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Sun A, Park P, Cole L, Vaidya H, Maegawa S, Keith K, Calendo G, Madzo J, Jelinek J, Jobin C, Issa JPJ. Non-pathogenic microbiota accelerate age-related CpG Island methylation in colonic mucosa. Epigenetics 2023; 18:2160568. [PMID: 36572998 PMCID: PMC9980687 DOI: 10.1080/15592294.2022.2160568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/11/2022] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is an epigenetic process altered in cancer and ageing. Age-related methylation drift can be used to estimate lifespan and can be influenced by extrinsic factors such as diet. Here, we report that non-pathogenic microbiota accelerate age-related methylation drift in the colon when compared with germ-free mice. DNA methylation analyses showed that microbiota and IL10KO were associated with changes in 5% and 4.1% of CpG sites, while mice with both factors had 18% alterations. Microbiota, IL10KO, and their combination altered 0.4%, 0.4%, and 4% of CpG island methylation, respectively. These are comparable to what is seen in colon cancer. Ageing changes were accelerated in the IL10KO mice with microbiota, and the affected genes were more likely to be altered in colon cancer. Thus, the microbiota affect DNA methylation of the colon in patterns reminiscent of what is observed in ageing and colorectal cancer.
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Affiliation(s)
- Ang Sun
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
| | - Pyounghwa Park
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Lauren Cole
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
| | - Himani Vaidya
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Shinji Maegawa
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Research Department of Pediatrics, University of Texas, MD Anderson Cancer Center Department of Pediatrics, University of Texas, MD Anderson Cancer CenterHouston, TX, USA
| | - Kelsey Keith
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Gennaro Calendo
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Jozef Madzo
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Jaroslav Jelinek
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Christian Jobin
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Jean-Pierre J. Issa
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
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Rav E, Maegawa S, Gopalakrishnan V, Gordon N. Overview of CD70 as a Potential Therapeutic Target for Osteosarcoma. J Immunol 2023; 211:1067-1072. [PMID: 37722095 DOI: 10.4049/jimmunol.2200591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/25/2023] [Indexed: 09/20/2023]
Abstract
Osteosarcoma is a primary malignant bone tumor. Effective chemotherapy regimens for refractory disease are scarce, accounting for no improvement in survival. Immune-based cell therapies have emerged as novel alternatives. However, advancements with these therapies have been seen mostly when immune cells are armed to target specific tumor Ags. Recent studies identified cluster of differentiation 70 (CD70) as a promising target to osteosarcoma particularly because CD70 is highly expressed in osteosarcoma lung metastases (Pahl et al. 2015. Cancer Cell Int. 15: 31), and its overexpression by tumors has been correlated with immune evasion and tumor proliferation (Yang et al. 2007. Blood 110: 2537-2544). However, the limited knowledge of the overall CD70 expression within normal tissues and the potential for off-target effect pose several challenges (Flieswasser et al. 2022. J. Exp. Clin. Cancer Res. 41: 12). Nonetheless, CD70-based clinical trials are currently ongoing and are preliminarily showing promising results for patients with osteosarcoma. The present review sheds light on the recent literature on CD70 as it relates to osteosarcoma and highlights the benefits and challenges of targeting this pathway.
