1
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Mulet-Lazaro R, van Herk S, Nuetzel M, Sijs-Szabo A, Díaz N, Kelly K, Erpelinck-Verschueren C, Schwarzfischer-Pfeilschifter L, Stanewsky H, Ackermann U, Glatz D, Raithel J, Fischer A, Pohl S, Rijneveld A, Vaquerizas JM, Thiede C, Plass C, Wouters BJ, Delwel R, Rehli M, Gebhard C. Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia. Nat Commun 2024; 15:5693. [PMID: 38972954 PMCID: PMC11228033 DOI: 10.1038/s41467-024-49811-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Leukemias with ambiguous lineage comprise several loosely defined entities, often without a clear mechanistic basis. Here, we extensively profile the epigenome and transcriptome of a subgroup of such leukemias with CpG Island Methylator Phenotype. These leukemias exhibit comparable hybrid myeloid/lymphoid epigenetic landscapes, yet heterogeneous genetic alterations, suggesting they are defined by their shared epigenetic profile rather than common genetic lesions. Gene expression enrichment reveals similarity with early T-cell precursor acute lymphoblastic leukemia and a lymphoid progenitor cell of origin. In line with this, integration of differential DNA methylation and gene expression shows widespread silencing of myeloid transcription factors. Moreover, binding sites for hematopoietic transcription factors, including CEBPA, SPI1 and LEF1, are uniquely inaccessible in these leukemias. Hypermethylation also results in loss of CTCF binding, accompanied by changes in chromatin interactions involving key transcription factors. In conclusion, epigenetic dysregulation, and not genetic lesions, explains the mixed phenotype of this group of leukemias with ambiguous lineage. The data collected here constitute a useful and comprehensive epigenomic reference for subsequent studies of acute myeloid leukemias, T-cell acute lymphoblastic leukemias and mixed-phenotype leukemias.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Stanley van Herk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Margit Nuetzel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Aniko Sijs-Szabo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Renewable Marine Resources Department, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Katherine Kelly
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Erpelinck-Verschueren
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Hanna Stanewsky
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Ute Ackermann
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Dagmar Glatz
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Johanna Raithel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Alexander Fischer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Sandra Pohl
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Anita Rijneveld
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital 8 Campus, London, United Kingdom
| | - Christian Thiede
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bas J Wouters
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany.
| | - Claudia Gebhard
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany.
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2
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Yamamoto H, Watanabe Y, Arai H, Umemoto K, Tateishi K, Sunakawa Y. Microsatellite instability: A 2024 update. Cancer Sci 2024; 115:1738-1748. [PMID: 38528657 PMCID: PMC11145116 DOI: 10.1111/cas.16160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024] Open
Abstract
Deficient mismatch repair (dMMR) results in microsatellite instability (MSI), a pronounced mutator phenotype. High-frequency MSI (MSI-H)/dMMR is gaining increasing interest as a biomarker for advanced cancer patients to determine their eligibility for immune checkpoint inhibitors (ICIs). Various methods based on next-generation sequencing (NGS) have been developed to assess the MSI status. Comprehensive genomic profiling (CGP) testing can precisely ascertain the MSI status as well as genomic alterations in a single NGS test. The MSI status can be also ascertained through the liquid biopsy-based CGP assays. MSI-H has thus been identified in various classes of tumors, resulting in a greater adoption of immunotherapy, which is hypothesized to be effective against malignancies that possess a substantial number of mutations and/or neoantigens. NGS-based studies have also characterized MSI-driven carcinogenesis, including significant rates of fusion kinases in colorectal cancers (CRCs) with MSI-H that are targets for therapeutic kinase inhibitors, particularly in MLH1-methylated CRCs with wild-type KRAS/BRAF. NTRK fusion is linked to the colorectal serrated neoplasia pathway. Recent advances in investigations of MSI-H malignancies have resulted in the development of novel diagnostic or therapeutic techniques, such as a synthetic lethal therapy that targets the Werner gene. DNA sensing in cancer cells is required for antitumor immunity induced by dMMR, opening up novel avenues and biomarkers for immunotherapy. Therefore, clinical relevance exists for analyses of MSI and MSI-H-associated genomic alterations in malignancy. In this article, we provide an update on MSI-driven carcinogenesis, with an emphasis on unique landscapes of diagnostic and immunotherapeutic strategies.
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Affiliation(s)
- Hiroyuki Yamamoto
- Department of BioinformaticsSt. Marianna University Graduate School of MedicineKawasakiJapan
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
| | - Yoshiyuki Watanabe
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
- Department of Internal MedicineKawasaki Rinko General HospitalKawasakiJapan
| | - Hiroyuki Arai
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
| | - Kumiko Umemoto
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
| | - Keisuke Tateishi
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
| | - Yu Sunakawa
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
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3
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Lee AV, Nestler KA, Chiappinelli KB. Therapeutic targeting of DNA methylation alterations in cancer. Pharmacol Ther 2024; 258:108640. [PMID: 38570075 DOI: 10.1016/j.pharmthera.2024.108640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
DNA methylation is a critical component of gene regulation and plays an important role in the development of cancer. Hypermethylation of tumor suppressor genes and silencing of DNA repair pathways facilitate uncontrolled cell growth and synergize with oncogenic mutations to perpetuate cancer phenotypes. Additionally, aberrant DNA methylation hinders immune responses crucial for antitumor immunity. Thus, inhibiting dysregulated DNA methylation is a promising cancer therapy. Pharmacologic inhibition of DNA methylation reactivates silenced tumor suppressors and bolster immune responses through induction of viral mimicry. Now, with the advent of immunotherapies and discovery of the immune-modulatory effects of DNA methylation inhibitors, there is great interest in understanding how targeting DNA methylation in combination with other therapies can enhance antitumor immunity. Here, we describe the role of aberrant DNA methylation in cancer and mechanisms by which it promotes tumorigenesis and modulates immune responses. Finally, we review the initial discoveries and ongoing efforts to target DNA methylation as a cancer therapeutic.
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Affiliation(s)
- Abigail V Lee
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Kevin A Nestler
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.
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4
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Park PH, Keith K, Calendo G, Jelinek J, Madzo J, Gharaibeh RZ, Ghosh J, Sapienza C, Jobin C, Issa JPJ. Association between gut microbiota and CpG island methylator phenotype in colorectal cancer. Gut Microbes 2024; 16:2363012. [PMID: 38860458 PMCID: PMC11174071 DOI: 10.1080/19490976.2024.2363012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
The intestinal microbiota is an important environmental factor implicated in CRC development. Intriguingly, modulation of DNA methylation by gut microbiota has been reported in preclinical models, although the relationship between tumor-infiltrating bacteria and CIMP status is currently unexplored. In this study, we investigated tumor-associated bacteria in 203 CRC tumor cases and validated the findings using The Cancer Genome Atlas datasets. We assessed the abundance of Bacteroides fragilis, Escherichia coli, Fusobacterium nucleatum, and Klebsiella pneumoniae through qPCR analysis and observed enrichment of all four bacterial species in CRC samples. Notably, except for E. coli, all exhibited significant enrichment in cases of CIMP. This enrichment was primarily driven by a subset of cases distinguished by high levels of these bacteria, which we labeled as "Superhigh". The bacterial Superhigh status showed a significant association with CIMP (odds ratio 3.1, p-value = 0.013) and with MLH1 methylation (odds ratio 4.2, p-value = 0.0025). In TCGA CRC cases (393 tumor and 45 adj. normal), bacterial taxa information was extracted from non-human whole exome sequencing reads, and the bacterial Superhigh status was similarly associated with CIMP (odds ratio 2.9, p < 0.001) and MLH1 methylation (odds ratio 3.5, p < 0.001). Finally, 16S ribosomal RNA gene sequencing revealed high enrichment of Bergeyella spp. C. concisus, and F. canifelinum in CIMP-Positive tumor cases. Our findings highlight that specific bacterial taxa may influence DNA methylation, particularly in CpG islands, and contribute to the development and progression of CIMP in colorectal cancer.
