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Sala-Torra O, Reddy S, Hung LH, Beppu L, Wu D, Radich J, Yeung KY, Yeung CCS. Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing. PLOS Glob Public Health 2023; 3:e0002267. [PMID: 37699001 PMCID: PMC10497132 DOI: 10.1371/journal.pgph.0002267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/17/2023] [Indexed: 09/14/2023]
Abstract
Recurrent gene fusions are common drivers of disease pathophysiology in leukemias. Identifying these structural variants helps stratify disease by risk and assists with therapy choice. Precise molecular diagnosis in low-and-middle-income countries (LMIC) is challenging given the complexity of assays, trained technical support, and the availability of reliable electricity. Current fusion detection methods require a long turnaround time (7-10 days) or advance knowledge of the genes involved in the fusions. Recent technology developments have made sequencing possible without a sophisticated molecular laboratory, potentially making molecular diagnosis accessible to remote areas and low-income settings. We describe a long-read sequencing DNA assay designed with CRISPR guides to select and enrich for recurrent leukemia fusion genes, that does not need a priori knowledge of the abnormality present. By applying rapid sequencing technology based on nanopores, we sequenced long pieces of genomic DNA and successfully detected fusion genes in cell lines and primary specimens (e.g., BCR::ABL1, PML::RARA, CBFB::MYH11, KMT2A::AFF1) using cloud-based bioinformatics workflows with novel custom fusion finder software. We detected fusion genes in 100% of cell lines with the expected breakpoints and confirmed the presence or absence of a recurrent fusion gene in 12 of 14 patient cases. With our optimized assay and cloud-based bioinformatics workflow, these assays and analyses could be performed in under 8 hours. The platform's portability, potential for adaptation to lower-cost devices, and integrated cloud analysis make this assay a candidate to be placed in settings like LMIC to bridge the need of bedside rapid molecular diagnostics.
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Affiliation(s)
- Olga Sala-Torra
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- University of Washington, Seattle, Washington, United States of America
| | - Shishir Reddy
- University of Washington, Seattle, Washington, United States of America
| | - Ling-Hong Hung
- University of Washington, Seattle, Washington, United States of America
| | - Lan Beppu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - David Wu
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, Washington, United States of America
| | - Jerald Radich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, Washington, United States of America
| | - Ka Yee Yeung
- University of Washington, Seattle, Washington, United States of America
| | - Cecilia C. S. Yeung
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, Washington, United States of America
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Cassaday RD, Zarling LC, Garcia KLA, Sala-Torra O, Stevenson PA, Martino CH, Liu YJ, Fang M, Percival MEM, Halpern AB, Becker PS, Oehler VG, Shustov AR, Cooper JP, Orozco JJ, Hendrie PC, Walter RB, Radich JP, Soma LA, Estey EH. Phase II study of dose-adjusted EPOCH as initial therapy for adults with high-risk acute lymphoblastic leukemia. Leuk Lymphoma 2023; 64:927-937. [PMID: 36938892 PMCID: PMC10357946 DOI: 10.1080/10428194.2023.2189803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/15/2023] [Accepted: 02/25/2023] [Indexed: 03/21/2023]
Abstract
Treatments for adults with newly-diagnosed acute lymphoblastic leukemia (ALL) may be prohibitively toxic and/or resource-intense. To address this, we performed a phase II study of dose-adjusted etoposide, prednisone, vincristine, cyclophosphamide, and doxorubicin (DA-EPOCH). Imatinib or dasatinib was added for Ph + disease; rituximab was added when CD20+. Fifty-three patients were evaluable: 28 with Ph + disease, and 25 with Ph-. All patients had ≥1 high-risk clinical feature. Measurable residual disease-negativity by multiparameter flow cytometry within 4 cycles was achieved in 71% in patients with Ph + ALL and 64% in Ph - ALL. Median overall survival (OS) was 49 months, with a 2-year OS of 71%. Median relapse-free survival (RFS) in the 47 patients that attained morphologic remission was 24 months, with a 2-year RFS of 57%. Early mortality was 2%. In summary, DA-EPOCH yields deep and durable remissions in adults with ALL comparable to some resource-intense strategies but with a low rate of treatment-related death.