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Affiliation(s)
- Emily Rav
- Division of Pediatrics, Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shinji Maegawa
- Division of Pediatrics, Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vidya Gopalakrishnan
- Division of Pediatrics, Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nancy Gordon
- Division of Pediatrics, Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX
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Tricarico R, Madzo J, Scher G, Cohen M, Jelinek J, Maegawa S, Nagarathinam R, Scher C, Chang WC, Nicolas E, Slifker M, Zhou Y, Devarajan K, Cai KQ, Kwok T, Nakajima P, Xu J, Mancuso P, Doneddu V, Bagella L, Williams R, Balachandran S, Maskalenko N, Campbell K, Ma X, Cañadas I, Viana-Errasti J, Moreno V, Valle L, Grivennikov S, Peshkova I, Kurilenko N, Mazitova A, Koltsova E, Lee H, Walsh M, Duttweiler R, Whetstine JR, Yen TJ, Issa JP, Bellacosa A. TET1 and TDG Suppress Inflammatory Response in Intestinal Tumorigenesis: Implications for Colorectal Tumors With the CpG Island Methylator Phenotype. Gastroenterology 2023; 164:921-936.e1. [PMID: 36764492 PMCID: PMC10586516 DOI: 10.1053/j.gastro.2023.01.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 12/28/2022] [Accepted: 01/14/2023] [Indexed: 02/12/2023]
Abstract
BACKGROUND & AIMS Aberrant DNA methylation is frequent in colorectal cancer (CRC), but underlying mechanisms and pathologic consequences are poorly understood. METHODS We disrupted active DNA demethylation genes Tet1 and/or Tdg from ApcMin mice and characterized the methylome and transcriptome of colonic adenomas. Data were compared to human colonic adenocarcinomas (COAD) in The Cancer Genome Atlas. RESULTS There were increased numbers of small intestinal adenomas in ApcMin mice expressing the TdgN151A allele, whereas Tet1-deficient and Tet1/TdgN151A-double heterozygous ApcMin colonic adenomas were larger with features of erosion and invasion. We detected reduction in global DNA hypomethylation in colonic adenomas from Tet1- and Tdg-mutant ApcMin mice and hypermethylation of CpG islands in Tet1-mutant ApcMin adenomas. Up-regulation of inflammatory, immune, and interferon response genes was present in Tet1- and Tdg-mutant colonic adenomas compared to control ApcMin adenomas. This up-regulation was also seen in murine colonic organoids and human CRC lines infected with lentiviruses expressing TET1 or TDG short hairpin RNA. A 127-gene inflammatory signature separated colonic adenocarcinomas into 4 groups, closely aligned with their microsatellite or chromosomal instability and characterized by different levels of DNA methylation and DNMT1 expression that anticorrelated with TET1 expression. Tumors with the CpG island methylator phenotype (CIMP) had concerted high DNMT1/low TET1 expression. TET1 or TDG knockdown in CRC lines enhanced killing by natural killer cells. CONCLUSIONS Our findings reveal a novel epigenetic regulation, linked to the type of genomic instability, by which TET1/TDG-mediated DNA demethylation decreases methylation levels and inflammatory/interferon/immune responses. CIMP in CRC is triggered by an imbalance of methylating activities over demethylating activities. These mice represent a model of CIMP CRC.
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Affiliation(s)
- Rossella Tricarico
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Gabrielle Scher
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Maya Cohen
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Shinji Maegawa
- University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Carly Scher
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Wen-Chi Chang
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Emmanuelle Nicolas
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael Slifker
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yan Zhou
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Karthik Devarajan
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Kathy Q Cai
- Experimental Histopathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Tim Kwok
- Cell Culture Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Pamela Nakajima
- Cell Culture Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jinfei Xu
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Pietro Mancuso
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Valentina Doneddu
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania
| | - Riley Williams
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Siddharth Balachandran
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Nicholas Maskalenko
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Kerry Campbell
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Xueying Ma
- Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Israel Cañadas
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Julen Viana-Errasti
- Hereditary Cancer Program Catalan Institute of Oncology, Oncobell Program, Investigación Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology, Oncobell Program, Investigación Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Laura Valle