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Affiliation(s)
- Pyoung Hwa Park
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Kelsey Keith
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Gennaro Calendo
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Jaroslav Jelinek
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Jozef Madzo
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Raad Z. Gharaibeh
- Department of Medicine, University of Florida, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Carmen Sapienza
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Jean-Pierre J. Issa
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
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5
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Asari Y, Yamazaki J, Thandar O, Suzuki T, Aoshima K, Takeuchi K, Kinoshita R, Kim S, Hosoya K, Ishizaki T, Kagawa Y, Jelinek J, Yokoyama S, Sasaki N, Ohta H, Nakamura K, Takiguchi M. Diverse genome-wide DNA methylation alterations in canine hepatocellular tumours. Vet Med Sci 2023; 9:2006-2014. [PMID: 37483163 PMCID: PMC10508506 DOI: 10.1002/vms3.1204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 06/02/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Canine hepatocellular tumours (HCTs) are common primary liver tumours. However, the exact mechanisms of tumourigenesis remain unclear. Although some genetic mutations have been reported, DNA methylation alterations in canine HCT have not been well studied. OBJECTIVES In this study, we aimed to analyse the DNA methylation status of canine HCT. METHODS Tissues from 33 hepatocellular carcinomas, 3 hepatocellular adenomas, 1 nodular hyperplasia, 21 non-tumour livers from the patients and normal livers from 5 healthy dogs were used. We analysed the DNA methylation levels of 72,367 cytosine-guanine dinucleotides (CpG sites) in all 63 samples. RESULTS AND CONCLUSIONS Although a large fraction of CpG sites that were highly methylated in the normal liver became hypomethylated in tumours from most patients, we also found some patients with less remarkable change or no change in DNA methylation. Hierarchical clustering analysis revealed that 32 of 37 tumour samples differed from normal livers, although the remaining 5 tumour livers fell into the same cluster as normal livers. In addition, the number of hypermethylated genes in tumour livers varied among tumour cases, suggesting various DNA methylation patterns in different tumour groups. However, patient and clinical parameters, such as age, were not associated with DNA methylation status. In conclusion, we found that HCTs undergo aberrant and diverse patterns of genome-wide DNA methylation compared with normal liver tissue, suggesting a complex epigenetic mechanism in canine HCT.
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Affiliation(s)
- Yu Asari
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Jumpei Yamazaki
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
| | - Oo Thandar
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Tamami Suzuki
- Laboratory of Comparative Pathology, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Keisuke Aoshima
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
- Laboratory of Comparative Pathology, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Kyosuke Takeuchi
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Ryohei Kinoshita
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
| | - Sangho Kim
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
- Laboratory of Veterinary Surgery, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Kenji Hosoya
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
- Laboratory of Veterinary Surgery, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Teita Ishizaki
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- Laboratory of Comparative Pathology, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- North LabSapporoJapan
| | | | | | - Shoko Yokoyama
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
| | - Noboru Sasaki
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Hiroshi Ohta
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Kensuke Nakamura
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Mitsuyoshi Takiguchi
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
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6
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Ohnmacht AJ, Rajamani A, Avar G, Kutkaite G, Gonçalves E, Saur D, Menden MP. The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity. Commun Biol 2023; 6:825. [PMID: 37558831 PMCID: PMC10412573 DOI: 10.1038/s42003-023-05198-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023] Open
Abstract
Aberrant DNA methylation accompanies genetic alterations during oncogenesis and tumour homeostasis and contributes to the transcriptional deregulation of key signalling pathways in cancer. Despite increasing efforts in DNA methylation profiling of cancer patients, there is still a lack of epigenetic biomarkers to predict treatment efficacy. To address this, we analyse 721 cancer cell lines across 22 cancer types treated with 453 anti-cancer compounds. We systematically detect the predictive component of DNA methylation in the context of transcriptional and mutational patterns, i.e., in total 19 DNA methylation biomarkers across 17 drugs and five cancer types. DNA methylation constitutes drug sensitivity biomarkers by mediating the expression of proximal genes, thereby enhancing biological signals across multi-omics data modalities. Our method reproduces anticipated associations, and in addition, we find that the NEK9 promoter hypermethylation may confer sensitivity to the NEDD8-activating enzyme (NAE) inhibitor pevonedistat in melanoma through downregulation of NEK9. In summary, we envision that epigenomics will refine existing patient stratification, thus empowering the next generation of precision oncology.
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Affiliation(s)
- Alexander Joschua Ohnmacht
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Anantharamanan Rajamani
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Ismaninger Str. 22, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Göksu Avar
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Ginte Kutkaite
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Emanuel Gonçalves
- Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001, Lisbon, Portugal
- INESC-ID, 1000-029, Lisbon, Portugal
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Ismaninger Str. 22, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Michael Patrick Menden
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany.
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany.
- Department of Biochemistry and Pharmacology, University of Melbourne, Victoria, VIC, 3010, Australia.
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7
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Gunn K, Myllykoski M, Cao JZ, Ahmed M, Huang B, Rouaisnel B, Diplas BH, Levitt MM, Looper R, Doench JG, Ligon KL, Kornblum HI, McBrayer SK, Yan H, Duy C, Godley LA, Koivunen P, Losman JA. (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers. Cancer Discov 2023; 13:1478-1497. [PMID: 36847506 PMCID: PMC10238656 DOI: 10.1158/2159-8290.cd-22-0825] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/21/2022] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
Oncogenic mutations in isocitrate dehydrogenase 1 (IDH1) and IDH2 occur in a wide range of cancers, including acute myeloid leukemia (AML) and glioma. Mutant IDH enzymes convert 2-oxoglutarate (2OG) to (R)-2-hydroxyglutarate [(R)-2HG], an oncometabolite that is hypothesized to promote cellular transformation by dysregulating 2OG-dependent enzymes. The only (R)-2HG target that has been convincingly shown to contribute to transformation by mutant IDH is the myeloid tumor suppressor TET2. However, there is ample evidence to suggest that (R)-2HG has other functionally relevant targets in IDH-mutant cancers. Here, we show that (R)-2HG inhibits KDM5 histone lysine demethylases and that this inhibition contributes to cellular transformation in IDH-mutant AML and IDH-mutant glioma. These studies provide the first evidence of a functional link between dysregulation of histone lysine methylation and transformation in IDH-mutant cancers. SIGNIFICANCE Mutant IDH is known to induce histone hypermethylation. However, it is not known if this hypermethylation is functionally significant or is a bystander effect of (R)-2HG accumulation in IDH-mutant cells. Here, we provide evidence that KDM5 inhibition by (R)-2HG contributes to mutant IDH-mediated transformation in AML and glioma. This article is highlighted in the In This Issue feature, p. 1275.
