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Armstrong RN, Steeples V, Singh S, Sanchi A, Boultwood J, Pellagatti A. Splicing factor mutations in the myelodysplastic syndromes: target genes and therapeutic approaches. Adv Biol Regul 2017; 67:13-29. [PMID: 28986033 DOI: 10.1016/j.jbior.2017.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 10/25/2022]
Abstract
Mutations in splicing factor genes (SF3B1, SRSF2, U2AF1 and ZRSR2) are frequently found in patients with myelodysplastic syndromes (MDS), suggesting that aberrant spliceosome function plays a key role in the pathogenesis of MDS. Splicing factor mutations have been shown to result in aberrant splicing of many downstream target genes. Recent functional studies have begun to characterize the splicing dysfunction in MDS, identifying some key aberrantly spliced genes that are implicated in disease pathophysiology. These findings have led to the development of therapeutic strategies using splicing-modulating agents and rapid progress is being made in this field. Splicing inhibitors are promising agents that exploit the preferential sensitivity of splicing factor-mutant cells to these compounds. Here, we review the known target genes associated with splicing factor mutations in MDS, and discuss the potential of splicing-modulating therapies for these disorders.
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Yip BH, Steeples V, Repapi E, Armstrong RN, Llorian M, Roy S, Shaw J, Dolatshad H, Taylor S, Verma A, Bartenstein M, Vyas P, Cross NC, Malcovati L, Cazzola M, Hellström-Lindberg E, Ogawa S, Smith CW, Pellagatti A, Boultwood J. The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes. J Clin Invest 2017; 127:3557. [PMID: 28862641 DOI: 10.1172/jci96202] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Unnikrishnan A, Papaemmanuil E, Beck D, Deshpande NP, Verma A, Kumari A, Woll PS, Richards LA, Knezevic K, Chandrakanthan V, Thoms JAI, Tursky ML, Huang Y, Ali Z, Olivier J, Galbraith S, Kulasekararaj AG, Tobiasson M, Karimi M, Pellagatti A, Wilson SR, Lindeman R, Young B, Ramakrishna R, Arthur C, Stark R, Crispin P, Curnow J, Warburton P, Roncolato F, Boultwood J, Lynch K, Jacobsen SEW, Mufti GJ, Hellstrom-Lindberg E, Wilkins MR, MacKenzie KL, Wong JWH, Campbell PJ, Pimanda JE. Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes. Cell Rep 2017; 20:572-585. [PMID: 28723562 DOI: 10.1016/j.celrep.2017.06.067] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/20/2017] [Accepted: 06/22/2017] [Indexed: 11/30/2022] Open
Abstract
Myelodysplastic syndromes and chronic myelomonocytic leukemia are blood disorders characterized by ineffective hematopoiesis and progressive marrow failure that can transform into acute leukemia. The DNA methyltransferase inhibitor 5-azacytidine (AZA) is the most effective pharmacological option, but only ∼50% of patients respond. A response only manifests after many months of treatment and is transient. The reasons underlying AZA resistance are unknown, and few alternatives exist for non-responders. Here, we show that AZA responders have more hematopoietic progenitor cells (HPCs) in the cell cycle. Non-responder HPC quiescence is mediated by integrin α5 (ITGA5) signaling and their hematopoietic potential improved by combining AZA with an ITGA5 inhibitor. AZA response is associated with the induction of an inflammatory response in HPCs in vivo. By molecular bar coding and tracking individual clones, we found that, although AZA alters the sub-clonal contribution to different lineages, founder clones are not eliminated and continue to drive hematopoiesis even in complete responders.
