Dataset Information

Chromothripsis in Patient WHIM-09

ABSTRACT:

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 CXCR4^R334X who has been disease-free for 20 years and who lacks CXCR4^R334X 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 CXCR4^R334X 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.

PROVIDER: phs000856 | dbGaP |

SECONDARY ACCESSION(S): PRJNA272464PRJNA272463

REPOSITORIES: dbGaP

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	GapExchange_phs000856.v1.p1.xml	Xml
	dbGaPEx2.1.5.xsd	Other
	Study_Report.phs000856.Chromothripsis_WHIM.v1.p1.MULTI.pdf	Pdf
	manifest_phs000856.Chromothripsis_WHIM.v1.p1.c1.GRU-IRB.pdf	Pdf
	datadict_v2.xsl	Other

Items per page:

1 - 5 of 15

Similar Datasets

Project description:Current therapies for metastatic colorectal cancer only prolong life for approximately 2 years. A more innovative therapy that prolongs life significantly or even cures is needed. Bone marrow transplantation is a curative therapy for patients with leukemias and lymphomas. Tumor eradication in the case of transplantation of the patient’s own marrow (autologous transplantation) is based on the intensive chemotherapy and/or radiotherapy used for conditioning. Tumor eradication in the case of transplantation using the marrow of a normal donor is based on both tumor reduction from conditioning and the immune elimination of tumor cells by T cells in the donor transplant that recognize the foreign tissue antigens expressed by the tumor cells and kill these cells. The use of bone marrow transplantation to treat tumors other than leukemia and lymphoma has been limited, and studies of transplantation of the patient’s own marrow for the treatment of advanced /metastatic breast cancer have not conclusively shown benefit beyond conventional therapy. Recently, the Strober lab developed a preclinical model that effectively treated colon cancer in mice by combining immunotherapy and autologous bone marrow transplantation in order to markedly augment the anti-tumor potency of immunotherapy. They used the CT26 colon cancer as the therapeutic target either as a single subcutaneous tumor nodule, as a disseminated tumor in the lungs and peritoneum, or as a metastatic tumor in the liver depending on the route of administration of the tumor cells in BALB/c mice. Mice were vaccinated mice with established primary tumors or disseminated/ metastatic disease with irradiated tumor cells mixed with the adjuvant CpG, and found that vaccination alone had no effect on tumor growth. Similarly radiation conditioning of tumor bearing hosts followed by transplantation of bone marrow and spleen cells or purified T cells and hematopoietic stem cells from unvaccinated donors of the same strain had no effect. In contrast, radiation conditioning of mice followed by transplantation of hematopoietic and immune cells from donors of the same strain vaccinated with tumor cells and CpG cured almost all subcutaneous primary as well as disseminated and metastatic tumors in the hosts. A similar result was obtained after autologous transplantation of hematopoietic and immune cells from tumor bearing mice that had been vaccinated after tumor establishment. Investigation of tumor infiltrating cells showed that the injected donor T cells do not accumulate in the tumors unless the host has been irradiated before injection. Based on this model, we have assembled a team of Stanford University faculty members with expertise in gastrointestinal cancers, immunotherapy, radiation oncology, and bone marrow transplantation in the Departments of Medicine and Pathology to translate the preclinical findings into a Phase I safety and feasibility clinical study for the treatment of 10 patients with metastatic colorectal cancer. Resected tumor cells will be irradiated and mixed with CpG to create a vaccine. Patients will receive subcutaneous vaccination at weeks 1 and 2 after resection. Six weeks later, immune T cells and then G-CSF "mobilized" purified blood progenitor cells will be harvested from the blood and cryopreserved. If needed patients will receive chemotherapy for tumor reduction. When disease is controlled off chemotherapy, patients will receive a conditioning regimen of fludarabine (30mg/m2 daily x 3 days) followed by intensive fractionated total body irradiation. The dose of fTBI will be escalated using a 3+3 design to ensure safety and will range from 400 to 800 gray. The patient will then undergo hematopoietic and immune cell rescue. They will undergo a third vaccination within 7-14 days after transplant. Thereafter, serial monitoring of tumor burden will continue. Immune monitoring will occur before and after vaccination as well as after transplantation. Tests will include in vitro anti-tumor immune responses of T cells (proliferation, cytotoxicity, cytokine secretion etc.) to stimulation with whole tumor cells and tumor cell lysates pulsed on to antigen presenting cells, anti-tumor antibody responses, and immune reconstitution after transplantation.

Project description:The paper describes a model of tumor invasion to bone marrow. Created by COPASI 4.26 (Build 213) This model is described in the article: Modeling invasion of metastasizing cancer cells to bone marrow utilizing ecological principles Kun-Wan Chen, Kenneth J Pienta Theoretical Biology and Medical Modelling 2011, 8:36 Abstract: Background: The invasion of a new species into an established ecosystem can be directly compared to the steps involved in cancer metastasis. Cancer must grow in a primary site, extravasate and survive in the circulation to then intravasate into target organ (invasive species survival in transport). Cancer cells often lay dormant at their metastatic site for a long period of time (lag period for invasive species) before proliferating (invasive spread). Proliferation in the new site has an impact on the target organ microenvironment (ecological impact) and eventually the human host (biosphere impact). Results: Tilman has described mathematical equations for the competition between invasive species in a structured habitat. These equations were adapted to study the invasion of cancer cells into the bone marrow microenvironment as a structured habitat. A large proportion of solid tumor metastases are bone metastases, known to usurp hematopoietic stem cells (HSC) homing pathways to establish footholds in the bone marrow. This required accounting for the fact that this is the natural home of hematopoietic stem cells and that they already occupy this structured space. The adapted Tilman model of invasion dynamics is especially valuable for modeling the lag period or dormancy of cancer cells. Conclusions: The Tilman equations for modeling the invasion of two species into a defined space have been modified to study the invasion of cancer cells into the bone marrow microenvironment. These modified equations allow a more flexible way to model the space competition between the two cell species. The ability to model initial density, metastatic seeding into the bone marrow and growth once the cells are present, and movement of cells out of the bone marrow niche and apoptosis of cells are all aspects of the adapted equations. These equations are currently being applied to clinical data sets for verification and further refinement of the models. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Dataset Information

Chromothripsis in Patient WHIM-09

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets