Chromothripsis in Patient WHIM-09

We are studying the natural history, pathogenesis and treatment of patients with WHIM syndrome, an immunodeficiency disorder characterized by warts, hypogammaglobulinemia, recurrent infections and neutropenia usually due to autosomal dominant gain-of-function mutations in chemokine receptor CXCR4. We have identified a patient born with WHIM syndrome and the WHIM mutation CXCR4R334X who has been disease-free for 20 years and who lacks CXCR4R334X in myeloid cells, the cells that drive disease manifestations. She is a genetic and hematopoietic mosaic, since she still has the mutation in lymphoid cells and non-hematopoietic cells. Cytogenetics and microarray analysis revealed that the mechanism of loss of the mutation was deletion of the mutant allele from one copy of chromosome 2. Whole genome sequencing of patient neutrophil and skin fibroblast genomic DNA revealed that the mechanism of deletion was chromothripsis, a process of chromosome shattering resulting in deletions and rearrangements of the non-deleted chromosomal segments. In the patient, this process evidently occurred in a single hematopoietic stem cell (HSC), resulting in deletion of the disease allele CXCR4R334X and one copy of 163 other genes on chromosome 2. This HSC evidently acquired a growth advantage and repopulated the HSC population and the myeloid lineage. Consistent with this, studies using gene targeted mice in competitive bone marrow transplantation experiments revealed that selective Cxcr4 haploinsufficiency (inactivation of one copy of Cxcr4 and not of any other genes) was sufficient to confer a strong engraftment advantage over bone marrow cells from wild type mice as well as bone marrow cells from a mouse model of WHIM syndrome. These results suggest that CXCR4 knockdown may be a useful strategy to enhance bone marrow engraftment in the absence of toxic bone marrow conditioning regimens.]]>
Inclusion criteria: patients with warts, hypogammaglobulinemia, recurrent infections and neutropenia with mutations in CXCR4. Exclusion criteria: none]]>
The first patient ever described with WHIM syndrome, designated WHIM-09, came to the NIH requesting evaluation of two of her three daughters, both of whom have WHIM syndrome. We identified the WHIM mutation CXCR4R334X in whole blood DNA from both daughters but not in the mother who indicated that ~20 years prior to the visit her warts had resolved and her recurrent infections had stopped. Analysis of the medical record indicated that the absolute neutrophil and monocyte counts in the blood of patient WHIM-09, were markedly deficient until ~20 years before coming to NIH, consistent with WHIM syndrome, then began to rise spontaneously reaching a plateau about twice the upper limit of normal. The lymphocyte levels rose minimally during this time. Accordingly, we found that WHIM-09 is a genetic and hematopoietic mosaic, since she still has the mutation CXCR4R334X in lymphoid cells and non-hematopoietic cells. Cytogenetics and microarray analysis revealed that the mechanism of loss of the mutation was deletion of the mutant allele from one copy of chromosome 2. Whole genome sequencing of patient neutrophil and skin fibroblast genomic DNA revealed that the mechanism of deletion was chromothripsis, a process of chromosome shattering resulting in deletions and rearrangements of the non-deleted chromosomal segments. In the patient, this process evidently occurred in a single hematopoietic stem cell (HSC), resulting in deletion of the disease allele CXCR4R334X and one copy of 163 other genes on chromosome 2. This HSC evidently acquired a growth advantage and repopulated the HSC population and the myeloid lineage, but not the lymphoid lineage. Consistent with this, studies using gene targeted mice in competitive bone marrow transplantation experiments revealed that selective Cxcr4 haploinsufficiency (inactivation of one copy of Cxcr4 and not of any other genes) was sufficient to confer a strong engraftment advantage over bone marrow cells from a mouse model of WHIM syndrome as well as bone marrow cells from wild type mice. These results suggest that CXCR4 knockdown may be useful as a general strategy to enhance bone marrow engraftment in the absence of toxic bone marrow conditioning regimens.]]>