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Bhagat TD, Chen S, Bartenstein M, Barlowe AT, Von Ahrens D, Choudhary GS, Tivnan P, Amin E, Marcondes AM, Sanders MA, Hoogenboezem RM, Kambhampati S, Ramachandra N, Mantzaris I, Sukrithan V, Laurence R, Lopez R, Bhagat P, Giricz O, Sohal D, Wickrema A, Yeung C, Gritsman K, Aplan P, Hochedlinger K, Yu Y, Pradhan K, Zhang J, Greally JM, Mukherjee S, Pellagatti A, Boultwood J, Will B, Steidl U, Raaijmakers MHGP, Deeg HJ, Kharas MG, Verma A. Epigenetically Aberrant Stroma in MDS Propagates Disease via Wnt/β-Catenin Activation. Cancer Res 2017; 77:4846-4857. [PMID: 28684528 DOI: 10.1158/0008-5472.can-17-0282] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/06/2017] [Accepted: 06/30/2017] [Indexed: 11/16/2022]
Abstract
The bone marrow microenvironment influences malignant hematopoiesis, but how it promotes leukemogenesis has not been elucidated. In addition, the role of the bone marrow stroma in regulating clinical responses to DNA methyltransferase inhibitors (DNMTi) is also poorly understood. In this study, we conducted a DNA methylome analysis of bone marrow-derived stromal cells from myelodysplastic syndrome (MDS) patients and observed widespread aberrant cytosine hypermethylation occurring preferentially outside CpG islands. Stroma derived from 5-azacytidine-treated patients lacked aberrant methylation and DNMTi treatment of primary MDS stroma enhanced its ability to support erythroid differentiation. An integrative expression analysis revealed that the WNT pathway antagonist FRZB was aberrantly hypermethylated and underexpressed in MDS stroma. This result was confirmed in an independent set of sorted, primary MDS-derived mesenchymal cells. We documented a WNT/β-catenin activation signature in CD34+ cells from advanced cases of MDS, where it associated with adverse prognosis. Constitutive activation of β-catenin in hematopoietic cells yielded lethal myeloid disease in a NUP98-HOXD13 mouse model of MDS, confirming its role in disease progression. Our results define novel epigenetic changes in the bone marrow microenvironment, which lead to β-catenin activation and disease progression of MDS. Cancer Res; 77(18); 4846-57. ©2017 AACR.
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Choudhary GS, Bhagat TD, Samson MES, Gordon S, Ahrens DV, Pradhan K, Shastri A, Pellagatti A, Boutlwood J, Booher RN, Steidl U, Verma A. Abstract 127: Efficacy of novel IRAK4 inhibitor CA4948 in AML and MDS. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Myelodysplastic syndrome (MDS) & Acute Myeloid Leukemia (AML) are hematologic malignancies that arise from a population of aberrant hematopoietic stem cells (HSCs). Overactivated innate immune signaling pathways such as IRAK1, TRAF6, IL1RAP, S100A9 and IL8 have been demonstrated in MDS/AML and play important roles in propagation of disease. IRAK4 (interleukin-1 receptor-associated kinase 4), is a protein kinase involved in signaling innate immune responses and forms a critical signaling complex with IRAK1. To determine its role in disease pathobiology, we analyzed transcriptomic data from CD34+ stem and progenitor cells from 183 MDS patients and found significantly increased expression of IRAK4 in MDS samples belonging to the high risk RAEB category (Refractory anemia with excess of blasts, N=80, P Value <0.05 when compared to healthy controls). Furthermore, increased IRAK4 expression was predictive of significantly adverse prognosis (P value < 0.05, median survival of 2.6 years compared to 5.2 years for group with lower IRAK4). Clinical correlations revealed that MDS patients with higher IRAK4 expression in stem/progenitor cells had significantly higher transfusion dependence and had higher leukemic blast counts (Mean Blast Count 9.3% vs 3.9%, P<0.05), further demonstrating IRAK4 to be an adverse prognostic marker in MDS. IRAK4 was also overexpressed in highly purified FACS sorted disease initiating stem cell populations (Long Term-HSC, CD34+/CD38-/CD90+/Lin –ve) from AML patients with complex cytogenetics when compared to healthy controls.
To functionally determine the role of IRAK4 in MDS/AML pathogenesis, we utilized CA-4948, a potent, oral, small-molecule inhibitor of IRAK4, to assess the effect of inhibiting IRAK4 catalytic activity. In vitro, CA-4948 blocked downstream NF-κB pathway signaling, including secretion of proinflammatory cytokines, in Toll-like receptor stimulated THP1 leukemic cells. CA-4948 was tested in clonogenic assays from primary MDS and AML samples. MDS and AML are associated with block in differentiation that leads to cytopenias that are the cause of morbidity in these patients. Treatment with CA-4948 led to increased erythroid and myeloid differentiation in a majority of samples. Furthermore, drug treatment led to decreased viability of MDS/AML stem cells (CD34+/CD38-/Lin-ve) In vivo studies using a THP1 leukemia xenograft model in NSG mice demonstrated that CA-4948 was well tolerated and led to significantly decreased disease burden after 6 weeks of treatment.
In conclusion, we demonstrate that IRAK4 is upregulated in stem and progenitor cells in MDS and AML and is an adverse prognostic marker. Importantly, a novel, specific, inhibitor of IRAK4 shows preclinical in vitro and in vivo efficacy in MDS and AML models.
Citation Format: Gaurav S. Choudhary, Tushar D. Bhagat, Maria Elena S. Samson, Shanisha Gordon, Dagny Von Ahrens, Kith Pradhan, Aditi Shastri, Andrea Pellagatti, Jacqueline Boutlwood, Robert N. Booher, Ulrich Steidl, Amit Verma. Efficacy of novel IRAK4 inhibitor CA4948 in AML and MDS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 127. doi:10.1158/1538-7445.AM2017-127
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Yip BH, Steeples V, Repapi E, Armstrong RN, Llorian M, Roy S, Shaw J, Dolatshad H, Taylor S, Verma A, Bartenstein M, Vyas P, Cross NC, Malcovati L, Cazzola M, Hellström-Lindberg E, Ogawa S, Smith CW, Pellagatti A, Boultwood J. The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes. J Clin Invest 2017; 127:2206-2221. [PMID: 28436936 PMCID: PMC5451246 DOI: 10.1172/jci91363] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/21/2017] [Indexed: 12/23/2022] Open
Abstract
Mutations of the splicing factor–encoding gene U2AF1 are frequent in the myelodysplastic syndromes (MDS), a myeloid malignancy, and other cancers. Patients with MDS suffer from peripheral blood cytopenias, including anemia, and an increasing percentage of bone marrow myeloblasts. We studied the impact of the common U2AF1S34F mutation on cellular function and mRNA splicing in the main cell lineages affected in MDS. We demonstrated that U2AF1S34F expression in human hematopoietic progenitors impairs erythroid differentiation and skews granulomonocytic differentiation toward granulocytes. RNA sequencing of erythroid and granulomonocytic colonies revealed that U2AF1S34F induced a higher number of cassette exon splicing events in granulomonocytic cells than in erythroid cells. U2AF1S34F altered mRNA splicing of many transcripts that were expressed in both cell types in a lineage-specific manner. In hematopoietic progenitors, the introduction of isoform changes identified in the U2AF1S34F target genes H2AFY, encoding an H2A histone variant, and STRAP, encoding serine/threonine kinase receptor–associated protein, recapitulated phenotypes associated with U2AF1S34F expression in erythroid and granulomonocytic cells, suggesting a causal link. Furthermore, we showed that isoform modulation of H2AFY and STRAP rescues the erythroid differentiation defect in U2AF1S34F MDS cells, suggesting that splicing modulators could be used therapeutically. These data have critical implications for understanding MDS phenotypic heterogeneity and support the development of therapies targeting splicing abnormalities.