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Affiliation(s)
- Kathryn Gunn
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matti Myllykoski
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland; Oulu Center for Cell-Matrix Research, University of Oulu, FI-90220, Oulu, Finland
| | - John Z. Cao
- Committee on Cancer Biology, Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Manna Ahmed
- Cancer Signaling and Epigenetics Program, Cancer Epigenetic Institute, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Bofu Huang
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Betty Rouaisnel
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bill H. Diplas
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael M. Levitt
- Children’s Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ryan Looper
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - John G. Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Keith L. Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Boston Children’s Hospital and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Harley I. Kornblum
- Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
| | - Samuel K. McBrayer
- Children’s Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hai Yan
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cihangir Duy
- Cancer Signaling and Epigenetics Program, Cancer Epigenetic Institute, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Lucy A. Godley
- Committee on Cancer Biology, Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland; Oulu Center for Cell-Matrix Research, University of Oulu, FI-90220, Oulu, Finland
| | - Julie-Aurore Losman
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
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8
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Tong X, Li M, Jin J, Li Y, Li L, Peng Y, Huang L, Xu B, Meng F, Mao X, Huang L, Huang W, Zhang D. Cladribine- and decitabine-containing conditioning regimen has a low post-transplant relapse rate in patients with relapsed or refractory acute myeloid leukemia and high-risk myelodysplastic syndrome. Int J Cancer 2023; 152:2123-2133. [PMID: 36594582 DOI: 10.1002/ijc.34419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/24/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023]
Abstract
To reduce the risk of relapse after allogeneic hematopoietic stem cell transplantation (allo-HSCT), there have been continuing efforts to optimize the conditioning regimens. Our study aimed to analyze the risk factors associated with the relapse of relapsed/refractory (R/R), high-risk acute myeloid leukemia (AML) and high-risk myelodysplastic syndrome (MDS) post-transplant and the efficacy of a new conditioning regimen involving decitabine and cladribine. Clinical data of 125 patients with R/R AML, high-risk AML and high-risk MDS who underwent allo-HSCT were collected. In addition, 35 patients with R/R AML, high-risk AML and high-risk MDS received treatment with a new conditioning regimen including decitabine and cladribine. Cox regression analysis was used to identify risk factors associated with OS, RFS and relapse. Among 125 patients who underwent allo-HSCT, CR before allo-HSCT and matched sibling donors were independent protective factors for OS. DNMT3A abnormality was an independent risk factor for both relapse and RFS. Among 35 patients who received a new conditioning regimen containing decitabine and cladribine, only six patients relapsed and 1-year cumulative incidence of relapse was 11.7%. Moreover, this new regimen showed efficient MRD clearance early after allo-HSCT. The combined decitabine- and cladribine-based conditioning regimen showed a low relapse rate and a high survival without an increased incidence of GVHD or adverse effects and thus has potential for use in allo-HSCT for R/R AML, high-risk AML and high-risk MDS.
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Affiliation(s)
- Xiwen Tong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mengyuan Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jie Jin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yizhou Peng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lifang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bin Xu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fankai Meng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xia Mao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Donghua Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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9
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Shin HJ, Hua JT, Li H. Recent advances in understanding DNA methylation of prostate cancer. Front Oncol 2023; 13:1182727. [PMID: 37234978 PMCID: PMC10206257 DOI: 10.3389/fonc.2023.1182727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Epigenetic modifications, such as DNA methylation, is widely studied in cancer. DNA methylation patterns have been shown to distinguish between benign and malignant tumors in various cancers, including prostate cancer. It may also contribute to oncogenesis, as it is frequently associated with downregulation of tumor suppressor genes. Aberrant patterns of DNA methylation, in particular the CpG island hypermethylator phenotype (CIMP), have shown associative evidence with distinct clinical features and outcomes, such as aggressive subtypes, higher Gleason score, prostate-specific antigen (PSA), and overall tumor stage, overall worse prognosis, as well as reduced survival. In prostate cancer, hypermethylation of specific genes is significantly different between tumor and normal tissues. Methylation patterns could distinguish between aggressive subtypes of prostate cancer, including neuroendocrine prostate cancer (NEPC) and castration resistant prostate adenocarcinoma. Further, DNA methylation is detectable in cell-free DNA (cfDNA) and is reflective of clinical outcome, making it a potential biomarker for prostate cancer. This review summarizes recent advances in understanding DNA methylation alterations in cancers with the focus on prostate cancer. We discuss the advanced methodology used for evaluating DNA methylation changes and the molecular regulators behind these changes. We also explore the clinical potential of DNA methylation as prostate cancer biomarkers and its potential for developing targeted treatment of CIMP subtype of prostate cancer.
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Affiliation(s)
- Hyun Jin Shin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
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10
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ARID1A loss-of-function induces CpG island methylator phenotype. Cancer Lett 2022; 532:215587. [DOI: 10.1016/j.canlet.2022.215587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/26/2021] [Accepted: 02/03/2022] [Indexed: 11/22/2022]
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11
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Paweł K, Maria Małgorzata S. CpG Island Methylator Phenotype-A Hope for the Future or a Road to Nowhere? Int J Mol Sci 2022; 23:ijms23020830. [PMID: 35055016 PMCID: PMC8777692 DOI: 10.3390/ijms23020830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
The CpG island methylator phenotype (CIMP) can be regarded as the most notable emanation of epigenetic instability in cancer. Since its discovery in the late 1990s, CIMP has been extensively studied, mainly in colorectal cancers (CRC) and gliomas. Consequently, knowledge on molecular and pathological characteristics of CIMP in CRC and other tumour types has rapidly expanded. Concordant and widespread hypermethylation of multiple CpG islands observed in CIMP in multiple cancers raised hopes for future epigenetically based diagnostics and treatments of solid tumours. However, studies on CIMP in solid tumours were hampered by a lack of generalisability and reproducibility of epigenetic markers. Moreover, CIMP was not a satisfactory marker in predicting clinical outcomes. The idea of targeting epigenetic abnormalities such as CIMP for cancer therapy has not been implemented for solid tumours, either. Twenty-one years after its discovery, we aim to cover both the fundamental and new aspects of CIMP and its future application as a diagnostic marker and target in anticancer therapies.
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12
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Shen FL, Zhao YN, Yu XL, Wang BL, Wu XL, Lan GC, Gao RL. Chinese Medicine Regulates DNA Methylation to Treat Haematological Malignancies: A New Paradigm of "State-Target Medicine". Chin J Integr Med 2021; 28:560-566. [PMID: 34241803 DOI: 10.1007/s11655-021-3316-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2021] [Indexed: 12/19/2022]
Abstract
Aberrant regulation of DNA methylation plays a crucial causative role in haematological malignancies (HMs). Targeted therapy, aiming for DNA methylation, is an effective mainstay of modern medicine; however, many issues remain to be addressed. The progress of epigenetic studies and the proposed theory of "state-target medicine" have provided conditions to form a new treatment paradigm that combines the "body state adjustment" of CM with targeted therapy. We discussed the correlation between Chinese medicine (CM) syndromes/states and DNA methylation in this paper. Additionally, the latest research findings on the intervention and regulation of DNA methylation in HMs, including the core targets, therapy status, CM compounds and active components of the Chinese materia medica were concisely summarized to establish a theoretical foundation of "state-target synchronous conditioning" pattern of integrative medicine for HMs, simultaneously leading a new perspective in clinical diagnosis and therapy.
