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Eulalio T, Sun MW, Gevaert O, Greicius MD, Montine TJ, Nachun D, Montgomery SB. regionalpcs: improved discovery of DNA methylation associations with complex traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.590171. [PMID: 38746367 PMCID: PMC11092597 DOI: 10.1101/2024.05.01.590171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
We have developed the regional principal components (rPCs) method, a novel approach for summarizing gene-level methylation. rPCs address the challenge of deciphering complex epigenetic mechanisms in diseases like Alzheimer's disease (AD). In contrast to traditional averaging, rPCs leverage principal components analysis to capture complex methylation patterns across gene regions. Our method demonstrated a 54% improvement in sensitivity over averaging in simulations, offering a robust framework for identifying subtle epigenetic variations. Applying rPCs to the AD brain methylation data in ROSMAP, combined with cell type deconvolution, we uncovered 838 differentially methylated genes associated with neuritic plaque burden-significantly outperforming conventional methods. Integrating methylation quantitative trait loci (meQTL) with genome-wide association studies (GWAS) identified 17 genes with potential causal roles in AD, including MS4A4A and PICALM. Our approach is available in the Bioconductor package regionalpcs, opening avenues for research and facilitating a deeper understanding of the epigenetic landscape in complex diseases.
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Affiliation(s)
- Tiffany Eulalio
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Min Woo Sun
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Olivier Gevaert
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Michael D Greicius
- Department of Neurology & Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Daniel Nachun
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
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Taib N, Merhi M, Inchakalody V, Mestiri S, Hydrose S, Makni-Maalej K, Raza A, Sahir F, Azizi F, Nizamuddin PB, Fernandes Q, Yoosuf ZSKM, Almoghrabi S, Al-Zaidan L, Shablak A, Uddin S, Maccalli C, Al Homsi MU, Dermime S. Treatment with decitabine induces the expression of stemness markers, PD-L1 and NY-ESO-1 in colorectal cancer: potential for combined chemoimmunotherapy. J Transl Med 2023; 21:235. [PMID: 37004094 PMCID: PMC10067322 DOI: 10.1186/s12967-023-04073-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND The mechanism of tumor immune escape and progression in colorectal cancer (CRC) is widely investigated in-vitro to help understand and identify agents that might play a crucial role in response to treatment and improve the overall survival of CRC patients. Several mechanisms of immune escape and tumor progression, including expression of stemness markers, inactivation of immunoregulatory genes by methylation, and epigenetic silencing, have been reported in CRC, indicating the potential of demethylating agents as anti-cancer drugs. Of these, a chemotherapeutic demethylating agent, Decitabine (DAC), has been reported to induce a dual effect on both DNA demethylation and histone changes leading to an increased expression of target biomarkers, thus making it an attractive anti-tumorigenic drug. METHODS We compared the effect of DAC in primary 1076 Col and metastatic 1872 Col cell lines isolated and generated from patients' tumor tissues. Both cell lines were treated with DAC, and the expression of the NY-ESO-1 cancer-testis antigen, the PD-L1 immunoinhibitory marker, and the CD44, Nanog, KLF-4, CD133, MSI-1 stemness markers were analyzed using different molecular and immunological assays. RESULTS DAC treatment significantly upregulated stemness markers in both primary 1076 Col and meta-static 1872 Col cell lines, although a lower effect occurred on the latter: CD44 (7.85 fold; ***p = 0.0001 vs. (4.19 fold; *p = 0.0120), Nanog (4.1 fold; ***p < 0.0001 vs.1.69 fold; ***p = 0.0008), KLF-4 (4.33 fold; ***p < 0.0001 vs.2.48 fold; ***p = 0.0005), CD133 (16.77 fold; ***p = 0.0003 vs.6.36 fold; *p = 0.0166), and MSI-1 (2.33 fold; ***p = 0.0003 vs.2.3 fold; ***p = 0.0004), respectively. Interestingly, in the metastatic 1872 Col cells treated with DAC, the expression of both PD-L1 and NY-ESO-1 was increased tenfold (*p = 0.0128) and fivefold (***p < 0.0001), respectively. CONCLUSIONS We conclude that the upregulation of both stemness and immune checkpoint markers by DAC treatment on CRC cells might represent a mechanism of immune evasion. In addition, induction of NY-ESO-1 may represent an immuno-therapeutic option in metastatic CRC patients. Finally, the combination of DAC and anti-PD-1/anti-PD-L1 antibodies treatment should represent a potential therapeutic intervention for this group of patients.