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Shastri A, Teixeira M, Bhattacharya S, Ramachandra N, Lopez R, Ravipati G, Bhagat T, Choudhary G, Bartenstein M, Gordon-Mitchell S, Pradhan K, Pellagatti A, Boultwood J, Kim Y, Woessner R, Will B, Steidl U, Verma A. Therapeutic Targeting of MDS & AML Stem Cells with an Antisense Inhibitor of STAT3. Leuk Res 2017. [DOI: 10.1016/s0145-2126(17)30128-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Pellagatti A, Steeples V, Sharma E, Repapi E, Yip B, Armstrong R, Dolatshad H, Lockstone H, Taylor S, Giagounidis A, Vyas P, Papaemmanuil E, Woll P, Killick S, Malcovati L, Hellström-Lindberg E, Cazzola M, Smith C, Boultwood J. Identification of Aberrant Splicing Events in Myelodysplastic Syndrome Patients with Splicing Factor Gene Mutations. Leuk Res 2017. [DOI: 10.1016/s0145-2126(17)30129-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Scharenberg C, Giai V, Pellagatti A, Saft L, Dimitriou M, Jansson M, Jädersten M, Grandien A, Douagi I, Neuberg DS, LeBlanc K, Boultwood J, Karimi M, Jacobsen SEW, Woll PS, Hellström-Lindberg E. Progression in patients with low- and intermediate-1-risk del(5q) myelodysplastic syndromes is predicted by a limited subset of mutations. Haematologica 2016; 102:498-508. [PMID: 27884971 PMCID: PMC5394951 DOI: 10.3324/haematol.2016.152025] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 11/15/2016] [Indexed: 12/24/2022] Open
Abstract
A high proportion of patients with lower-risk del(5q) myelodysplastic syndromes will respond to treatment with lenalidomide. The median duration of transfusion-independence is 2 years with some long-lasting responses, but almost 40% of patients progress to acute leukemia by 5 years after starting treatment. The mechanisms underlying disease progression other than the well-established finding of small TP53-mutated subclones at diagnosis remain unclear. We studied a longitudinal cohort of 35 low- and intermediate-1-risk del(5q) patients treated with lenalidomide (n=22) or not (n=13) by flow cytometric surveillance of hematopoietic stem and progenitor cell subsets, targeted sequencing of mutational patterns, and changes in the bone marrow microenvironment. All 13 patients with disease progression were identified by a limited number of mutations in TP53, RUNX1, and TET2, respectively, with PTPN11 and SF3B1 occurring in one patient each. TP53 mutations were found in seven of nine patients who developed acute leukemia, and were documented to be present in the earliest sample (n=1) and acquired during lenalidomide treatment (n=6). By contrast, analysis of the microenvironment, and of hematopoietic stem and progenitor cells by flow cytometry was of limited prognostic value. Based on our data, we advocate conducting a prospective study aimed at investigating, in a larger number of cases of del(5q) myelodysplastic syndromes, whether the detection of such mutations before and after lenalidomide treatment can guide clinical decision-making.
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Valletta S, Dolatshad H, Bartenstein M, Yip BH, Bello E, Gordon S, Yu Y, Shaw J, Roy S, Scifo L, Schuh A, Pellagatti A, Fulga TA, Verma A, Boultwood J. ASXL1 mutation correction by CRISPR/Cas9 restores gene function in leukemia cells and increases survival in mouse xenografts. Oncotarget 2016; 6:44061-71. [PMID: 26623729 PMCID: PMC4792541 DOI: 10.18632/oncotarget.6392] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/08/2015] [Indexed: 12/03/2022] Open
Abstract
Recurrent somatic mutations of the epigenetic modifier and tumor suppressor ASXL1 are common in myeloid malignancies, including chronic myeloid leukemia (CML), and are associated with poor clinical outcome. CRISPR/Cas9 has recently emerged as a powerful and versatile genome editing tool for genome engineering in various species. We have used the CRISPR/Cas9 system to correct the ASXL1 homozygous nonsense mutation present in the CML cell line KBM5, which lacks ASXL1 protein expression. CRISPR/Cas9-mediated ASXL1 homozygous correction resulted in protein re-expression with restored normal function, including down-regulation of Polycomb repressive complex 2 target genes. Significantly reduced cell growth and increased myeloid differentiation were observed in ASXL1 mutation-corrected cells, providing new insights into the role of ASXL1 in human myeloid cell differentiation. Mice xenografted with mutation-corrected KBM5 cells showed significantly longer survival than uncorrected xenografts. These results show that the sole correction of a driver mutation in leukemia cells increases survival in vivo in mice. This study provides proof-of-concept for driver gene mutation correction via CRISPR/Cas9 technology in human leukemia cells and presents a strategy to illuminate the impact of oncogenic mutations on cellular function and survival.
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Pellagatti A, Boultwood J. Splicing factor gene mutations in the myelodysplastic syndromes: impact on disease phenotype and therapeutic applications. Adv Biol Regul 2016; 63:59-70. [PMID: 27639445 DOI: 10.1016/j.jbior.2016.08.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 01/05/2023]
Abstract
Splicing factor gene mutations are the most frequent mutations found in patients with the myeloid malignancy myelodysplastic syndrome (MDS), suggesting that spliceosomal dysfunction plays a major role in disease pathogenesis. The aberrantly spliced target genes and deregulated cellular pathways associated with the commonly mutated splicing factor genes in MDS (SF3B1, SRSF2 and U2AF1) are being identified, illuminating the molecular mechanisms underlying MDS. Emerging data from mouse modeling studies indicate that the presence of splicing factor gene mutations can lead to bone marrow hematopoietic stem/myeloid progenitor cell expansion, impaired hematopoiesis and dysplastic differentiation that are hallmarks of MDS. Importantly, recent evidence suggests that spliceosome inhibitors and splicing modulators may have therapeutic value in the treatment of splicing factor mutant myeloid malignancies.