- Hereditary Cancer Program Catalan Institute of Oncology, Oncobell Program, Investigación Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Sergei Grivennikov
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Iuliia Peshkova
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Natalia Kurilenko
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Aleksandra Mazitova
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ekaterina Koltsova
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Hayan Lee
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Martin Walsh
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Reuben Duttweiler
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Timothy J Yen
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Alfonso Bellacosa
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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Vaidya H, Jeong HS, Keith K, Maegawa S, Calendo G, Madzo J, Jelinek J, Issa JPJ. Author Correction: DNA methylation entropy as a measure of stem cell replication and aging. Genome Biol 2023; 24:104. [PMID: 37122020 PMCID: PMC10150501 DOI: 10.1186/s13059-023-02943-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Affiliation(s)
- Himani Vaidya
- Coriell Institute for Medical Research, Camden, NJ, 08013, USA
| | - Hye Seon Jeong
- Coriell Institute for Medical Research, Camden, NJ, 08013, USA
- Department of Neurology, Chungnam National University Hospital, Daejeon, South Korea
| | - Kelsey Keith
- Coriell Institute for Medical Research, Camden, NJ, 08013, USA
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Gennaro Calendo
- Coriell Institute for Medical Research, Camden, NJ, 08013, USA
| | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, NJ, 08013, USA
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Vaidya H, Jeong HS, Keith K, Maegawa S, Calendo G, Madzo J, Jelinek J, Issa JPJ. DNA methylation entropy as a measure of stem cell replication and aging. Genome Biol 2023; 24:27. [PMID: 36797759 PMCID: PMC9933260 DOI: 10.1186/s13059-023-02866-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 02/05/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Epigenetic marks are encoded by DNA methylation and accumulate errors as organisms age. This drift correlates with lifespan, but the biology of how this occurs is still unexplained. We analyze DNA methylation with age in mouse intestinal stem cells and compare them to nonstem cells. RESULTS Age-related changes in DNA methylation are identical in stem and nonstem cells, affect most prominently CpG islands and correlate weakly with gene expression. Age-related DNA methylation entropy, measured by the Jensen-Shannon Distribution, affects up to 25% of the detectable CpG sites and is a better measure of aging than individual CpG methylation. We analyze this entropy as a function of age in seven other tissues (heart, kidney, skeletal muscle, lung, liver, spleen, and blood) and it correlates strikingly with tissue-specific stem cell division rates. Thus, DNA methylation drift and increased entropy with age are primarily caused by and are sensors for, stem cell replication in adult tissues. CONCLUSIONS These data have implications for the mechanisms of tissue-specific functional declines with aging and for the development of DNA-methylation-based biological clocks.
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Affiliation(s)
- Himani Vaidya
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
| | - Hye Seon Jeong
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA ,grid.411665.10000 0004 0647 2279Department of Neurology, Chungnam National University Hospital, Daejeon, South Korea
| | - Kelsey Keith
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
| | - Shinji Maegawa
- grid.240145.60000 0001 2291 4776Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX USA
| | - Gennaro Calendo
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
| | - Jozef Madzo
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
| | - Jaroslav Jelinek
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
| | - Jean-Pierre J. Issa
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ 08013 USA
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Lee J, Savage H, Maegawa S, Ballarò R, Pareek S, Guerrouahen BS, Gopalakrishnan V, Schadler K. Exercise Promotes Pro-Apoptotic Ceramide Signaling in a Mouse Melanoma Model. Cancers (Basel) 2022; 14:cancers14174306. [PMID: 36077841 PMCID: PMC9454537 DOI: 10.3390/cancers14174306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Exercise has been shown to improve the efficacy of chemotherapy against several tumor models using mice through modulating tumor vascular perfusion, immune function, circulating growth factors, hypoxia, and metabolism in tumor cells and their surrounding microenvironment. However, little is known about the effect of exercise on tumor-cell-intrinsic death mechanisms, such as apoptosis. Ceramide is a bioactive lipid that can promote cell death. The strategy of increasing intracellular ceramide has potential as an anticancer treatment for melanoma with dysregulated ceramide metabolism, but there is not yet