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Affiliation(s)
- Nassiba Taib
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Maysaloun Merhi
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Varghese Inchakalody
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Sarra Mestiri
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Shereena Hydrose
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Karama Makni-Maalej
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Afsheen Raza
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Fairooz Sahir
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Fouad Azizi
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Parveen B Nizamuddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Queenie Fernandes
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- College of Medicine, Qatar University, 2713, Doha, Qatar
| | - Zeenath Safira K M Yoosuf
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, 34110, Doha, Qatar
| | - Salam Almoghrabi
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Lobna Al-Zaidan
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Alaaeldin Shablak
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, 2030, Doha, Qatar
- Laboratory Animal Research Center, Qatar University, 2713, Doha, Qatar
| | - Cristina Maccalli
- Laboratory of Immune and Biological Therapy, Human Immunology Department, Research Branch, Sidra Medicine, 26999, Doha, Qatar
| | | | - Said Dermime
- Translational Cancer Research Facility, National Center for Cancer Care and Research/Translational Research Institute, Hamad Medical Corporation, 2030, Doha, Qatar.
- National Center for Cancer Care and Research, Hamad Medical Corporation, 2030, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, 34110, Doha, Qatar.
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Benton CB, Thomas DA, Yang H, Ravandi F, Rytting M, O'Brien S, Franklin AR, Borthakur G, Dara S, Kwari M, Pierce SR, Jabbour E, Kantarjian H, Garcia-Manero G. Safety and clinical activity of 5-aza-2'-deoxycytidine (decitabine) with or without Hyper-CVAD in relapsed/refractory acute lymphocytic leukaemia. Br J Haematol 2014; 167:356-65. [PMID: 25066676 DOI: 10.1111/bjh.13050] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/23/2014] [Indexed: 12/31/2022]
Abstract
To test the safety and activity of 5-aza-2'-deoxycytidine (decitabine) in patients with relapsed/refractory acute lymphocytic leukaemia (ALL), we conducted a phase 1 study with two parts: administering decitabine alone or in combination with Hyper-CVAD (fractionated cyclophosphamide, vincristine, doxorubicin and dexamethasone alternating with high-dose methotrexate and cytarabine). Patients participated in either part of the study or in both parts sequentially. In the initial part, decitabine was administered intravenously at doses of 10-120 mg/m(2) per d for 5 d every other week in cycles of 28 d. In the combination part, patients were treated on the first 5 d of Hyper-CVAD with intravenous decitabine at 5-60 mg/m(2) per d. A total of 39 patients received treatment in the study: 14 in the first part only, 16 sequentially in both parts and 9 in the second part only. Decitabine was tolerated at all doses administered, and grade 3 or 4 toxic effects included non-life-threatening hepatotoxicity and hyperglycaemia. Induction of DNA hypomethylation was observed at doses of decitabine up to 80 mg/m(2) . Some patients who had previously progressed on Hyper-CVAD alone achieved a complete response when decitabine was added. Decitabine alone or given with Hyper-CVAD is safe and has clinical activity in patients with advanced ALL.
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Affiliation(s)
- Christopher B Benton
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Marrone A, Dokal I. Dyskeratosis congenita: a disorder of telomerase deficiency and its relationship to other diseases. ACTA ACUST UNITED AC 2014. [DOI: 10.1586/17469872.1.3.463] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Epigenetics in Friedreich's Ataxia: Challenges and Opportunities for Therapy. GENETICS RESEARCH INTERNATIONAL 2013; 2013:852080. [PMID: 23533785 PMCID: PMC3590757 DOI: 10.1155/2013/852080] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/10/2013] [Indexed: 11/17/2022]
Abstract
Friedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disorder caused by homozygous expansion of a GAA·TTC trinucleotide repeat within the first intron of the FXN gene, leading to reduced FXN transcription and decreased levels of frataxin protein. Recent advances in FRDA research have revealed the presence of several epigenetic modifications that are either directly or indirectly involved in this FXN gene silencing. Although epigenetic marks may be inherited from one generation to the next, modifications of DNA and histones can be reversed, indicating that they are suitable targets for epigenetic-based therapy. Unlike other trinucleotide repeat disorders, such as Huntington disease, the large expansions of GAA·TTC repeats in FRDA do not produce a change in the frataxin amino acid sequence, but they produce reduced levels of normal frataxin. Therefore, transcriptional reactivation of the FXN gene provides a good therapeutic option. The present paper will initially focus on the epigenetic changes seen in FRDA patients and their role in the silencing of FXN gene and will be concluded by considering the potential epigenetic therapies.