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McGraw K, Cheng CH, Chen A, Genovese G, Cluzeau T, Lin HY, Przychodzen B, Mallo M, Arenillas L, Mohamedali A, Ades L, Basiorka A, Irvine B, Sallman D, Padron E, Sokol L, Pellagatti A, Brest C, Raynaud S, Nilsson B, Boultwood J, Ebert B, Sole F, Fenaux P, Mufti G, Maciejewski J, Kanetsky P, List A. Abstract 2570: Identification of genetic polymorphisms associated with myelodysplastic syndromes by genome-wide association study. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The myelodysplastic syndromes (MDS) are senescence-dependent stem cell malignancies. Although germ line mutations in RUNX1, CEBPA, ETV6, or GATA2 may underlie familial cases, inherited genetic polymorphisms influencing MDS susceptibility has not been evaluated. We performed the first genome-wide association study (GWAS) to identify single nucleotide polymorphisms (SNPs) linked to MDS predisposition.
Methods: DNA from 1361 MDS patients from 9 international centers was genotyped on the Affymetrix Genome-Wide Human SNP Array 6.0; all patients signed informed consent. Data on 4597 healthy controls genotyped on the same platform were obtained from the Database of Genotypes and Phenotypes (dbGaP). Applying standard quality control metrics and limiting to individuals of European ancestry, we analysed 999 MDS patients and 4,309 controls at 545,924 markers. We used logistic regression to determine associations with MDS after appropriate adjustment assuming an additive genetic model.
Results: We identified 15 SNPs at 9 loci associated with MDS, including rs6780298 (3q13; p = 5.0×10-6) and rs1206819 (20q13; p = 1.54×10-6) that mapped to the intragenic regions of MORC1 and EYA2, respectively; and rs2473784 (1p31; p = 3.32×10-7) that mapped downstream of DEPDC1. Other hits (p≤5×10-6) at 4q28, 5p14, 9p22, 6p22, 10q21 are in or near SLC7A11, GUSBP1, SH3GL2, MOG and TRIM27, respectively. Using publicly available gene expression profiling data, we confirmed all of these genes are expressed in the hematopoietic compartment and MORC1, EYA2, DEPDC1, and SH3GL2 are increased in leukemic samples suggesting that variation in these genes may be functionally relevant in myeloid malignancies. Notably, EYA2 (20q13) flanks the commonly deleted region in del(20q) MDS and has oncogenic properties in solid tumors. SH3GL2 is very highly upregulated in leukemic samples and interacts with Dynamin-1, a GTP-binding protein involved in cellular trafficking and is similarly associated with solid tumorigenesis. To validate our observed associations, we analysed the 15 SNP markers in an independent set of 12,385 individuals of whom 117 developed hematologic malignancy (including MDS) during follow up. The markers at 1p31 including rs2473784 and 4 others in strong linkage disequilibrium were associated with individuals who developed hematologic malignancy (p<0.05). One other SNP (rs404660) showing an association in both the MDS GWAS analysis and the hematologic malignancy dataset is also currently under further investigation.
Conclusions: These data provide the first genome-wide identification of germline variants associated with MDS. Current work is underway to replicate these findings in an independent sample set of MDS patients and healthy controls. If confirmed, these SNPs may serve as biomarkers to identify individuals at risk for MDS and potentially support new prevention strategies.
Citation Format: Kathy McGraw, Chia-Ho Cheng, Ann Chen, Giulio Genovese, Thomas Cluzeau, Hui-Yi Lin, Bartlomiej Przychodzen, Mar Mallo, Leonor Arenillas, Azim Mohamedali, Lionel Ades, Ashley Basiorka, Brittany Irvine, David Sallman, Eric Padron, Lubomir Sokol, Andrea Pellagatti, Chimene Brest, Sophie Raynaud, Bjorn Nilsson, Jacqueline Boultwood, Benjamin Ebert, Francesc Sole, Pierre Fenaux, Ghulam Mufti, Jaroslaw Maciejewski, Peter Kanetsky, Alan List. Identification of genetic polymorphisms associated with myelodysplastic syndromes by genome-wide association study. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2570.