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Affiliation(s)
- Feng-Lin Shen
- Institute of Hematology Research, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310006, China
| | - Yan-Na Zhao
- Institute of Hematology Research, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310006, China
| | - Xiao-Ling Yu
- Institute of Hematology Research, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310006, China
| | - Bo-Lin Wang
- Institute of Hematology Research, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310006, China
| | - Xiao-Long Wu
- Institute of Hematology Research, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310006, China
| | - Gao-Chen Lan
- Institute of Hematology Research, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310006, China
| | - Rui-Lan Gao
- Institute of Hematology Research, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310006, China.
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13
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Krali O, Palle J, Bäcklin CL, Abrahamsson J, Norén-Nyström U, Hasle H, Jahnukainen K, Jónsson ÓG, Hovland R, Lausen B, Larsson R, Palmqvist L, Staffas A, Zeller B, Nordlund J. DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML). Genes (Basel) 2021; 12:895. [PMID: 34200630 PMCID: PMC8229099 DOI: 10.3390/genes12060895] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/31/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Pediatric acute myeloid leukemia (AML) is a heterogeneous disease composed of clinically relevant subtypes defined by recurrent cytogenetic aberrations. The majority of the aberrations used in risk grouping for treatment decisions are extensively studied, but still a large proportion of pediatric AML patients remain cytogenetically undefined and would therefore benefit from additional molecular investigation. As aberrant epigenetic regulation has been widely observed during leukemogenesis, we hypothesized that DNA methylation signatures could be used to predict molecular subtypes and identify signatures with prognostic impact in AML. To study genome-wide DNA methylation, we analyzed 123 diagnostic and 19 relapse AML samples on Illumina 450k DNA methylation arrays. We designed and validated DNA methylation-based classifiers for AML cytogenetic subtype, resulting in an overall test accuracy of 91%. Furthermore, we identified methylation signatures associated with outcome in t(8;21)/RUNX1-RUNX1T1, normal karyotype, and MLL/KMT2A-rearranged subgroups (p < 0.01). Overall, these results further underscore the clinical value of DNA methylation analysis in AML.
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Affiliation(s)
- Olga Krali
- Department of Medical Sciences, Molecular Precision Medicine and Science for Life Laboratory, Uppsala University, 752 37 Uppsala, Sweden;
| | - Josefine Palle
- Department of Medical Sciences, Molecular Precision Medicine and Science for Life Laboratory, Uppsala University, 752 37 Uppsala, Sweden;
- Department of Women’s and Children’s Health, Uppsala University, 752 37 Uppsala, Sweden
| | - Christofer L. Bäcklin
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, 751 85 Uppsala, Sweden; (C.L.B.); (R.L.)
| | - Jonas Abrahamsson
- Department of Pediatrics, Queen Silvia Children’s Hospital, 416 85 Gothenburg, Sweden;
| | - Ulrika Norén-Nyström
- Department of Clinical Sciences, Pediatrics, Umeå University Hospital, 901 85 Umeå, Sweden;
| | - Henrik Hasle
- Department of Pediatrics, Aarhus University Hospital, DK-8200 Aarhus, Denmark;
| | - Kirsi Jahnukainen
- Children’s Hospital, Helsinki University Central Hospital, Helsinki, and University of Helsinki, 00290 Helsinki, Finland;
| | - Ólafur Gísli Jónsson
- Department of Pediatrics, Landspitali University Hospital, 101 Reykjavík, Iceland;
| | - Randi Hovland
- Center of Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5009 Bergen, Norway;
| | - Birgitte Lausen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Rolf Larsson
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, 751 85 Uppsala, Sweden; (C.L.B.); (R.L.)
| | - Lars Palmqvist
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, 41346 Gothenburg, Sweden; (L.P.); (A.S.)
| | - Anna Staffas
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, 41346 Gothenburg, Sweden; (L.P.); (A.S.)
| | - Bernward Zeller
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0450 Oslo, Norway;
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Precision Medicine and Science for Life Laboratory, Uppsala University, 752 37 Uppsala, Sweden;
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14
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Wang Q, Pan S, Jiang Q, Li L, Tu W, Zhang Q, Zhou X. CircSPAG16 suppresses cadmium-induced transformation of human bronchial epithelial cells by decoying PIP5K1α to inactivate Akt. Mol Carcinog 2021; 60:582-594. [PMID: 34081812 DOI: 10.1002/mc.23325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 02/03/2023]
Abstract
Circular RNAs (circRNAs) have been implicated to have important regulatory functions in chemical carcinogenesis via sponging microRNAs to regulate gene expression. Our study revealed a novel mechanism of circRNA in cadmium carcinogenesis through directly binding with protein. Here, we used cadmium-transformed human bronchial epithelial BEAS-2B cells to study the involvement and mechanism of circRNA in lung carcinogenesis caused by cadmium. By high-throughput sequencing, circSPAG16 was identified to be the most significantly downregulated circRNA in cadmium-transformed cells. CircSPAG16 was downregulated at Week 8, 12, 16, and 20 during cadmium-induced cell transformation. In addition, circSPAG16 overexpression prevented cadmium-induced transformation of BEAS-2B cells. Mechanistically, circSPAG16 inhibited the function of phosphatidylinositol 4-phosphate 5-kinase type-1 α (PIP5K1α) by binding with it. We demonstrated that PIP5K1α acted as an oncogene to activate Akt and promoted cancer hallmarks including proliferation, migration, invasion, and anchorage-independent growth in cadmium-transformed cells. CircSPAG16 overexpression inactivates PIP5K1α/Akt signaling in the transformed cells. Furthermore, PIP5K1α overexpression significantly rescued the inhibitory effects of circSPAG16 overexpression on pAkt and cancer hallmarks in cadmium-transformed cells. Collectively, our results revealed that circSPAG16 could prevent cadmium-induced transformation through binding with PIP5K1α to inactivate Akt. These results provide a novel regulatory mechanism of circRNA into carcinogenesis induced by cadmium.
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Affiliation(s)
- Qin Wang
- Key Laboratory of Environment and Health, Ministry of Education, Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuya Pan
- Key Laboratory of Environment and Health, Ministry of Education, Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qi Jiang
- Key Laboratory of Environment and Health, Ministry of Education, Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Luyao Li
- Key Laboratory of Environment and Health, Ministry of Education, Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Tu
- Key Laboratory of Environment and Health, Ministry of Education, Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qian Zhang
- Key Laboratory of Environment and Health, Ministry of Education, Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xue Zhou
- Key Laboratory of Environment and Health, Ministry of Education, Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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15
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Giacopelli B, Wang M, Cleary A, Wu YZ, Schultz AR, Schmutz M, Blachly JS, Eisfeld AK, Mundy-Bosse B, Vosberg S, Greif PA, Claus R, Bullinger L, Garzon R, Coombes KR, Bloomfield CD, Druker BJ, Tyner JW, Byrd JC, Oakes CC. DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia. Genome Res 2021; 31:747-761. [PMID: 33707228 PMCID: PMC8092005 DOI: 10.1101/gr.269233.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/09/2021] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) is a molecularly complex disease characterized by heterogeneous tumor genetic profiles and involving numerous pathogenic mechanisms and pathways. Integration of molecular data types across multiple patient cohorts may advance current genetic approaches for improved subclassification and understanding of the biology of the disease. Here, we analyzed genome-wide DNA methylation in 649 AML patients using Illumina arrays and identified a configuration of 13 subtypes (termed “epitypes”) using unbiased clustering. Integration of genetic data revealed that most epitypes were associated with a certain recurrent mutation (or combination) in a majority of patients, yet other epitypes were largely independent. Epitypes showed developmental blockage at discrete stages of myeloid differentiation, revealing epitypes that retain arrested hematopoietic stem-cell-like phenotypes. Detailed analyses of DNA methylation patterns identified unique patterns of aberrant hyper- and hypomethylation among epitypes, with variable involvement of transcription factors influencing promoter, enhancer, and repressed regions. Patients in epitypes with stem-cell-like methylation features showed inferior overall survival along with up-regulated stem cell gene expression signatures. We further identified a DNA methylation signature involving STAT motifs associated with FLT3-ITD mutations. Finally, DNA methylation signatures were stable at relapse for the large majority of patients, and rare epitype switching accompanied loss of the dominant epitype mutations and reversion to stem-cell-like methylation patterns. These results show that DNA methylation-based classification integrates important molecular features of AML to reveal the diverse pathogenic and biological aspects of the disease.
