The controlled collection and processing of clinical specimens from patients with myeloid leukemia and myelodysplastic syndrome continues to be a critical activity forthe accurate, efficient, and comprehensive acquisition of genomic data required for this program project. Similarly, a repository of quality controlled and standardized gene expression, genomic copy number, genotyping, and epigenetic data corresponding to these specimens will continue to aid in elucidating the genomic basis of AML and MDS. Procedural enhancements and operation within a regulated laboratory environment will accelerate the transition of key genomic findings to application in clinical trials. Accordingly, this Core has two Specific Aims:
Specific Aim 1. We will collect, store, and process tissue specimens from patients and families with AML and MDS seen at this institution. We will include malignant cell populations from bone marrow aspirates, peripheral blood, and extramedullary sites as well as skin punch biopsy and buccal lavage specimens representing non-malignant cell populations. Serum and plasma will be collected for future proteomic biomarker studies. Specimens will be collected throughout each patient's disease course (initial presentation, remission, relapse/refractory disease) and where appropriate, archival specimens from previous malignancies will be retrieved. Specimens will be processed to cellular RNA (mRN/VncRNA), genomic DNA, and protein extracts as required for each study. Cellular populations will also be viably frozen for future xenograft studies. Particular attention to specimen procurement (e.g. rapid processing of leukemia cells to preserve transcript profiles) and high standards of quality control will be practiced.
Specific Aim 2 : Using microarray platforms, we will generate whole transcriptome expression (mRNA, miRNA), whole genome copy number and genotyping, and whole epigenome DNA methylation data. Affymetrix Exon 1 .OST and miRNA 2.0 arrays will be used to generate quantitative transcriptional profiles. Affymetrix SNP 6.0 arrays will generate genomic copy number, loss of heterozygosity (LOH), and genotype data, lllumina Infinium HumanMethylation450 arrays will generate epigenome-wide DNA methylation data. While massively parallel sequencing approaches will be performed for primary tumor specimens in Projects 1-4, use of these microarray platforms will be concentrated in experiments with multiple conditions (e.g., chemotherapy sensitivity, xenograft studies) and for susceptibility studies (Project 3) to best allocate grant resources.

Public Health Relevance

Core B will continue to provide several functions critical for the success of this Program Project and, ultimately, for the better understanding of the genetic and epigenetic basis of AML. We will continue to accrue a large inventory of patient material and to generate targeted gene expression, genotyping, and epigenetic microarray data for experiments proposed herein, all tracked and maintained by a state ofthe art database. While this growing catalog of patient biospecimens and associated molecular data will be of tremendous use to participants in this Program Project, the resources generated may be leveraged by other investigators focused on acute myeloid leukemias through other, independent initiatives.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Program Projects (P01)
Project #
2P01CA101937-10
Application #
8528767
Study Section
Special Emphasis Panel (ZCA1-RPRB-J (J1))
Project Start
Project End
Budget Start
2013-04-09
Budget End
2014-03-31
Support Year
10
Fiscal Year
2013
Total Cost
$225,309
Indirect Cost
$104,397
Name
Washington University
Department
Type
DUNS #
068552207
City
Saint Louis
State
MO
Country
United States
Zip Code
63130
Fisher, D A C; Malkova, O; Engle, E K et al. (2017) Mass cytometry analysis reveals hyperactive NF Kappa B signaling in myelofibrosis and secondary acute myeloid leukemia. Leukemia 31:1962-1974
Uy, G L; Duncavage, E J; Chang, G S et al. (2017) Dynamic changes in the clonal structure of MDS and AML in response to epigenetic therapy. Leukemia 31:872-881
Cole, Christopher B; Russler-Germain, David A; Ketkar, Shamika et al. (2017) Haploinsufficiency for DNA methyltransferase 3A predisposes hematopoietic cells to myeloid malignancies. J Clin Invest 127:3657-3674
Spencer, David H; Russler-Germain, David A; Ketkar, Shamika et al. (2017) CpG Island Hypermethylation Mediated by DNMT3A Is a Consequence of AML Progression. Cell 168:801-816.e13
Bandyopadhyay, Shovik; Li, Junjie; Traer, Elie et al. (2017) Cholesterol esterification inhibition and imatinib treatment synergistically inhibit growth of BCR-ABL mutation-independent resistant chronic myelogenous leukemia. PLoS One 12:e0179558
Duncavage, Eric J; Uy, Geoffrey L; Petti, Allegra A et al. (2017) Mutational landscape and response are conserved in peripheral blood of AML and MDS patients during decitabine therapy. Blood 129:1397-1401
Shirai, Cara Lunn; White, Brian S; Tripathi, Manorama et al. (2017) Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome. Nat Commun 8:14060
Schroeder, Mark A; Choi, Jaebok; Staser, Karl et al. (2017) The Role of Janus Kinase Signaling in Graft-Versus-Host Disease and Graft Versus Leukemia. Biol Blood Marrow Transplant :
Zhang, Jin; Griffith, Malachi; Miller, Christopher A et al. (2017) Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes. Exp Hematol 55:19-33
Ali, Alaa M; Weisel, Daniel; Gao, Feng et al. (2017) Patterns of infectious complications in acute myeloid leukemia and myelodysplastic syndromes patients treated with 10-day decitabine regimen. Cancer Med 6:2814-2821

Showing the most recent 10 out of 113 publications