a clinically relevant method to do so. We found that moderate aerobic exercise increases pro-apoptotic ceramide in melanoma in mice, and activates p53 signaling, promoting tumor cell apoptosis. This finding suggests that exercise may be most effective as an adjuvant therapy to sensitize cancer cells to anticancer treatments in tumors that exhibit downregulated ceramide generation to evade cell death. Abstract Ceramides are essential sphingolipids that mediate cell death and survival. Low ceramide content in melanoma is one mechanism of drug resistance. Thus, increasing the ceramide content in tumor cells is likely to increase their sensitivity to cytotoxic therapy. Aerobic exercise has been shown to modulate ceramide metabolism in healthy tissue, but the relationship between exercise and ceramide in tumors has not been evaluated. Here, we demonstrate that aerobic exercise causes tumor cell apoptosis and accumulation of pro-apoptotic ceramides in B16F10 but not BP melanoma models using mice. B16F10 tumor-bearing mice were treated with two weeks of moderate treadmill exercise, or were control, unexercised mice. A reverse-phase protein array was used to identify canonical p53 apoptotic signaling as a key pathway upregulated by exercise, and we demonstrate increased apoptosis in tumors from exercised mice. Consistent with this finding, pro-apoptotic C16-ceramide, and the ceramide generating enzyme ceramide synthase 6 (CerS6), were higher in B16F10 tumors from exercised mice, while pro-survival sphingosine kinase 1 (Sphk1) was lower. These data suggest that exercise contributes to B16F10 tumor cell death, possibly by modulating ceramide metabolism toward a pro-apoptotic ceramide/sphingosine-1-phosphate balance. However, these results are not consistent in BP tumors, demonstrating that exercise can have different effects on tumors of different patient or mouse origin with the same diagnosis. This work indicates that exercise might be most effective as a therapeutic adjuvant with therapies that kill tumor cells in a ceramide-dependent manner.
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Affiliation(s)
- Jonghae Lee
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hannah Savage
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shinji Maegawa
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Riccardo Ballarò
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sumedha Pareek
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bella Samia Guerrouahen
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vidya Gopalakrishnan
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Keri Schadler
- Department of Pediatrics Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: ; Tel.: +1-(713)-794-1035
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Hasebe T, Maegawa S, Bito K, Kamei S, Edelman E. Abstract No. 114 The newest generation of drug-eluting stent for below-the-knee atherosclerotic disease: hybrid nano-coating Ni-Ti stent. J Vasc Interv Radiol 2022. [DOI: 10.1016/j.jvir.2022.03.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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8
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Swaminathan J, Maegawa S, Shaik S, Sharma A, Bravo-Alegria J, Guo L, Xu L, Harmanci A, Gopalakrishnan V. Cross-Talk Between Histone Methyltransferases and Demethylases Regulate REST Transcription During Neurogenesis. Front Oncol 2022; 12:855167. [PMID: 35600406 PMCID: PMC9120943 DOI: 10.3389/fonc.2022.855167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
The RE1 Silencing Transcription Factor (REST) is a major regulator of neurogenesis and brain development. Medulloblastoma (MB) is a pediatric brain cancer characterized by a blockade of neuronal specification. REST gene expression is aberrantly elevated in a subset of MBs that are driven by constitutive activation of sonic hedgehog (SHH) signaling in cerebellar granular progenitor cells (CGNPs), the cells of origin of this subgroup of tumors. To understand its transcriptional deregulation in MBs, we first studied control of Rest gene expression during neuronal differentiation of normal mouse CGNPs. Higher Rest expression was observed in proliferating CGNPs compared to differentiating neurons. Interestingly, two Rest isoforms were expressed in CGNPs, of which only one showed a significant reduction in expression during neurogenesis. In proliferating CGNPs, higher MLL4 and KDM7A activities opposed by the repressive polycomb repressive complex 2 (PRC2) and the G9A/G9A-like protein (GLP) complex function allowed Rest homeostasis. During differentiation, reduction in MLL4 enrichment on chromatin, in conjunction with an increase in PRC2/G9A/GLP/KDM7A activities promoted a decline in Rest expression. These findings suggest a lineage-context specific paradoxical role for KDM7A in the regulation of Rest expression in CGNPs. In human SHH-MBs (SHH-α and SHH-β) where elevated REST gene expression is associated with poor prognosis, up- or downregulation of KDM7A caused a significant worsening in patient survival. Our studies are the first to implicate KDM7A in REST regulation and in MB biology.