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Affiliation(s)
- Ryan D Cassaday
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Lucas C Zarling
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Olga Sala-Torra
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Philip A Stevenson
- Clinical Statistics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Christen H Martino
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yajuan J Liu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Min Fang
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Mary-Elizabeth M Percival
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Anna B Halpern
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Pamela S Becker
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - Vivian G Oehler
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrei R Shustov
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jason P Cooper
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Johnnie J Orozco
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Paul C Hendrie
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Roland B Walter
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jerald P Radich
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Lorinda A Soma
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Elihu H Estey
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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3
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Reddy S, Hung LH, Sala-Torra O, Radich JP, Yeung CC, Yeung KY. A graphical, interactive and GPU-enabled workflow to process long-read sequencing data. BMC Genomics 2021; 22:626. [PMID: 34425749 PMCID: PMC8381503 DOI: 10.1186/s12864-021-07927-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/10/2021] [Indexed: 12/18/2022] Open
Abstract
Background Long-read sequencing has great promise in enabling portable, rapid molecular-assisted cancer diagnoses. A key challenge in democratizing long-read sequencing technology in the biomedical and clinical community is the lack of graphical bioinformatics software tools which can efficiently process the raw nanopore reads, support graphical output and interactive visualizations for interpretations of results. Another obstacle is that high performance software tools for long-read sequencing data analyses often leverage graphics processing units (GPU), which is challenging and time-consuming to configure, especially on the cloud. Results We present a graphical cloud-enabled workflow for fast, interactive analysis of nanopore sequencing data using GPUs. Users customize parameters, monitor execution and visualize results through an accessible graphical interface. The workflow and its components are completely containerized to ensure reproducibility and facilitate installation of the GPU-enabled software. We also provide an Amazon Machine Image (AMI) with all software and drivers pre-installed for GPU computing on the cloud. Most importantly, we demonstrate the potential of applying our software tools to reduce the turnaround time of cancer diagnostics by generating blood cancer (NB4, K562, ME1, 238 MV4;11) cell line Nanopore data using the Flongle adapter. We observe a 29x speedup and a 93x reduction in costs for the rate-limiting basecalling step in the analysis of blood cancer cell line data. Conclusions Our interactive and efficient software tools will make analyses of Nanopore data using GPU and cloud computing accessible to biomedical and clinical scientists, thus facilitating the adoption of cost effective, fast, portable and real-time long-read sequencing. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07927-1.
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Affiliation(s)
| | - Ling-Hong Hung
- School of Engineering and Technology, University of Washington, 98402, Tacoma, WA, USA
| | - Olga Sala-Torra
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 98109, Seattle, WA, USA
| | - Jerald P Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 98109, Seattle, WA, USA.,Clinical Research Division, Kurt Enslein Endowed Chair, Fred Hutchinson Cancer Research Center, 98109, Seattle, WA, USA.,Department of Medicine, University of Washington, 98109, Seattle, WA, USA
| | - Cecilia Cs Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 98109, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, University of Washington, 98109, Seattle, WA, USA
| | - Ka Yee Yeung
- School of Engineering and Technology, University of Washington, 98402, Tacoma, WA, USA.