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Bachegowda L, Morrone K, Winski SL, Mantzaris I, Bartenstein M, Ramachandra N, Giricz O, Sukrithan V, Nwankwo G, Shahnaz S, Bhagat T, Bhattacharyya S, Assal A, Shastri A, Gordon-Mitchell S, Pellagatti A, Boultwood J, Schinke C, Yu Y, Guha C, Rizzi J, Garrus J, Brown S, Wollenberg L, Hogeland G, Wright D, Munson M, Rodriguez M, Gross S, Chantry D, Zou Y, Platanias L, Burgess LE, Pradhan K, Steidl U, Verma A. Pexmetinib: A Novel Dual Inhibitor of Tie2 and p38 MAPK with Efficacy in Preclinical Models of Myelodysplastic Syndromes and Acute Myeloid Leukemia. Cancer Res 2016; 76:4841-4849. [PMID: 27287719 DOI: 10.1158/0008-5472.can-15-3062] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 05/20/2016] [Indexed: 11/16/2022]
Abstract
Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) suppress normal hematopoietic activity in part by enabling a pathogenic inflammatory milieu in the bone marrow. In this report, we show that elevation of angiopoietin-1 in myelodysplastic CD34(+) stem-like cells is associated with higher risk disease and reduced overall survival in MDS and AML patients. Increased angiopoietin-1 expression was associated with a transcriptomic signature similar to known MDS/AML stem-like cell profiles. In seeking a small-molecule inhibitor of this pathway, we discovered and validated pexmetinib (ARRY-614), an inhibitor of the angiopoietin-1 receptor Tie-2, which was also found to inhibit the proinflammatory kinase p38 MAPK (which is overactivated in MDS). Pexmetinib inhibited leukemic proliferation, prevented activation of downstream effector kinases, and abrogated the effects of TNFα on healthy hematopoietic stem cells. Notably, treatment of primary MDS specimens with this compound stimulated hematopoiesis. Our results provide preclinical proof of concept for pexmetinib as a Tie-2/p38 MAPK dual inhibitor applicable to the treatment of MDS/AML. Cancer Res; 76(16); 4841-9. ©2016 AACR.
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Radujkovic A, Dietrich S, Andrulis M, Benner A, Longerich T, Pellagatti A, Nanda K, Giese T, Germing U, Baldus S, Boultwood J, Ho AD, Dreger P, Luft T. Expression of CDKN1C in the bone marrow of patients with myelodysplastic syndrome and secondary acute myeloid leukemia is associated with poor survival after conventional chemotherapy. Int J Cancer 2016; 139:1402-13. [DOI: 10.1002/ijc.30181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/22/2016] [Accepted: 04/25/2016] [Indexed: 01/15/2023]
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Botezatu L, Michel LC, Makishima H, Schroeder T, Germing U, Haas R, van der Reijden B, Marneth AE, Bergevoet SM, Jansen JH, Przychodzen B, Wlodarski M, Niemeyer C, Platzbecker U, Ehninger G, Unnikrishnan A, Beck D, Pimanda J, Hellström-Lindberg E, Malcovati L, Boultwood J, Pellagatti A, Papaemmanuil E, Le Coutre P, Kaeda J, Opalka B, Möröy T, Dührsen U, Maciejewski J, Khandanpour C. GFI1(36N) as a therapeutic and prognostic marker for myelodysplastic syndrome. Exp Hematol 2016; 44:590-595.e1. [PMID: 27080012 PMCID: PMC4917888 DOI: 10.1016/j.exphem.2016.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 03/31/2016] [Accepted: 04/03/2016] [Indexed: 01/06/2023]
Abstract
Inherited gene variants play an important role in malignant diseases. The transcriptional repressor growth factor independence 1 (GFI1) regulates hematopoietic stem cell (HSC) self-renewal and differentiation. A single-nucleotide polymorphism of GFI1 (rs34631763) generates a protein with an asparagine (N) instead of a serine (S) at position 36 (GFI136N) and has a prevalence of 3%–5% among Caucasians. Because GFI1 regulates myeloid development, we examined the role of GFI136N on the course of MDS disease. To this end, we determined allele frequencies of GFI136N in four independent MDS cohorts from the Netherlands and Belgium, Germany, the ICGC consortium, and the United States. The GFI136N allele frequency in the 723 MDS patients genotyped ranged between 9% and 12%. GFI136N was an independent adverse prognostic factor for overall survival, acute myeloid leukemia-free survival, and event-free survival in a univariate analysis. After adjustment for age, bone marrow blast percentage, IPSS score, mutational status, and cytogenetic findings, GFI136N remained an independent adverse prognostic marker. GFI136S homozygous patients exhibited a sustained response to treatment with hypomethylating agents, whereas GFI136N patients had a poor sustained response to this therapy. Because allele status of GFI136N is readily determined using basic molecular techniques, we propose inclusion of GFI136N status in future prospective studies for MDS patients to better predict prognosis and guide therapeutic decisions. GFI136N is present in about 9%–12% of all Caucasian patients with myelodysplastic syndrome. GFI136N is an independent, adverse prognostic factor for survival. GFI136N patients with myelodysplastic syndrome respond poorly to hypomethylating agents.