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Iastrebner M, Jang JH, Nucifora E, Kim K, Sackmann F, Kim DH, Orlando S, Jung CW, Basquiera A, Klein G, Santini F, Bernard HI, Korin J, Taborda G. Decitabine in myelodysplastic syndromes and chronic myelomonocytic leukemia: Argentinian/South Korean multi-institutional clinical experience. Leuk Lymphoma 2010; 51:2250-7. [PMID: 20929328 DOI: 10.3109/10428194.2010.524324] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This multicenter, open-label study evaluated the efficacy and safety of decitabine in patients from Argentina and South Korea with myelodysplastic syndromes or chronic myelomonocytic leukemia. Of 106 patients who received decitabine 20 mg/m(2) intravenously over 1 h once daily for 5 days in 4-week cycles, 99 patients were evaluable after receiving at least two cycles. The overall improvement rate was 35% (19% complete response +4% marrow complete response +4% partial response +8% hematologic improvement). Overall survival at 2 years was 71%. Treatment-related adverse events included febrile neutropenia, thrombocytopenia and bleeding, asthenia, fatigue, and eosinophilia. After complete response (CR), three patients received an allogeneic stem cell transplant. Four patients who relapsed after CR responded to decitabine retreatment. Acute myelogenous leukemia developed during follow-up in 21% of patients. Decitabine in a 5-day outpatient administration schedule was effective and well tolerated in typical clinical practice settings in South America and Asia.
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Nolte F, Hofmann WK. Molecular mechanisms involved in the progression of myelodysplastic syndrome. Future Oncol 2010; 6:445-55. [PMID: 20222800 DOI: 10.2217/fon.09.175] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of diseases characterized by ineffective hematopoiesis presenting with peripheral cytopenias in combination with a hyperplastic bone marrow. MDS patients have an increased risk of disease evolution to acute leukemia. Strong efforts have been made to gain further insights into the pathobiology of MDS. Development and progression of MDS to acute myeloid leukemia is suggested to be a multistep alteration to hematopoietic stem cells consisting of class I and class II alterations: the former targeting genes that are involved in signal transduction (e.g., FLT3, RAS and KIT), whereas the latter affect transcription factors (e.g., RUNX, RARA, EVI1 and WT1). These alterations consist of not only genomic mutations but also epigenetic aberrations, which can lead to reversible gene silencing. However, whether numerical and structural alterations of chromosomes and/or single genes or epigenetic changes represent the initiating event or, more likely, secondary events remains part of the discussion. Accumulation of such defects may finally cause the leukemic transformation of MDS.
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Affiliation(s)
- Florian Nolte
- Department of Hematology & Oncology, University Hospital Mannheim, Theodor-Kutzer-Ufer 1–3, 68167 Mannheim, Germany
| | - Wolf-K Hofmann
- Department of Hematology & Oncology, University Hospital Mannheim, Theodor-Kutzer-Ufer 1–3, 68167 Mannheim, Germany
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Amatori S, Papalini F, Lazzarini R, Donati B, Bagaloni I, Rippo MR, Procopio A, Pelicci PG, Catalano A, Fanelli M. Decitabine, differently from DNMT1 silencing, exerts its antiproliferative activity through p21 upregulation in malignant pleural mesothelioma (MPM) cells. Lung Cancer 2009; 66:184-90. [PMID: 19233506 DOI: 10.1016/j.lungcan.2009.01.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 10/21/2008] [Accepted: 01/19/2009] [Indexed: 01/12/2023]
Abstract
Malignant pleural mesothelioma (MPM) is a locally aggressive neoplasm, principally linked to asbestos fibres exposure. Strong evidences associate this pollutant with induction of DNA breaks, aberrant chromosomes segregation and important chromosomal rearrangements, considered crucial events in malignant transformation. A considerable contribution to cellular transformation in MPM is also given by the presence of high genomic instability, as well as by the increased DNA methylation, and consequent decreased expression, of tumor-suppressor genes. In this study we first demonstrated that MPM cells are characterized by a decreased methylation level of pericentromeric DNA sequences which can justify, at least in part, the genomic instability observed in this neoplasia. Concomitantly, we found a paradoxical increased expression of DNMT1, the most expressed DNA methyltransferases in MPM cells, DNMT3a and all five isoforms of DNMT3b. Thus, we compared two experimental strategies, DNMT1 silencing and usage of a demethylating agent (5-aza-2'-deoxycytidine or Decitabine), both theoretically able to revert the locally hypermethylated phenotype and considered potential future therapeutic approaches for MPM. Interestingly, both strategies substantially decrease cell survival of MPM cells but the antitumor activity of Decitabine, differently from DNMT1 silencing, is mediated, at least in part, by a p53-independent p21 upregulation, and is characterized by the arrest of MPM cells at the G2/M phase of the cell cycle. These results indicate that the two approaches act probably through different mechanisms and, thus, that DNMT1 silencing can be considered an effective alternative to Decitabine for cancer treatment.