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Yeung C, Qu X, Sala-Torra O, Woolston D, Radich J, Fang M. Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing. Cancer Med 2021; 10:5629-5642. [PMID: 34288525 PMCID: PMC8366081 DOI: 10.1002/cam4.4101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/03/2022] Open
Abstract
Background Comprehensive molecular and cytogenetic profiling of acute lymphoblastic leukemia (ALL) is important and critical to the current standard of care for patients with B‐acute lymphoblastic leukemia (B‐ALL). Here we propose a rapid process for detecting gene fusions whereby FusionPlex RNA next‐generation sequencing (NGS) and DNA chromosome genomic array testing (CGAT) are combined for a more efficient approach in the management of patients with B‐ALL. Methods We performed RNA NGS and CGAT on 28 B‐ALL samples and, in four patients, compared fixed cell pellets to paired cryo‐preserved samples as a starting material to further assess the utility of cytogenetic fixed pellets for gene expression analysis. Results Among the fixed specimens, when using alternative techniques as references, including karyotype, fluorescence in situ hybridization, CGAT, and RT‐qPCR, fusions were detected by RNA NGS with 100% sensitivity and specificity. In the four paired fixed versus fresh cryopreserved samples, fusions were also 100% concordant. Four of the 28 patients showed mutations that were detected by RNA sequencing and three of four of these mutations had well‐known drug resistance implications. Conclusions We conclude that FusionPlex is a robust and reliable anchored multiplex RNA sequencing platform for use in the detection of fusions in both fresh cryopreserved and cytogenetic fixed pellets. Gene expression data could only be obtained from fresh samples and although limited variant data are available, critical hotspot variants can be determined in conjunction with the fusions.
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Affiliation(s)
- Cecilia Yeung
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA.,University of Washington, Seattle, WA, USA.,Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Xiaoyu Qu
- Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Olga Sala-Torra
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - David Woolston
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - Jerry Radich
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA.,University of Washington, Seattle, WA, USA.,Seattle Cancer Care Alliance, Seattle, WA, USA
| | - Min Fang
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA.,University of Washington, Seattle, WA, USA.,Seattle Cancer Care Alliance, Seattle, WA, USA
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Foss EJ, Radulovic D, Stirewalt DL, Radich J, Sala-Torra O, Pogosova-Agadjanyan EL, Hengel SM, Loeb KR, Deeg HJ, Meshinchi S, Goodlett DR, Bedalov A. Proteomic classification of acute leukemias by alignment-based quantitation of LC-MS/MS data sets. J Proteome Res 2012; 11:5005-10. [PMID: 22900933 DOI: 10.1021/pr300567r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Despite immense interest in the proteome as a source of biomarkers in cancer, mass spectrometry has yet to yield a clinically useful protein biomarker for tumor classification. To explore the potential of a particular class of mass spectrometry-based quantitation approaches, label-free alignment of liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) data sets, for the identification of biomarkers for acute leukemias, we asked whether a label-free alignment algorithm could distinguish known classes of leukemias on the basis of their proteomes. This approach to quantitation involves (1) computational alignment of MS1 peptide peaks across large numbers of samples; (2) measurement of the relative abundance of peptides across samples by integrating the area under the curve of the MS1 peaks; and (3) assignment of peptide IDs to those quantified peptide peaks on the basis of the corresponding MS2 spectra. We extracted proteins from blasts derived from four patients with acute myeloid leukemia (AML, acute leukemia of myeloid lineage) and five patients with acute lymphoid leukemia (ALL, acute leukemia of lymphoid lineage). Mobilized CD34+ cells purified from peripheral blood of six healthy donors and mononuclear cells (MNC) from the peripheral blood of two healthy donors were used as healthy controls. Proteins were analyzed by LC-MS/MS and quantified with a label-free alignment-based algorithm developed in our laboratory. Unsupervised hierarchical clustering of blinded samples separated the samples according to their known biological characteristics, with each sample group forming a discrete cluster. The four proteins best able to distinguish CD34+, AML, and ALL were all either known biomarkers or proteins whose biological functions are consistent with their ability to distinguish these classes. We conclude that alignment-based label-free quantitation of LC-MS/MS data sets can, at least in some cases, robustly distinguish known classes of leukemias, thus opening the possibility that large scale studies using such algorithms can lead to the identification of clinically useful biomarkers.