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Affiliation(s)
- Brian Giacopelli
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Min Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ada Cleary
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Yue-Zhong Wu
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Anna Reister Schultz
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Maximilian Schmutz
- Hematology and Oncology, Medical Faculty, University of Augsburg, 86159 Augsburg, Germany
| | - James S Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ann-Kathrin Eisfeld
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Bethany Mundy-Bosse
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, 80539 Munich, Germany.,Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Munich, Germany
| | - Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, 80539 Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rainer Claus
- Department of Medicine II, Stem Cell Transplantation Unit, Klinikum Augsburg, Ludwig-Maximilians University Munich, 86156 Munich, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumorimmunology, Charité-Universitätsmedizin, 13353 Berlin, Germany
| | - Ramiro Garzon
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Kevin R Coombes
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Clara D Bloomfield
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Christopher C Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
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16
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Gao H, He X, Li Q, Wang Y, Tian Y, Chen X, Wang J, Guo Y, Wang W, Li X. Genome-wide DNA methylome analysis reveals methylation subtypes with different clinical outcomes for acute myeloid leukemia patients. Cancer Med 2020; 9:6296-6305. [PMID: 32628355 PMCID: PMC7476826 DOI: 10.1002/cam4.3291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 03/11/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
Leukemia is the second common blood cancer after lymphoma, and its incidence rate has an increasing trend in recent years. Acute myeloid leukemia (AML) is one of the prevalent forms of leukemia. Although previous studies have investigated the methylation profile for AML patients, the AML methylation subtypes based on the genome‐wide methylome are still unclear. In the present study, we identified three methylation subtypes for AML samples based on the methylation profiles at CGI, CGI shore, CGI shelf, and opensea genomic contexts. Analyzing the molecular characteristics and clinical factors of the three subtypes revealed different methylation patterns and clinical outcomes between them. Further analysis revealed subtype dependent marker genes and their promoter CpG sites with regulatory function. Finally, we found that combining the AML patient age and methylation pattern brought better clinical outcome classification. In conclusion, we identified AML methylation subtypes and their marker genes, these results may help to excavate potential targets for clinical therapy and the development of precision medicine for AML patients.
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Affiliation(s)
- Haiyan Gao
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xin He
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Qiang Li
- Department of Paediatrics, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Ying Wang
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yaoyao Tian
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xi Chen
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jinghua Wang
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yan Guo
- Assessment Admittance Section, Heilongjiang Hospital Service Management Evaluation Center, Harbin, China
| | - Wei Wang
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xiaoyun Li
- Department of Hematology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
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17
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The Influence of Methylating Mutations on Acute Myeloid Leukemia: Preliminary Analysis on 56 Patients. Diagnostics (Basel) 2020; 10:diagnostics10050263. [PMID: 32365516 PMCID: PMC7277399 DOI: 10.3390/diagnostics10050263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 11/18/2022] Open
Abstract
Acute myeloid leukemia (AML) is a hematologic malignancy characterized by abnormal proliferation and a lack of differentiation of myeloid blasts. Considering the dismal prognosis this disease presents, several efforts have been made to better classify it and offer a tailored treatment to each subtype. This has been formally done by the World Health Organization (WHO) with the AML classification schemes from 2008 and 2016. Nonetheless, there are still mutations that are not currently included in the WHO AML classification, as in the case of some mutations that influence methylation. In this regard, the present study aimed to determine if some of the mutations that influence DNA methylation can be clustered together regarding methylation, expression, and clinical profile. Data from the TCGA LAML cohort were downloaded via cBioPortal. The analysis was performed using R 3.5.2, and the necessary packages for classical statistics, dimensionality reduction, and machine learning. We included only patients that presented mutations in DNMT3A, TET2, IDH1/2, ASXL1, WT1, and KMT2A. Afterwards, mutations that were present in too few patients were removed from the analysis, thus including a total of 57 AML patients. We observed that regarding expression, methylation, and clinical profile, patients with mutated TET2, IDH1/2, and WT1 presented a high degree of similarity, indicating the equivalence that these mutations present between themselves. Nonetheless, we did not observe this similarity between DNMT3A- and KMT2A-mutated AML. Moreover, when comparing the hypermethylating group with the hypomethylating one, we also observed important differences regarding expression, methylation, and clinical profile. In the current manuscript we offer additional arguments for the similarity of the studied hypermethylating mutations and suggest that those should be clustered together in further classifications. The hypermethylating and hypomethylating groups formed above were shown to be different from each other considering overall survival, methylation profile, expression profile, and clinical characteristics. In this manuscript, we present additional arguments for the similarity of the effect generated by TET2, IDH1/2, and WT1 mutations in AML patients. Thus, we hypothesize that hypermethylating mutations skew the AML cells to a similar phenotype with a possible sensitivity to hypermethylating agents.
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18
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SERS assessment of the cancer-specific methylation pattern of genomic DNA: towards the detection of acute myeloid leukemia in patients undergoing hematopoietic stem cell transplantation. Anal Bioanal Chem 2019; 411:7907-7913. [PMID: 31745615 DOI: 10.1007/s00216-019-02213-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/04/2019] [Accepted: 10/14/2019] [Indexed: 10/25/2022]
Abstract
In this label-free surface-enhanced Raman scattering (SERS) study of genomic DNA, we demonstrate that the cancer-specific DNA methylation pattern translates into specific spectral differences. Thus, DNA extracted from an acute myeloid leukemia (AML) cell line presented a decreased intensity of the 1005 cm-1 band of 5-methylcytosine compared to normal DNA, in line with the well-described hypomethylation of cancer DNA. The unique methylation pattern of cancer DNA also influences the DNA adsorption geometry, resulting in higher adenine SERS intensities for cancer DNA. The possibility of detecting cancer DNA based on its SERS spectrum was validated on peripheral blood genomic DNA samples from n = 17 AML patients and n = 17 control samples, yielding an overall classification of 82% based on the 1005 cm-1 band of 5-methylcytosine. By demonstrating the potential of SERS in assessing the methylation status in the case of real-life DNA samples, the study paves the way for novel methods of diagnosing cancer. Graphical abstract.
