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Blood, Vol. 113, Issue 3, 646-648, January 15, 2009
Specific JAK2 mutation (JAK2R683) and multiple gene deletions in Down syndrome acute lymphoblastic leukemia
Blood Kearney et al.
113: 646
Supplemental materials for: Kearney et al
The predicted structure of the JAK2 pseudokinase domain was determined by running the PHYRE protein threading program, based on the crystal structure of ephrin a2 tyrosine kinase which shares 23% sequence identity. Arginine 683 is modelled at the N-terminus of a loop connecting the b7 and b8 antiparallel b-strands within the C-lobe which also accommodates the REED insertion which has been reported as deleted in one DS-ALL case12. The arginine side chain is solvent exposed and possibly interacts with the side chain of Phe 611. However, it does not interact with the Glu-Glu-Asp motif immediately C-terminal to it. Since this domain lacks activity, mutation of Arg683 to either Gly or Ser must influence the activity of the C-terminal domain. One could assume that these mutations (missense and deletion) must alter the inter-domain interactions with the C-terminal kinase domain, in some manner releasing the inhibitory effects exerted by the pseudokinase domain. Alternatively, the mutations could induce an activating conformational change in the kinase. A definitive explanation of how the mutation promotes leukaemia awaits knowledge of the crystal structure.
Files in this Data Supplement:
- Table S1. Clinical and cytogenetic details of DS-ALL cases sequenced for JAK2R683 mutation (PDF, 84.3 KB)
- Table S2. Sequences (PDF, 93.2 KB) -
(A) Primers for candidate gene sequencing. (B) Primer sequences for pyrosequencing analysis.
- Table S3. High-resolution SNP array analysis of DS-ALL cases showing regions of loss or gain (PDF, 38.6 KB)
- Figure S1. 250K Sty SNP array plots from leukaemic DNA of patient 13 showing focal deletion of the PAX5 (A) and ETV6 gene (B) respectively (arrows) (JPG, 53.3 KB)
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GTYPE (Affymetrix) was used for analysis of signal intensity and for genotype calling. For copy number estimates and identification of regions with UPD, the in-house Genome Orientated Laboratory File (GOLF) software package was used (available online at http://bioinformatics.cancerresearchuk.org/cazier01/). Hybridization values were normalized to the median value on each array. Copy number was determined based on the log2 ratio of the signal intensity from the leukemia sample versus the remission sample and was done by visual inspection. Only putative copy-number changes involving at least three SNPs were included. In cases where no remission DNA was available, we used pooled signal intensity of 15 unrelated non-leukaemic DNA samples. In (A) and (B), each dot represents the log2 ratio of one SNP with a moving average of three SNPs. The bottom line represents a log2 ratio of 1, the middle a log2 ratio of 2 and the top a log2 ratio of 4. For PAX5, there was a hemizygous deletion of approximately 120 kb, whereas for ETV6, there was a homozygous deletion involving 5 SNPs. Full SNP genotype data is available at www.icr.ac.uk/array/array.html.
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