CNKSR3, and MIR4435-2HG are also overexpressed in relapse samples. Finally, MIR4435-2HG overexpression, together with positive minimal residual disease, is associated with poorer survival, and together with high expression of DAPK1 and ASCL2, it could improve the risk classification of patients with normal karyotype. In conclusion, MIR4435-2HG is a potential predictive and prognostic biomarker in children with B-ALL, and its detection at diagnosis could improve survival rates in our patients
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| Overall design |
26 fresh bone marrow samples.
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| Contributor(s) |
Torres-Llanos YX, Zabaleta J, Cruz-Rodriguez N, Quijano SM, Guzman PC, de los Reyes I, Poveda N, Infante A, Lopez L, Combita AL |
| Citation(s) |
38745909 |
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| Submission date |
Apr 05, 2023 |
| Last update date |
May 22, 2024 |
| Contact name |
Jovanny Zabaleta |
| E-mail(s) |
jzabal@lsuhsc.edu
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| Phone |
504-210 2979
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| Organization name |
Louisiana State University Health Sciences Center
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| Department |
Cancer Center/Interdiscipliary Oncology
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| Lab |
LCRC 909
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| Street address |
1700 Tulane Ave.
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| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
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| Platforms (1) |
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| Samples (26)
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| This SubSeries is part of SuperSeries: |
| GSE229056 |
MIR4435-2HG as a novel predictive biomarker of chemotherapy response and death in pediatric B-cell ALL |
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| Relations |
| BioProject |
PRJNA952635 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE229046_XimenaTorresLlanos_AllSamples_Raw_counts.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE229046_XimenaTorres_Llanos_AllSamples_Normalized_counts.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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