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19
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Chung W, Kelly AD, Kropf P, Fung H, Jelinek J, Su XY, Roboz GJ, Kantarjian HM, Azab M, Issa JPJ. Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia. Clin Epigenetics 2019; 11:106. [PMID: 31331399 PMCID: PMC6647096 DOI: 10.1186/s13148-019-0704-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023] Open
Abstract
Background Guadecitabine is a novel DNA methyltransferase (DNMT) inhibitor with improved pharmacokinetics and clinical activity in a subset of patients with relapsed/refractory acute myeloid leukemia (r/r AML), but identification of this subset remains difficult. Methods To search for biomarkers of response, we measured genome-wide DNA methylation, mutations of 54 genes, and expression of a panel of 7 genes in pre-treatment samples from 128 patients treated at therapeutic doses in a phase I/II study. Results Response rate to guadecitabine was 17% (2 complete remission (CR), 3 CR with incomplete blood count recovery (CRi), or CR with incomplete platelets recovery (CRp)) in the phase I component and 23% (14 CR, 9 CRi/CRp) in phase II. There were no strong mutation or methylation predictors of response. Gene expression clustering defined a subset of patients (~ 20%) that had (i) high DNMT3B and low CDKN2B, CTCF, and CDA expression; (ii) enrichment for KRAS/NRAS mutations; (iii) frequent CpG island hypermethylation; (iv) low long interspersed nuclear element 1 (LINE-1) hypomethylation after treatment; and (v) resistance to guadecitabine in both phase I (response rate 0% vs. 33%, p = 0.07) and phase II components of the study (response rate 5% vs. 30%, p = 0.02). Multivariate analysis identified peripheral blood (PB) blasts and hemoglobin as predictors of response and cytogenetics, gene expression, RAS mutations, and hemoglobin as predictors of survival. Conclusions A subset of patients (~ 20%) with r/r AML is unlikely to benefit from guadecitabine as a single agent. In the remaining 80%, guadecitabine is a viable option with a median survival of 8 months and a 2-year survival rate of 21%. Trial registration NCT01261312. Electronic supplementary material The online version of this article (10.1186/s13148-019-0704-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Woonbok Chung
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA. .,Present address: Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA.
| | - Andrew D Kelly
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA
| | - Patricia Kropf
- Fox Chase Cancer Center, Temple Health, Philadelphia, PA, USA
| | - Henry Fung
- Fox Chase Cancer Center, Temple Health, Philadelphia, PA, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA.,Present address: Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA
| | | | - Gail J Roboz
- Weill Cornell Medicine, Division of Hematology and Oncology, The New York Presbyterian Hospital, New York, NY, USA
| | | | | | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, USA.,Present address: Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA
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20
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Gu Y, Zhou JD, Xu ZJ, Zhang TJ, Wen XM, Ma JC, Ji RB, Yuan Q, Zhang W, Chen Q, Lin J, Qian J. Promoter methylation of the candidate tumor suppressor gene TCF21 in myelodysplastic syndrome and acute myeloid leukemia. Am J Transl Res 2019; 11:3450-3460. [PMID: 31312357 PMCID: PMC6614633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/12/2019] [Indexed: 06/10/2023]
Abstract
Transcription factor 21 (TCF21) has been identified as a candidate tumor suppressor gene which was epigenetically inactivated in a variety of human cancers. However, TCF21 methylation pattern remains unknown in hematologic malignancies. The aim of this study was to investigate TCF21 methylation and its clinical relevance in myelodysplastic syndrome (MDS) and non-M3 acute myeloid leukemia (AML). A total cohort of 33 MDS patients, 100 non-M3 AML patients and 25 healthy donors were enrolled in the study. Targeted bisulfite sequencing assay was performed to identify the methylation pattern of CpG islands within the promoter of TCF21 gene. The bioinformatics analyses were based on The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO). The results showed that there were significant differences in the methylation levels of TCF21 between MDS, non-M3 AML and controls (P = 0.003 and < 0.001, respectively). TCF21 hypermethylation might be served as a promising biomarker which could distinguish MDS/AML from normal controls (P < 0.001 and = 0.003, respectively). There was a significant difference in cytogenetic risk categories between TCF21 hypermethylation and non-hypermethylation AML patients (P = 0.032). Notably, TCF21 hypermethylation occurred frequently in AML patients with adverse risk category, compared with those with favorable and intermediate categories, respectively (67% vs 44% and 29%). TCF21 non-hypermethylation AML patients showed a higher probability of normal karyotype than abnormal karyotype (P = 0.003). The rate of DNMT3A gene mutation was significantly higher in the non-hypermethylation AML patients than that in the hypermethylation (8/44 vs 0/34, P = 0.020). These results suggested that aberrant DNA promoter methylation of TCF21 was frequent event in MDS and non-M3 AML, and TCF21 hypermathylation was associated with adverse risk karyotype in AML.
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Affiliation(s)
- Yu Gu
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Jing-Dong Zhou
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Zi-Jun Xu
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Ting-Juan Zhang
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Xiang-Mei Wen
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Ji-Chun Ma
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Ren-Bi Ji
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
| | - Qian Yuan
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Wei Zhang
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Qin Chen
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Jiang Lin
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Jun Qian
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
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21
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Young CR, Adler S, Eary JF, Lindenberg ML, Jacobs PM, Collins J, Kummar S, Kurdziel KA, Choyke PL, Mena E. Biodistribution, Tumor Detection, and Radiation Dosimetry of 18F-5-Fluoro-2'-Deoxycytidine with Tetrahydrouridine in Solid Tumors. J Nucl Med 2018; 60:492-496. [PMID: 30389817 DOI: 10.2967/jnumed.118.216994] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/12/2018] [Indexed: 01/27/2023] Open
Abstract
In preclinical studies, 5-fluoro-2'-deoxycytidine (FdCyd), an inhibitor of DNA methyltransferase and DNA hypermethylation, has shown treatment efficacy against multiple malignancies by suppressing epigenetic hypermethylation in tumor cells. Several ongoing clinical trials are using FdCyd, and although some patients may respond to this drug, in most patients it is ineffective. Thus, establishing a noninvasive imaging modality to evaluate the distribution of the drug may provide insight into the variable responses. A novel experimental radiopharmaceutical, 18F-labeled FdCyd, was developed as a companion imaging agent to the nonradioactive form of the drug, FdCyd. We present the first-in-humans radiation dosimetry results and biodistribution of 18F-FdCyd, administered along with tetrahydrouridine, an inhibitor of cytidine/deoxycytidine deaminase, in patients with a variety of solid tumors undergoing FdCyd therapy. Methods: This phase 0 imaging trial examined the 18F-FdCyd biodistribution and radiation dosimetry in 5 human subjects enrolled in companion therapy trials. In each subject, 4 sequential PET scans were acquired to estimate whole-body and individual organ effective dose, using OLINDA/EXM, version 1.0. Tumor-to-background ratios were also calculated for the tumor sites visualized on PET/CT imaging. Results: The average whole-body effective dose for the experimental radiopharmaceutical 18F-FdCyd administered in conjunction with tetrahydrouridine was 2.12E-02 ± 4.15E-03 mSv/MBq. This is similar to the radiation dose estimates for 18F-FDG PET. The critical organ, with the highest absorbed radiation dose, was the urinary bladder wall at 7.96E-02 mSv/MBq. Other organ doses of note were the liver (6.02E-02mSv/MBq), kidneys (5.26E-02 mSv/MBq), and gallbladder (4.05E-02 mSv/MBq). Tumor target-to-background ratios ranged from 2.4 to 1.4, which potentially enable tumor visualization in static PET images. Conclusion: This phase 0 imaging clinical trial provides evidence that 18F-FdCyd administered in conjunction with tetrahydrouridine yields acceptable individual organ and whole-body effective doses, as well as modest tumor-to-background ratios that potentially enable tumor visualization. Dose estimates for 18F-FdCyd are comparable to those for other PET radiopharmaceuticals, such as 18F-FDG. Further studies with larger study populations are warranted to assess 18F-FdCyd imaging as a predictor of FdCyd treatment effectiveness.