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Smith H, Board M, Pellagatti A, Turley H, Boultwood J, Callaghan R. The Effects of Severe Hypoxia on Glycolytic Flux and Enzyme Activity in a Model of Solid Tumors. J Cell Biochem 2016; 117:1890-901. [PMID: 26755257 DOI: 10.1002/jcb.25488] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/06/2016] [Indexed: 12/14/2022]
Abstract
Solid tumors contend with, and adapt to, a hostile micro-environment that includes limited availability of nutrient fuels and oxygen. The presence of hypoxia (O2 <5%) stabilizes the transcription factor Hif1 and results in numerous cellular adaptations including increased flux of glucose through glycolysis. Increasingly, more sophisticated analysis of tumor oxygenation has revealed large gradients of oxygen tension and significant regions under severe hypoxia (O2 ∼0.1%). The present investigation has demonstrated a significant increase in the glycolytic flux rate when tumor spheroids were exposed to 0.1% O2 . The severe hypoxia was associated with uniform pimonidazole adduct formation and elevated levels of Hif1α and c-Myc. This resulted in elevated expression of GLUT and MCT transporters, in addition to increased activity of PFK1 in comparison to that observed in normoxia. However, the protein expression and enzymatic capacity of HK2, G6PDH, PK, and LDH were all reduced by severe hypoxia. Clearly, the effects of exposure to severe hypoxia lead to a significantly abridged Hif1 response, yet one still able to elevate glycolytic flux and prevent loss of intermediates to anabolism. J. Cell. Biochem. 117: 1890-1901, 2016. © 2016 Wiley Periodicals, Inc.
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Boultwood J, Pellagatti A. Clinical associations of CSNK1A1 mutation in myelodysplastic syndrome. LANCET HAEMATOLOGY 2015; 2:e182-3. [PMID: 26688092 DOI: 10.1016/s2352-3026(15)00070-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 11/17/2022]
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Dolatshad H, Pellagatti A, Fernandez-Mercado M, Yip BH, Malcovati L, Attwood M, Przychodzen B, Sahgal N, Kanapin AA, Lockstone H, Scifo L, Vandenberghe P, Papaemmanuil E, Smith CWJ, Campbell PJ, Ogawa S, Maciejewski JP, Cazzola M, Savage KI, Boultwood J. Disruption of SF3B1 results in deregulated expression and splicing of key genes and pathways in myelodysplastic syndrome hematopoietic stem and progenitor cells. Leukemia 2015; 29:1798. [PMID: 26242354 PMCID: PMC5780642 DOI: 10.1038/leu.2015.178] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Pellagatti A, Dolatshad H, Yip BH, Valletta S, Boultwood J. Application of genome editing technologies to the study and treatment of hematological disease. Adv Biol Regul 2015; 60:122-134. [PMID: 26433620 DOI: 10.1016/j.jbior.2015.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/07/2015] [Accepted: 09/09/2015] [Indexed: 11/29/2022]
Abstract
Genome editing technologies have advanced significantly over the past few years, providing a fast and effective tool to precisely manipulate the genome at specific locations. The three commonly used genome editing technologies are Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), and the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Cas9 (CRISPR/Cas9) system. ZFNs and TALENs consist of endonucleases fused to a DNA-binding domain, while the CRISPR/Cas9 system uses guide RNAs to target the bacterial Cas9 endonuclease to the desired genomic location. The double-strand breaks made by these endonucleases are repaired in the cells either by non-homologous end joining, resulting in the introduction of insertions/deletions, or, if a repair template is provided, by homology directed repair. The ZFNs, TALENs and CRISPR/Cas9 systems take advantage of these repair mechanisms for targeted genome modification and have been successfully used to manipulate the genome in human cells. These genome editing tools can be used to investigate gene function, to discover new therapeutic targets, and to develop disease models. Moreover, these genome editing technologies have great potential in gene therapy. Here, we review the latest advances in the application of genome editing technology to the study and treatment of hematological disorders.