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Affiliation(s)
- Jyothishmathi Swaminathan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Shavali Shaik
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Ajay Sharma
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Javiera Bravo-Alegria
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX, United States
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Department of Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Brain Tumor Center - University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Center for Cancer Epigenetics - University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- MD Anderson-UTHealth Science Center Graduate School of Biomedical Sciences, Houston, TX, United States
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Affiliation(s)
- Shinji Maegawa
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Vidya Gopalakrishnan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,Corresponding Author: Vidya Gopalakrishnan, PhD, 1515 Holcombe Blvd, Unit 853, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 ()
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10
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Shaik S, Maegawa S, Gopalakrishnan V. Medulloblastoma: novel insights into emerging therapeutic targets. Expert Opin Ther Targets 2021; 25:615-619. [PMID: 34602009 DOI: 10.1080/14728222.2021.1982896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Shavali Shaik
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shinji Maegawa
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vidya Gopalakrishnan
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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11
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Shaik S, Maegawa S, Haltom AR, Wang F, Xiao X, Dobson T, Sharma A, Yang Y, Swaminathan J, Kundra V, Li XN, Schadler K, Harmanci A, Xu L, Gopalakrishnan V. REST promotes ETS1-dependent vascular growth in medulloblastoma. Mol Oncol 2021; 15:1486-1506. [PMID: 33469989 PMCID: PMC8096796 DOI: 10.1002/1878-0261.12903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/22/2020] [Accepted: 01/15/2021] [Indexed: 01/03/2023] Open
Abstract
Expression of the RE1‐silencing transcription factor (REST), a master regulator of neurogenesis, is elevated in medulloblastoma (MB) tumors. A cell‐intrinsic function for REST in MB tumorigenesis is known. However, a role for REST in the regulation of MB tumor microenvironment has not been investigated. Here, we implicate REST in remodeling of the MB vasculature and describe underlying mechanisms. Using RESTTG mice, we demonstrate that elevated REST expression in cerebellar granule cell progenitors, the cells of origin of sonic hedgehog (SHH) MBs, increased vascular growth. This was recapitulated in MB xenograft models and validated by transcriptomic analyses of human MB samples. REST upregulation was associated with enhanced secretion of proangiogenic factors. Surprisingly, a REST‐dependent increase in the expression of the proangiogenic transcription factor E26 oncogene homolog 1, and its target gene encoding the vascular endothelial growth factor receptor‐1, was observed in MB cells, which coincided with their localization at the tumor vasculature. These observations were confirmed by RNA‐Seq and microarray analyses of MB cells and SHH‐MB tumors. Thus, our data suggest that REST elevation promotes vascular growth by autocrine and paracrine mechanisms.