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Affiliation(s)
- Eric J Foss
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
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6
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Reynaud D, Pietras E, Barry-Holson K, Mir A, Binnewies M, Jeanne M, Sala-Torra O, Radich JP, Passegué E. IL-6 controls leukemic multipotent progenitor cell fate and contributes to chronic myelogenous leukemia development. Cancer Cell 2011; 20:661-73. [PMID: 22094259 PMCID: PMC3220886 DOI: 10.1016/j.ccr.2011.10.012] [Citation(s) in RCA: 242] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 08/09/2011] [Accepted: 10/13/2011] [Indexed: 11/24/2022]
Abstract
Using a mouse model recapitulating the main features of human chronic myelogenous leukemia (CML), we uncover the hierarchy of leukemic stem and progenitor cells contributing to disease pathogenesis. We refine the characterization of CML leukemic stem cells (LSCs) to the most immature long-term hematopoietic stem cells (LT-HSCs) and identify some important molecular deregulations underlying their aberrant behavior. We find that CML multipotent progenitors (MPPs) exhibit an aberrant B-lymphoid potential but are redirected toward the myeloid lineage by the action of the proinflammatory cytokine IL-6. We show that BCR/ABL activity controls Il-6 expression thereby establishing a paracrine feedback loop that sustains CML development. These results describe how proinflammatory tumor environment affects leukemic progenitor cell fate and contributes to CML pathogenesis.
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MESH Headings
- Animals
- Feedback, Physiological
- Fusion Proteins, bcr-abl/metabolism
- Fusion Proteins, bcr-abl/physiology
- Interleukin-6/genetics
- Interleukin-6/metabolism
- Interleukin-6/physiology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Mice
- Multipotent Stem Cells/pathology
- Precursor Cells, B-Lymphoid/metabolism
- Precursor Cells, B-Lymphoid/pathology
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Affiliation(s)
- Damien Reynaud
- The Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, 94143, USA
- Co-corresponding authors: Emmanuelle Passegué, PhD () Damien Reynaud, PhD () University of California San Francisco 35 Medical Way, Regeneration Medicine Building (RMB), Rm. 1017, Box 0667 San Francisco, CA 94143, USA Phone: 415-476-2426 Fax: 415-476-9273
| | - Eric Pietras
- The Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, 94143, USA
| | - Keegan Barry-Holson
- The Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, 94143, USA
| | - Alain Mir
- Fluidigm Corporation, South San Francisco, California, 94080, USA
| | - Mikhail Binnewies
- The Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, 94143, USA
| | - Marion Jeanne
- The Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, 94143, USA
| | - Olga Sala-Torra
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Jerald P. Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Emmanuelle Passegué
- The Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, 94143, USA
- Co-corresponding authors: Emmanuelle Passegué, PhD () Damien Reynaud, PhD () University of California San Francisco 35 Medical Way, Regeneration Medicine Building (RMB), Rm. 1017, Box 0667 San Francisco, CA 94143, USA Phone: 415-476-2426 Fax: 415-476-9273
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Advani AS, Gundacker HM, Sala-Torra O, Radich JP, Lai R, Slovak ML, Lancet JE, Coutre SE, Stuart RK, Mims MP, Stiff PJ, Appelbaum FR. Southwest Oncology Group Study S0530: a phase 2 trial of clofarabine and cytarabine for relapsed or refractory acute lymphocytic leukaemia. Br J Haematol 2010; 151:430-4. [PMID: 21113977 PMCID: PMC3058291 DOI: 10.1111/j.1365-2141.2010.08387.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Clofarabine and cytarabine target different steps in DNA synthesis and replication, are synergistic in vivo, and have non-overlapping toxicities, making this combination a potentially promising treatment for acute lymphocytic leukaemia. Thirty-seven patients were treated. The median age was 41 years, 44% of patients were either in ≥2nd relapse or had refractory disease and 59% of patients had poor risk cytogenetics. Six out of 36 patients (17%) achieved a complete remission with or without complete count recovery; median overall survival was 3 months. Nucleoside transporter expression did not predict outcome. This regimen lacked sufficient activity to warrant further testing.
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Affiliation(s)
- Anjali S Advani
- Hematologic Oncology and Blood Disorders, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44195, USA.