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Cabrero M, Yu Y, Verma A, Yang H, Colla S, Jia Y, Zheng H, Bohannan Z, Ganan-Gomez I, Futreal A, Takahashi K, Chin L, Kantarjian H, Pellagatti A, Bowman T, Boultwood J, Garcia-Manero G, Wei Y. Downregulation of Protection of Telomeres 1 expression in myelodysplastic syndromes with 7q deletion. Br J Haematol 2015; 173:161-5. [PMID: 26105212 DOI: 10.1111/bjh.13574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bello E, Pellagatti A, Shaw J, Mecucci C, Kušec R, Killick S, Giagounidis A, Raynaud S, Calasanz MJ, Fenaux P, Boultwood J. CSNK1A1 mutations and gene expression analysis in myelodysplastic syndromes with del(5q). Br J Haematol 2015; 171:210-214. [PMID: 26085061 PMCID: PMC4744770 DOI: 10.1111/bjh.13563] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/26/2015] [Indexed: 01/16/2023]
Abstract
Mutations of CSNK1A1, a gene mapping to the commonly deleted region of the 5q‐ syndrome, have been recently described in patients with del(5q) myelodysplastic syndromes (MDS). Haploinsufficiency of Csnk1a1 in mice has been shown to result in β‐catenin activation and expansion of haematopoietic stem cells (HSC). We have screened a large cohort of 104 del(5q) MDS patients and have identified mutations of CSNK1A1 in five cases (approximately 5%). We have shown up‐regulation of β‐catenin target genes in the HSC of patients with del(5q) MDS. Our data further support a central role of CSNK1A1 in the pathogenesis of MDS with del(5q).
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Pellagatti A, Roy S, Di Genua C, Burns A, McGraw K, Valletta S, Larrayoz MJ, Fernandez-Mercado M, Mason J, Killick S, Mecucci C, Calasanz MJ, List A, Schuh A, Boultwood J. Targeted resequencing analysis of 31 genes commonly mutated in myeloid disorders in serial samples from myelodysplastic syndrome patients showing disease progression. Leukemia 2015; 30:247-50. [PMID: 25991409 PMCID: PMC4705423 DOI: 10.1038/leu.2015.129] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Pellagatti A, Dolatshad H, Valletta S, Boultwood J. Application of CRISPR/Cas9 genome editing to the study and treatment of disease. Arch Toxicol 2015; 89:1023-34. [DOI: 10.1007/s00204-015-1504-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 03/05/2015] [Indexed: 12/14/2022]
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Pellagatti A, Roy S, Di Genua C, Burns A, McGraw K, Larrayoz M, Fernandez-Mercado M, Valletta S, Mason J, Killick S, Mecucci C, Calasanz M, List A, Schuh A, Boultwood J. 52 TARGETED RE-SEQUENCING ANALYSIS OF 31 GENES COMMONLY MUTATED IN MYELOID DISORDERS IN SERIAL SAMPLES FROM MYELODYSPLASTIC SYNDROME PATIENTS WITH DISEASE PROGRESSION. Leuk Res 2015. [DOI: 10.1016/s0145-2126(15)30053-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Pellagatti A, Boultwood J. The molecular pathogenesis of the myelodysplastic syndromes. Eur J Haematol 2015; 95:3-15. [DOI: 10.1111/ejh.12515] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2014] [Indexed: 02/07/2023]
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