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Affiliation(s)
- Shavali Shaik
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Amanda R Haltom
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Feng Wang
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xue Xiao
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tara Dobson
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Ajay Sharma
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Yanwen Yang
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Vikas Kundra
- Departments of Abdominal Imaging and Cancer Systems, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Xiao Nan Li
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Keri Schadler
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX, USA
| | - Lin Xu
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA.,Department of Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA.,Brain Tumor Center, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
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12
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Cheng D, Taylor P, Gireud M, Maegawa S, Yang Y, Majumder S, Gopalakrishnan V. MBRS-64. STUDY OF ARGININE METHYL TRANSFERASES IN MEDULLOBLASTOMA. Neuro Oncol 2020. [PMCID: PMC7715249 DOI: 10.1093/neuonc/noaa222.568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Medulloblastoma is the most common malignant pediatric cancer and a leading cause of childhood cancer-related mortality. There is dire need for new therapies. Molecular sub-classification of medulloblastomas has identified chromatin modifiers as potential drivers of tumorigenesis. Expression of the RE1 Silencing Transcription Factor (REST), a hub for assembly of repressive chromatin remodelers and a known regulator of neurogenesis, is elevated in a subset of human sonic hedgehog (SHH) subgroup medulloblastomas, and is associated with poor prognosis. Using a novel transgenic mouse model, we showed REST to be a driver of medulloblastoma development. Surprisingly, our studies also revealed a role for REST in promoting proliferation of granule cell progenitors (GCPs), the cells of origin of SHH-driven medulloblastoma, and a concomitant loss of telomeres and increased genomic instability. We performed a gain of function screen using a library of chromatin modifiers to understand the mechanism by which proliferative potential was maintained, despite the loss of telomeres. This screen identified the Protein Arginine Methyltransferase 6 (PRMT6) as a high confidence hit. PRMT6 upregulation caused a reduction in CDKN2A, an important regulator of replicative senescence. Evasion of senescence is frequently implicated in tumor progression. Using a chemical screen, we also identified a novel, selective, reversible and competitive inhibitor of PRMT6. The consequence of genetic and pharmacological inhibition of PRMT6 on cell proliferation and senescence will be reported. Thus, our studies are the first to demonstrate a role for arginine methyl transferase family of chromatin modifiers in medulloblastoma genesis.
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Affiliation(s)
- Donghang Cheng
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Pete Taylor
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Monica Gireud
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Yanwen Yang
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Sadhan Majumder
- Department of Genetics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
- Department of Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
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13
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Maegawa S, Dobson T, Lu Y, Estecio M, Harmanci A, Gopalakrishnan V. MBRS-70. FUNCTIONAL DEPENDENCY BETWEEN REST AND DNMT1 IN MEDULLOBLASTOMA. Neuro Oncol 2020. [PMCID: PMC7715790 DOI: 10.1093/neuonc/noaa222.574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Medulloblastomas exhibit poor neuronal lineage specification. Expression of RE1 Silencing Transcription Factor (REST), a repressor of neurogenesis, is aberrantly elevated in human sonic hedgehog (SHH) medulloblastomas. Constitutive REST expression in mice (RESTTG) drives medulloblastoma genesis and promotes tumor progression in the context of Ptch1 haploinsufficiency (Ptch+/−), implicating it as a driver of tumorigenesis. Tumor formation in Ptch+/−/RESTTG mice showed significantly decreased latency and increased penetrance compared to that in Ptch+/− mice. Since REST silences gene expression by chromatin remodeling, we sought to identify cooperating epigenetic events that contributed to its oncogenic activity. To this end, we performed a loss of function screen employing a bar-coded library of short hairpin RNAs against epigenes, to identify candidates whose loss could create a proliferative vulnerability in the context of REST-elevation. This screen identified DNA methyltransferase 1 (DNMT1) as a high-priority epigenetic modifier. DNMT1 and the Ubiquitin like with PHD and Ring finger domain 1 (UHRF1) proteins are essential for methylation of hemi-methylated DNA at the replication fork during S-phase. Their expression is downregulated during neuronal differentiation. In human SHH-medulloblastoma tumors, REST and UHRF1 expression are positively correlated with higher levels of both genes noted specifically in the SHH-beta subtype, and is associated with poor prognosis. The requirement for DNMT1/UHRF1 in the context of REST elevation, was established by RNA-Seq and Reduced Representation Bisulfite Sequencing (RRBS), which revealed hypermethylation and downregulated expression of REST-target genes needed for neurogenesis. Thus, DNMT1/UHRF1 is a functional and potential therapeutic vulnerability in REST-elevated SHH medulloblastomas.