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Affiliation(s)
- Colin R Young
- Department of Radiology, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Stephen Adler
- Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, Maryland
| | - Janet F Eary
- Cancer Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - M Liza Lindenberg
- Molecular Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Paula M Jacobs
- Cancer Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jerry Collins
- Developmental Therapeutics Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Shivaani Kummar
- Stanford University School of Medicine, Palo Alto, California
| | - Karen A Kurdziel
- Molecular Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Peter L Choyke
- Molecular Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Esther Mena
- Molecular Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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22
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Gao M, Lin Y, Liu X, Li Y, Zhang C, Wang Z, Wang Z, Wang Y, Guo Z. ISG20 promotes local tumor immunity and contributes to poor survival in human glioma. Oncoimmunology 2018; 8:e1534038. [PMID: 30713788 PMCID: PMC6343791 DOI: 10.1080/2162402x.2018.1534038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/20/2022] Open
Abstract
Recent evidence has confirmed that a mutation of the isocitrate dehydrogenase (IDH) gene occurs early in gliomagenesis and contributes to suppressed immunity. The present study aimed to determine the candidate genes associated with IDH mutation status that could serve as biomarkers of immune suppression for improved prognosis prediction. Clinical information and RNA-seq gene expression data were collected for 932 glioma samples from the CGGA and TCGA databases, and differentially expressed genes in both lower-grade glioma (LGG) and glioblastoma (GBM) samples were identified according to IDH mutation status. Only one gene, interferon-stimulated exonuclease gene 20 (ISG20), with reduced expression in IDH mutant tumors, demonstrated significant prognostic value. ISG20 expression level significantly increased with increasing tumor grade, and its high expression was associated with a poor clinical outcome. Moreover, increased ISG20 expression was associated with increased infiltration of monocyte-derived macrophages and neutrophils, and suppressed adaptive immune response. ISG20 expression was also positively correlated with PD-1, PD-L1, and CTLA4 expression, along with the levels of several chemokines. We conclude that ISG20 is a useful biomarker to identify IDH-mediated immune processes in glioma and may serve as a potential therapeutic target.
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Affiliation(s)
- Mengqi Gao
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Yi Lin
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Xing Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Yiming Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Chuanbao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Zheng Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Zhiliang Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Yulin Wang
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Zongze Guo
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
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23
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Kelly AD, Madzo J, Madireddi P, Kropf P, Good CR, Jelinek J, Issa JPJ. Demethylator phenotypes in acute myeloid leukemia. Leukemia 2018; 32:2178-2188. [PMID: 29556023 PMCID: PMC6128790 DOI: 10.1038/s41375-018-0084-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 01/29/2018] [Accepted: 02/06/2018] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) often harbors mutations in epigenetic regulators, and also has frequent DNA hypermethylation, including the presence of CpG island methylator phenotypes (CIMPs). Although global hypomethylation is well known in cancer, the question of whether distinct demethylator phenotypes (DMPs) exist remains unanswered. Using Illumina 450k arrays for 194 patients from The Cancer Genome Atlas, we identified two distinct DMPs by hierarchical clustering: DMP.1 and DMP.2. DMP.1 cases harbored mutations in NPM1 (94%), FLT3 (71%) and DNMT3A (61%). Surprisingly, only 40% of patients with DNMT3A mutations were DMP.1, which has implications for mechanisms of transformation by this mutation. In contrast, DMP.2 AML was comprised of patients with t(8;21), inv(16) or t(15;17), suggesting common methylation defects connect these disparate rearrangements. RNA-seq revealed upregulated genes functioning in immune response (DMP.1) and development (DMP.2). We confirmed these findings by integrating independent 450k data sets (236 additional cases), and found prognostic effects by DMP status, independent of age and cytogenetics. The existence of DMPs has implications for AML pathogenesis and may augment existing tools in risk stratification.
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Affiliation(s)
- Andrew D Kelly
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Jozef Madzo
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Priyanka Madireddi
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Patricia Kropf
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Charly R Good
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA.
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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24
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Abstract
Epigenetic alterations such as DNA methylation defects and aberrant covalent histone modifications occur within all cancers and are selected for throughout the natural history of tumor formation, with changes being detectable in early onset, progression, and ultimately recurrence and metastasis. The ascertainment and use of these marks to identify at-risk patient populations, refine diagnostic criteria, and provide prognostic and predictive factors to guide treatment decisions are of growing clinical relevance. Furthermore, the targetable nature of epigenetic modifications provides a unique opportunity to alter treatment paradigms and provide new therapeutic options for patients whose malignancies possess these aberrant epigenetic modifications, paving the way for new and personalized medicine. DNA methylation has proven to be of significant clinical utility for its stability and relative ease of testing. The intent of this review is to elaborate upon well-supported examples of epigenetic precision medicine and how the field is moving forward, primarily in the context of aberrant DNA methylation.
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Affiliation(s)
- Rachael J Werner
- From the *Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
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25
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Abstract
Next year will mark 60 years since Dr. Leslie Foulds outlined his hypothesis that cancer is "a dynamic process advancing through stages that are qualitatively different," leading the way to our view of cancer progression as we know it today. Our understanding of the mechanisms of these stages has been continuously evolving this past half-century, and there has always been an active discussion of the roles of both genetic and epigenetic changes in directing this progression. In this review, we focus on the roles one particular epigenetic mark-DNA methylation-plays in these various "discontinuous" stages of cancer. Understanding these steps not only gives us a better picture of how this fascinating biological process operates, but also opens the doors to new prognostic biomarkers and therapies against these malignancies.
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26
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Abstract
The immune system is characterized by the generation of structurally and functionally heterogeneous immune cells that constitute complex innate and adaptive immunity. This heterogeneity of immune cells results from changes in the expression of genes without altering DNA sequence. To achieve this heterogeneity, immune cells orchestrate the expression and functional status of transcription factor (TF) networks, which can be broadly categorized into 3 classes: pioneer TFs that facilitate initial commitment and differentiation of hematopoietic cells, subset-specific TFs that promote the generation of selected cell lineages, and immune-signaling TFs that regulate specialized function in differentiated cells. Epigenetic mechanisms are known to be critical for organizing the TF networks, thereby controlling immune cell lineage-fate decisions, plasticity, and function. The effects of epigenetic regulators can be heritable during cell mitosis, primarily through the modification of DNA and histone methylation patterns at gene loci. By doing so, the immune system is enabled to mount a selective but robust response to stimuli, such as pathogens, tumor cells, autoantigens, or allogeneic antigens in the setting of transplantation, while preserving the immune cell reservoir necessary for protecting the host against numerous other unexpected stimuli and limit detrimental effect of systemic inflammatory reactions.
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27
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Liu B, Narurkar R, Hanmantgad M, Zafar W, Song Y, Liu D. Venetoclax and low-dose cytarabine induced complete remission in a patient with high-risk acute myeloid leukemia: a case report. Front Med 2018; 12:593-599. [PMID: 29785506 DOI: 10.1007/s11684-018-0635-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/27/2018] [Indexed: 12/19/2022]
Abstract
Conventional combination therapies have not resulted in considerable progress in the treatment of acute myeloid leukemia (AML). Elderly patients with AML and poor risk factors have grave prognosis. Midostaurin has been recently approved for the treatment of FLT-3-mutated AML. Venetoclax, a BCL-2 inhibitor, has been approved for the treatment of relapsed and/or refractory chronic lymphoid leukemia. Clinical trials on applying venetoclax in combination with cytarabine and other agents to treat various hematological malignancies are currently underway. Here, we present a case of a male patient with poor performance status and who developed AML following allogeneic hematopoietic stem cell transplant for high-risk myelodysplasia. The patient with high risk AML achieved complete response to the combined treatment regimen of low-dose cytarabine and venetoclax. Furthermore, we reviewed current clinical trials on the use of venetoclax for hematological malignancies.