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Affiliation(s)
- S Amatori
- Molecular Pathology and Oncology Lab. M.Paola, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61032 Fano, PU, Italy
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Koppel A, Schiller G. Myelodysplastic syndrome: An update on diagnosis and therapy. Curr Hematol Malig Rep 2009; 4:10-6. [PMID: 20425433 DOI: 10.1007/s11899-009-0002-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Myelodysplastic syndromes (MDS) are a diverse group of disorders characterized by disorderly and ineffective hematopoiesis. Patients suffer morbidity from associated cytopenias that result in an increased risk of infection, transfusion-dependent anemia, and bleeding. Despite the variable risk of transformation to acute leukemia, the majority of deaths are due to bone marrow failure. No truly effective treatment exists for MDS, and therapy usually focuses on reducing or preventing complications of the disease. Identification of potential cellular and molecular targets, such as epigenetic modification, has led to novel therapeutic approaches in recent years. An increasing number of diagnostic markers, prognostic parameters, and therapeutic strategies are available and becoming widely accepted.
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Affiliation(s)
- Ahrin Koppel
- Department of Hematology/Oncology, University of California, Los Angeles, Box 957059, Suite 2333 PVUB, Los Angeles, CA 90095, USA.
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Abstract
Myelodysplastic syndromes (MDS) are a diverse group of disorders characterized by disorderly and ineffective hematopoiesis. Patients suffer morbidity from associated cytopenias that result in an increased risk of infection, transfusion-dependent anemia, and bleeding. Despite the variable risk of transformation to acute leukemia, the majority of deaths are due to bone marrow failure. No truly effective treatment exists for MDS, and therapy usually focuses on reducing or preventing complications of the disease. Identification of potential cellular and molecular targets, such as epigenetic modification, has led to novel therapeutic approaches in recent years. An increasing number of diagnostic markers, prognostic parameters, and therapeutic strategies are available and becoming widely accepted.
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Affiliation(s)
- Ahrin Koppel
- Department of Hematology/Oncology, University of California, Los Angeles, Box 957059, Suite 2333 PVUB, Los Angeles, CA 90095, USA.
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12
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Epi-drugs to fight cancer: from chemistry to cancer treatment, the road ahead. Int J Biochem Cell Biol 2008; 41:199-213. [PMID: 18790076 DOI: 10.1016/j.biocel.2008.08.020] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 08/08/2008] [Accepted: 08/08/2008] [Indexed: 12/16/2022]
Abstract
In addition to genetic events, a variety of epigenetic events have been widely reported to contribute to the onset of many diseases including cancer. DNA methylation and histone modifications (such as acetylation, methylation, sumoylation, and phosphorylation) involving chromatin remodelling are among the most studied epigenetic mechanisms for regulation of gene expression leading, when altered, to some diseases. Epigenetic therapy tries to reverse the aberrations followed to the disruption of the balance of the epigenetic signalling ways through the use of both natural compounds and synthetic molecules, active on specific epi-targets. Such epi-drugs are, for example, inhibitors of DNA methyltransferases, histone deacetylases, histone acetyltransferases, histone methyltransferases, and histone demethylases. In this review we will focus on the chemical aspects of such molecules, joined to their effective (or potential) application in cancer therapy.
