Contributions
Abstract: EP319
Type: E-Poster Presentation
Session title: Acute lymphoblastic leukemia - Biology & Translational Research
Background
Intrachromosomal amplification of chromosome 21 (iAMP21) is a rare, but high-risk subtype of pediatric B-cell acute lymphoblastic leukemia (B-ALL). iAMP21 was discovered by routine screening for the ETV6-RUNX1 fusion, resulting in the current definition of iAMP21 as three or more extra copies of RUNX1 on a single abnormal chromosome 21. Using copy number profiling, iAMP21 can also be detected as regions of amplifications, deletions and inversions. It is currently unknown how the abnormal chromosome 21 contributes to development of leukemia.
Aims
We aimed to determine the common region of amplification in iAMP21 patients. In addition, by correlating the chromosome 21 copy number gain, and resulting gene expression change, to genome wide gene expression, we aimed to shed light on the potential leukemic target of the abnormal chromosome 21.
Methods
Copy number aberrations were determined in a population based pediatric B-ALL cohort using array Comparative Genomic Hybridization (aCGH). As an independent cohort, the supplementary SNP array data from Gu et al (Nature genetics, 2020) was used. Gene expression was evaluated using Affymetrix U133 Plus2 expression arrays. Differential gene expression was evaluated using Limma and Globaltest was used to evaluate genome wide gene expression correlations. As an independent cohort, publicly available RNA expression data from B-other and BCR-ABL1-like B-ALL patients from the PeCan database was used.
Results
Within our population based aCGH cohort, 12 out of 398 patients showed an aCGH profile suggestive of iAMP21 (median age = 8.5 years, range = 5-14; median white blood cell count = 7.6 x 109/L, range = 2-129). By scoring their chromosome 21 copy number gain per probe, we identified three regions of a total of 3.9 Mb that were commonly amplified (at least 2 copies gained). A similar strategy was applied to the supplementary SNP array data of 34 pediatric and young adult iAMP21 patients from Gu et al (Nature Genetics, 2019). Combined with the common region of amplification (CRA) determined by Rand et al (n = 18, Blood, 2011), it resulted in a narrowed down CRA of 1.5 Mb, containing 12 protein-coding genes. Interestingly, the CRA was located telomeric from RUNX1, but did not include this gene. Although gained in all patients, in 4 of our 12 iAMP21 patients the highest amplified region was located telomeric from RUNX1. In accordance, RUNX1 expression did not correlate with copy number (p = 0.371, spearman correlation) and was only moderately overexpressed in iAMP21 cases, both in our samples (n = 155 of which 12 iAMP21, fold change (FC) = 1.6, adjusted p-value = 0.030), as well as in the independent PeCan dataset (n = 246 of which 17 iAMP21, FC = 1.4, p-value < 0.001). Only 7 of these 12 protein-coding genes were significantly upregulated (adjusted p-value < 0.01). RIPPLY3 was the highest overexpressed gene (FC = 4.2) within the CRA, confirmed in the independent PeCan dataset (FC = 9.8). The expression of RIPPLY3 was most correlated to the expression of the 1128 differentially expressed probesets in iAMP21 (R = 0.59).
Conclusion
We narrowed down the common region of amplification in iAMP21 B-ALL to 1.5 Mb which surprisingly did not include the RUNX1 gene. Our data suggest that RIPPLY3, a negative regulator of the transcriptional activity of TBX1 and suggested to regulate STAT3 transcriptional activity, is the potential target of the iAMP21 transformation, making it an interesting gene for further functional studies.
Keyword(s): B cell acute lymphoblastic leukemia, Expression, Genomics, Pediatric
Abstract: EP319
Type: E-Poster Presentation
Session title: Acute lymphoblastic leukemia - Biology & Translational Research
Background
Intrachromosomal amplification of chromosome 21 (iAMP21) is a rare, but high-risk subtype of pediatric B-cell acute lymphoblastic leukemia (B-ALL). iAMP21 was discovered by routine screening for the ETV6-RUNX1 fusion, resulting in the current definition of iAMP21 as three or more extra copies of RUNX1 on a single abnormal chromosome 21. Using copy number profiling, iAMP21 can also be detected as regions of amplifications, deletions and inversions. It is currently unknown how the abnormal chromosome 21 contributes to development of leukemia.
Aims
We aimed to determine the common region of amplification in iAMP21 patients. In addition, by correlating the chromosome 21 copy number gain, and resulting gene expression change, to genome wide gene expression, we aimed to shed light on the potential leukemic target of the abnormal chromosome 21.
Methods
Copy number aberrations were determined in a population based pediatric B-ALL cohort using array Comparative Genomic Hybridization (aCGH). As an independent cohort, the supplementary SNP array data from Gu et al (Nature genetics, 2020) was used. Gene expression was evaluated using Affymetrix U133 Plus2 expression arrays. Differential gene expression was evaluated using Limma and Globaltest was used to evaluate genome wide gene expression correlations. As an independent cohort, publicly available RNA expression data from B-other and BCR-ABL1-like B-ALL patients from the PeCan database was used.
Results
Within our population based aCGH cohort, 12 out of 398 patients showed an aCGH profile suggestive of iAMP21 (median age = 8.5 years, range = 5-14; median white blood cell count = 7.6 x 109/L, range = 2-129). By scoring their chromosome 21 copy number gain per probe, we identified three regions of a total of 3.9 Mb that were commonly amplified (at least 2 copies gained). A similar strategy was applied to the supplementary SNP array data of 34 pediatric and young adult iAMP21 patients from Gu et al (Nature Genetics, 2019). Combined with the common region of amplification (CRA) determined by Rand et al (n = 18, Blood, 2011), it resulted in a narrowed down CRA of 1.5 Mb, containing 12 protein-coding genes. Interestingly, the CRA was located telomeric from RUNX1, but did not include this gene. Although gained in all patients, in 4 of our 12 iAMP21 patients the highest amplified region was located telomeric from RUNX1. In accordance, RUNX1 expression did not correlate with copy number (p = 0.371, spearman correlation) and was only moderately overexpressed in iAMP21 cases, both in our samples (n = 155 of which 12 iAMP21, fold change (FC) = 1.6, adjusted p-value = 0.030), as well as in the independent PeCan dataset (n = 246 of which 17 iAMP21, FC = 1.4, p-value < 0.001). Only 7 of these 12 protein-coding genes were significantly upregulated (adjusted p-value < 0.01). RIPPLY3 was the highest overexpressed gene (FC = 4.2) within the CRA, confirmed in the independent PeCan dataset (FC = 9.8). The expression of RIPPLY3 was most correlated to the expression of the 1128 differentially expressed probesets in iAMP21 (R = 0.59).
Conclusion
We narrowed down the common region of amplification in iAMP21 B-ALL to 1.5 Mb which surprisingly did not include the RUNX1 gene. Our data suggest that RIPPLY3, a negative regulator of the transcriptional activity of TBX1 and suggested to regulate STAT3 transcriptional activity, is the potential target of the iAMP21 transformation, making it an interesting gene for further functional studies.
Keyword(s): B cell acute lymphoblastic leukemia, Expression, Genomics, Pediatric