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Affiliation(s)
- Bingshan Liu
- The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450003, China
| | - Roshni Narurkar
- Department of Medicine, New York Medical College and Westchester Medical Center, Valhalla, NY, 10595, USA
| | - Madhura Hanmantgad
- Department of Medicine, New York Medical College and Westchester Medical Center, Valhalla, NY, 10595, USA
| | - Wahib Zafar
- Department of Medicine, New York Medical College and Westchester Medical Center, Valhalla, NY, 10595, USA
| | - Yongping Song
- The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450003, China
| | - Delong Liu
- The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450003, China.
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28
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Ramsawhook A, Ruzov A, Coyle B. Wilms' Tumor Protein 1 and Enzymatic Oxidation of 5-Methylcytosine in Brain Tumors: Potential Perspectives. Front Cell Dev Biol 2018; 6:26. [PMID: 29623275 PMCID: PMC5874295 DOI: 10.3389/fcell.2018.00026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/05/2018] [Indexed: 12/24/2022] Open
Abstract
The patterns of 5-methylcytosine (5mC) and its oxidized derivatives, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine (5caC) are reportedly altered in a range of cancers. Likewise, Wilms' Tumor protein 1 (WT1), a transcription factor essential for urogenital, epicardium, and kidney development exhibits aberrant expression in multiple tumors. Interestingly, WT1 directly interacts with TET proteins that catalyze the enzymatic oxidation of 5mC and exhibits high affinity for 5caC-containing DNA substrates in vitro. Here we review recent developments in the fields of Tet-dependent 5mC oxidation and WT1 biology and explore potential perspectives for studying the interplay between TETs and WT1 in brain tumors.
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Affiliation(s)
- Ashley Ramsawhook
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Alexey Ruzov
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Beth Coyle
- Children's Brain Tumour Research Centre, Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
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29
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Ginder GD, Williams DC. Readers of DNA methylation, the MBD family as potential therapeutic targets. Pharmacol Ther 2017; 184:98-111. [PMID: 29128342 DOI: 10.1016/j.pharmthera.2017.11.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA methylation represents a fundamental epigenetic modification that regulates chromatin architecture and gene transcription. Many diseases, including cancer, show aberrant methylation patterns that contribute to the disease phenotype. DNA methylation inhibitors have been used to block methylation dependent gene silencing to treat hematopoietic neoplasms and to restore expression of developmentally silenced genes. However, these inhibitors disrupt methylation globally and show significant off-target toxicities. As an alternative approach, we have been studying readers of DNA methylation, the 5-methylcytosine binding domain family of proteins, as potential therapeutic targets to restore expression of aberrantly and developmentally methylated and silenced genes. In this review, we discuss the role of DNA methylation in gene regulation and cancer development, the structure and function of the 5-methylcytosine binding domain family of proteins, and the possibility of targeting the complexes these proteins form to treat human disease.
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Affiliation(s)
- Gordon D Ginder
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, United States; Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, United States.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
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30
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Abstract
Glioblastoma is the most aggressive brain tumor and, even with the current multimodal therapy, is an invariably lethal cancer with a life expectancy that depends on the tumor subtype but, even in the most favorable cases, rarely exceeds 2 years. Epigenetic factors play an important role in gliomagenesis, are strong predictors of outcome, and are important determinants for the resistance to radio- and chemotherapy. The latest addition to the epigenetic machinery is the noncoding RNA (ncRNA), that is, RNA molecules that are not translated into a protein and that exert their function by base pairing with other nucleic acids in a reversible and nonmutational mode. MicroRNAs (miRNA) are a class of ncRNA of about 22 bp that regulate gene expression by binding to complementary sequences in the mRNA and silence its translation into proteins. MicroRNAs reversibly regulate transcription through nonmutational mechanisms; accordingly, they can be considered as epigenetic effectors. In this review, we will discuss the role of miRNA in glioma focusing on their role in drug resistance and on their potential applications in the therapy of this tumor.
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31
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Wiehle L, Raddatz G, Pusch S, Gutekunst J, von Deimling A, Rodríguez-Paredes M, Lyko F. mIDH-associated DNA hypermethylation in acute myeloid leukemia reflects differentiation blockage rather than inhibition of TET-mediated demethylation. Cell Stress 2017; 1:55-67. [PMID: 31225434 PMCID: PMC6551656 DOI: 10.15698/cst2017.10.106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Isocitrate dehydrogenases 1 and 2 (IDH1/2) are recurrently mutated in acute myeloid leukemia (AML), but their mechanistic role in leukemogenesis is poorly understood. The inhibition of TET enzymes by D-2-hydroxyglutarate (D-2-HG), which is produced by mutant IDH1/2 (mIDH1/2), has been suggested to promote epigenetic deregulation during tumorigenesis. In addition, mIDH also induces a differentiation block in various cell culture and mouse models. Here we analyze the genomic methylation patterns of AML patients with mIDH using Infinium 450K data from a large AML cohort and found that mIDH is associated with pronounced DNA hypermethylation at tens of thousands of CpGs. Interestingly, however, myeloid leukemia cells overexpressing mIDH, cells that were cultured in the presence of D-2-HG or TET2 mutant AML patients did not show similar methylation changes. In further analyses, we also characterized the methylation landscapes of myeloid progenitor cells and analyzed their relationship to mIDH-associated hypermethylation. Our findings identify the differentiation state of myeloid cells, rather than inhibition of TET-mediated DNA demethylation, as a major factor of mIDH-associated hypermethylation in AML. Furthermore, our results are also important for understanding the mode of action of currently developed mIDH inhibitors.
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Affiliation(s)
- Laura Wiehle
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center; 69120 Heidelberg, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center; 69120 Heidelberg, Germany
| | - Stefan Pusch
- German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center; 69120 Heidelberg, Germany
| | - Andreas von Deimling
- German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center; 69120 Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center; 69120 Heidelberg, Germany
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Kelly AD, Issa JPJ. The promise of epigenetic therapy: reprogramming the cancer epigenome. Curr Opin Genet Dev 2017; 42:68-77. [PMID: 28412585 DOI: 10.1016/j.gde.2017.03.015] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 02/07/2023]
Abstract
Epigenetics refers to heritable molecular determinants of phenotype independent of DNA sequence. Epigenetic features include DNA methylation, histone modifications, non-coding RNAs, and chromatin structure. The epigenetic status of cells plays a crucial role in determining their differentiation state and proper function within multicellular organisms. Disruption of these processes is now understood to be a major contributor to cancer development and progression, and recent efforts have attempted to pharmacologically reverse such altered epigenetics. In this mini-review we introduce the concept of epigenetic drivers of cancer and discuss how aberrant DNA methylation, histone modifications, and chromatin states are being targeted using drugs either in preclinical, or clinical development, and how they fit in the context of existing therapies.
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Affiliation(s)
- Andrew D Kelly
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
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