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Al-Ali HK, Brand R, van Biezen A, Finke J, Boogaerts M, Fauser AA, Egeler M, Cahn JY, Arnold R, Biersack H, Niederwieser D, de Witte T. A retrospective comparison of autologous and unrelated donor hematopoietic cell transplantation in myelodysplastic syndrome and secondary acute myeloid leukemia: a report on behalf of the Chronic Leukemia Working Party of the European Group for Blood and Marrow Transplantation (EBMT). Leukemia 2007; 21:1945-51. [PMID: 17611571 DOI: 10.1038/sj.leu.2404774] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hematopoietic cell transplantation (HCT) is an effective treatment for myelodysplasia (MDS) and secondary acute myeloid leukemia (sAML). In this study, outcome of 593 patients with MDS/sAML after autologous and allogeneic HCT from a matched unrelated donor (MUD) were compared. A total of 167 (28%) patients received HCT from MUD without prior chemotherapy (MUD-U). The rest received HCT in first complete remission (CR1) (Autologous (Auto-CR1), n=290 (49%), HCT from MUD (MUD-CR1), n=136 (23%)). Survival at 3 years was best in MUD-CR1 (50%) compared to Auto-CR1 (41%) and MUD-U (40%) (P=0.01). Similarly, disease-free survival was 44% for MUD-CR1 compared to Auto-CR1 (28%) and MUD-U (34%) (P=0.03). Treatment-related mortality was 17% in Auto-CR1 compared to MUD-CR1 (38%) and MUD-U (49%) (P<0.001). Relapse for Auto-CR1 was 62% compared to 24 and 30% for MUD-CR1 and MUD-U, respectively (P<0.001). Outcome was best for patients with low tumor burden transplanted 6-12 months after diagnosis. Factors influencing outcome at 3 years were mainly significant in the first 6 months. Only, relapse after autologous HCT remained constant over time. Outcomes after allogeneic HCT in patients of 20-40 and >40 years were similar. Autologous and Allogeneic HCT from MUD offer the possibility of long-term survival to patients with MDS/sAML.
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Affiliation(s)
- H K Al-Ali
- Department of Hematology/Oncology, University of Leipzig, Leipzig, Germany.
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Fenaux P, Raza A, Mufti GJ, Aul C, Germing U, Kantarjian H, Cripe L, Kerstens R, De Porre P, Kurzrock R. A multicenter phase 2 study of the farnesyltransferase inhibitor tipifarnib in intermediate- to high-risk myelodysplastic syndrome. Blood 2007; 109:4158-63. [PMID: 17264294 DOI: 10.1182/blood-2006-07-035725] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
This multicenter phase 2 study evaluated the use of tipifarnib (R115777) in patients with poor-risk myelodysplastic syndrome (MDS; French-American-British classification). Patients (n = 82) received tipifarnib 300 mg orally twice daily for the first 21 days of each 28-day cycle. Twenty-six patients (32%) responded to tipifarnib: 12 (15%) complete responses (CRs) and 14 (17%) hematologic improvements; 37 patients (45%) had stable disease (modified International Working Group criteria, 2006). Among the 12 CRs, the median response duration was 11.5 months (range, 2.0-21.9 months), the median time to progression was 12.4 months (range, 3.9-23.8 months), and 7 were still alive at time of analysis (all > 3 years). Median overall survival was 11.7 months (95% CI, 9.4-15.0). Grade 3-4 neutropenia (18%) and thrombocytopenia (32%) were the most common treatment-related adverse events; severe nonhematologic adverse events were rarely reported. In this study, durable responses and acceptable side effects were observed. Tipifarnib is an active agent for the treatment of patients with intermediate- to high-risk MDS.
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Gore SD, Baylin S, Sugar E, Carraway H, Miller CB, Carducci M, Grever M, Galm O, Dauses T, Karp JE, Rudek MA, Zhao M, Smith BD, Manning J, Jiemjit A, Dover G, Mays A, Zwiebel J, Murgo A, Weng LJ, Herman JG. Combined DNA methyltransferase and histone deacetylase inhibition in the treatment of myeloid neoplasms. Cancer Res 2006; 66:6361-9. [PMID: 16778214 DOI: 10.1158/0008-5472.can-06-0080] [Citation(s) in RCA: 413] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Optimal reexpression of most genes silenced through promoter methylation requires the sequential application of DNA methyltransferase inhibitors followed by histone deacetylase inhibitors in tumor cell cultures. Patients with myelodysplastic syndrome or acute myeloid leukemia (AML) were treated with the methyltransferase inhibitor 5-azacitidine (aza-CR) followed by the histone deacetylase inhibitor sodium phenylbutyrate. Major responses associated with cytogenetic complete response developed in patients receiving prolonged dosing schedules of aza-CR. Bisulfite sequencing of the p15 promoter in marrow DNA during the first cycle of treatment showed heterogeneous allelic demethylation in three responding patients, suggesting ongoing demethylation within the tumor clone, but no demethylation in two nonresponders. Six of six responding patients with pretreatment methylation of p15 or CDH-1 promoters reversed methylation during the first cycle of therapy (methylation-specific PCR), whereas none of six nonresponders showed any demethylation. Gene demethylation correlated with the area under the aza-CR plasma concentration-time curve. Administration of both drugs was associated with induction of acetylation of histones H3 and H4. This study provides the first demonstration that molecular mechanisms responsible for responses to DNA methyltransferase/histone deacetylase inhibitor combinations may include reversal of aberrant epigenetic gene silencing. The promising percentage of major hematologic responses justifies the testing of such combinations in prospective randomized trials.