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8
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Sala-Torra O, Gundacker HM, Stirewalt DL, Ladne PA, Pogosova-Agadjanyan EL, Slovak ML, Willman CL, Heimfeld S, Boldt DH, Radich JP. Connective tissue growth factor (CTGF) expression and outcome in adult patients with acute lymphoblastic leukemia. Blood 2007; 109:3080-3. [PMID: 17170128 PMCID: PMC1852221 DOI: 10.1182/blood-2006-06-031096] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We compared the gene expression profile of adult acute lymphoblastic leukemia (ALL) to normal hematopoietic and non-ALL samples using oligonucleotide arrays. Connective tissue growth factor (CTGF) was the highest overexpressed gene in B-cell ALL compared with the other groups, and displayed heterogeneous expression, suggesting it might have prognostic relevance. CTGF expression was examined by quantitative reverse transcriptase-polymerase chain reaction (ORT-PCR) on 79 adult ALL specimens. CTGF expression levels were significantly increased in ALL cases with B-lineage (P < .001), unfavorable cytogenetics (P < .001), and blasts expressing CD34 (P < .001). In a multivariate proportional hazards model, higher CTGF expression levels corresponded to worsening of overall survival (OS; hazard ratio 1.36, for each 10-fold increase in expression; P = .019). Further studies are ongoing to confirm the prognostic value of CTGF expression in ALL and to investigate its role in normal and abnormal lymphocyte biology.
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Affiliation(s)
- Olga Sala-Torra
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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Sala-Torra O, Hanna C, Loken MR, Flowers MED, Maris M, Ladne PA, Mason JR, Senitzer D, Rodriguez R, Forman SJ, Deeg HJ, Radich JP. Evidence of Donor-Derived Hematologic Malignancies after Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2006; 12:511-7. [PMID: 16635786 DOI: 10.1016/j.bbmt.2006.01.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Accepted: 01/12/2006] [Indexed: 01/25/2023]
Abstract
Increasing the upper age limit for recipients of hematopoietic stem cell transplantation (HCT) naturally has also increased the age of the corresponding related donor population. Because aging is a risk factor for malignancies, the risk of transferring preexisting malignant or premalignant hemopoietic clones in the process of HCT might be expected to increase as well. Anecdotal clinical cases of malignancies derived from donor cells in patients undergoing HCT have been published since 1971. In this article, we report 12 new cases that fit 2 different categories: (1) cases in which clones with characteristics of lymphohemopoietic malignancies were transferred from the donors to the recipients and (2) cases in which the malignant clone evolved from healthy donor cells once transplanted into the recipient. Donors in the first group were significantly older than donors in the second group. A more systematic examination of the prevalence and biology of donor malignancies would merit study.
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Affiliation(s)
- Olga Sala-Torra
- Division of Clinical Research, Program in Genetics and Genomics, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
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10
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Stirewalt DL, Pogosova-Agadjanyan EL, Khalid N, Hare DR, Ladne PA, Sala-Torra O, Zhao LP, Radich JP. Single-stranded linear amplification protocol results in reproducible and reliable microarray data from nanogram amounts of starting RNA. Genomics 2004; 83:321-31. [PMID: 14706461 DOI: 10.1016/j.ygeno.2003.08.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The range of scientific questions utilizing DNA microarray techniques is limited by the fact that these methods require 5-40 microg of high-quality total RNA. Thus, methods that reliably amplify the starting RNA amount could expand the applicability of DNA microarray technology. We developed a single-stranded linear amplification protocol (SLAP) that combines the reproducibility of in vitro transcription and the amplification robustness of polymerase chain reactions. We compared SLAP to the NIH-IVT amplification protocol. SLAP displayed excellent conservation of the 5'/3' signal and demonstrated the most robust amplification, producing the recommended amounts of biotin-labeled RNA with as little as 0.002 microg of starting RNA. Both SLAP and NIH-IVT methods demonstrated good reproducibility, but SLAP maintained the highest level of reliability with RNA starting amounts of <0.05 microg. These results suggest that SLAP is an excellent alternative to IVT-based amplification protocols when RNA is limited by small sample size.
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Affiliation(s)
- Derek L Stirewalt
- Clinical Research Division, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98109, USA.
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