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Affiliation(s)
- Steven D Gore
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland 21287, USA.
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Kantarjian H, Issa JPJ, Rosenfeld CS, Bennett JM, Albitar M, DiPersio J, Klimek V, Slack J, de Castro C, Ravandi F, Helmer R, Shen L, Nimer SD, Leavitt R, Raza A, Saba H. Decitabine improves patient outcomes in myelodysplastic syndromes: results of a phase III randomized study. Cancer 2006; 106:1794-803. [PMID: 16532500 DOI: 10.1002/cncr.21792] [Citation(s) in RCA: 1162] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Aberrant DNA methylation, which results in leukemogenesis, is frequent in patients with myelodysplastic syndromes (MDS) and is a potential target for pharmacologic therapy. Decitabine indirectly depletes methylcytosine and causes hypomethylation of target gene promoters. METHODS A total of 170 patients with MDS were randomized to receive either decitabine at a dose of 15 mg/m2 given intravenously over 3 hours every 8 hours for 3 days (at a dose of 135 mg/m2 per course) and repeated every 6 weeks, or best supportive care. Response was assessed using the International Working Group criteria and required that response criteria be met for at least 8 weeks. RESULTS Patients who were treated with decitabine achieved a significantly higher overall response rate (17%), including 9% complete responses, compared with supportive care (0%) (P < .001). An additional 12 patients who were treated with decitabine (13%) achieved hematologic improvement. Responses were durable (median, 10.3 mos) and were associated with transfusion independence. Patients treated with decitabine had a trend toward a longer median time to acute myelogenous leukemia (AML) progression or death compared with patients who received supportive care alone (all patients, 12.1 mos vs. 7.8 mos [P = 0.16]; those with International Prognostic Scoring System intermediate-2/high-risk disease, 12.0 mos vs. 6.8 mos [P = 0.03]; those with de novo disease, 12.6 mos vs. 9.4 mos [P = 0.04]; and treatment-naive patients, 12.3 mos vs. 7.3 mos [P = 0.08]). CONCLUSIONS Decitabine was found to be clinically effective in the treatment of patients with MDS, provided durable responses, and improved time to AML transformation or death. The duration of decitabine therapy may improve these results further.
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Affiliation(s)
- Hagop Kantarjian
- Department of Leukemia, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA.
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Current Awareness in Hematological Oncology. Hematol Oncol 2005. [DOI: 10.1002/hon.731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Issa JP. Optimizing therapy with methylation inhibitors in myelodysplastic syndromes: dose, duration, and patient selection. ACTA ACUST UNITED AC 2005; 2 Suppl 1:S24-9. [PMID: 16341237 DOI: 10.1038/ncponc0355] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Accepted: 08/30/2005] [Indexed: 11/09/2022]
Abstract
Azacitidine (Vidaza, Pharmion Corp., Boulder, CO, USA) and decitabine (Dacogentrade mark, SuperGen, Inc., Dublin, CA, USA, and MGI Pharma, Inc., Bloomington, MN, USA) are DNA methyltransferase (DNMT) inhibitors that have clinical activity in patients with myelodysplastic syndromes. Mechanism-based laboratory studies suggest that clinical optimization of therapy with DNMT inhibitors needs to include optimizing intracellular drug uptake and maximizing drug exposure over time while still using lower doses to avoid cytotoxicity. Clinical studies suggest that increased dose intensity and multiple cycles of administration substantially increase response rates. Other strategies for optimizing the efficacy of DNMT inhibitor therapy also include identification of patients that are best qualified for treatment, and defining in vivo mechanisms of patient responses. In the future, combination strategies to increase gene reactivation and to take advantage of increased expression of target genes may be critical for achieving optimal results.
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Affiliation(s)
- Jean-Pierre Issa
- Section of Translational Research, Department of Leukemia at the MD Anderson Cancer Center, University of Texas, Houston 77030, USA.
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