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Affiliation(s)
- Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Tara Dobson
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Marcos Estecio
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
- Department of Leukemia, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Arif Harmanci
- School of Biomedical Informatics, Center for Precision Health, University of Texas Health Science Center, Houston, TX, USA
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
- Department of Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
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14
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Shaik S, Maegawa S, Haltom A, Dobson T, Schadler K, Gopalakrishnan V. MBRS-53. CONTROL OF MEDULLOBLASTOMA VASCULATURE BY A REGULATOR OF NEUROGENESIS. Neuro Oncol 2020. [PMCID: PMC7715809 DOI: 10.1093/neuonc/noaa222.559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Medulloblastomas are characterized by poor neuronal lineage specification. Expression of the RE1 Silencing Transcription Factor (REST), a regulator of neurogenesis, is aberrantly elevated in human sonic hedgehog (SHH) medulloblastomas. Using a novel transgenic mouse (RESTTG) model, we demonstrated that REST is a driver of medulloblastoma genesis and promotes tumor progression in mice with loss of an allele of Ptch1 (Ptch+/−). Tumor formation in Ptch+/−/RESTTG mice occurred with 100% penetrance and a latency of 10–90 days in contrast to Ptch+/− mice, which developed tumors at a frequency of 15–20% at 6–9 months of age. Histopathological analyses showed leptomeningeal dissemination of tumors in Ptch+/−/RESTTG mice, in addition to a significant increase in tumor vasculature compared to tumors in Ptch+/− mice. These findings were recapitulated in xenografted tumors of isogenic low and high-REST medulloblastomas in mice. Proteome profiler human angiogenesis array analyses revealed a REST-dependent increase in vascular endothelial growth factor (VEGF) and placental growth factor (PLGF). Surprisingly, REST elevation also caused co-localization of tumor cells with tumor vasculature, specifically endothelial cells, and was associated with upregulated expression of a number of pro-angiogenic genes, including receptor VEGFR1 and the positive regulator of endothelial differentiation, E26 transformation specific-1 (ETS1), in tumor cells. In addition, expression of several anti-angiogenic molecules was downregulated. Knockdown of ETS1 reversed the above findings. Thus, our data demonstrate that REST elevation not only blocks neurogenesis in medulloblastoma cells, but also modulates the tumor microenvironment by mechanisms that likely involve vascular mimicry.
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Affiliation(s)
- Shavali Shaik
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Amanda Haltom
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Tara Dobson
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Keri Schadler
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
- Department of Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
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15
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Gong S, Maegawa S, Yang Y, Gopalakrishnan V, Zheng G, Cheng D. Licochalcone A is a Natural Selective Inhibitor of Arginine Methyltransferase 6. Biochem J 2020; 478:BCJ20200411. [PMID: 33245113 PMCID: PMC7850898 DOI: 10.1042/bcj20200411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Arginine methylation is a post-translational modification that is implicated in multiple biological functions including transcriptional regulation. The expression of protein arginine methyltransferases (PRMT) has been shown to be upregulated in various cancers. PRMTs have emerged as attractive targets for the development of new cancer therapies. Here, we describe the identification of a natural compound, licochalcone A, as a novel, reversible and selective inhibitor of PRMT6. Since expression of PRMT6 is upregulated in human breast cancers and is associated with oncogenesis, we used the human breast cancer cell line system to study the effect of licochalcone A treatment on PRMT6 activity, cell viability, cell cycle, and apoptosis. We demonstrated that licochalcone A is a non-S-adenosyl L-methionine (SAM) binding site competitive inhibitor of PRMT6. In MCF-7 cells, it inhibited PRMT6-dependent methylation of histone H3 at arginine 2 (H3R2), which resulted in a significant repression of estrogen receptor activity. Licochalcone A exhibited cytotoxicity towards human MCF-7 breast cancer cells, but not MCF-10A human breast epithelial cells, by upregulating p53 expression and blocking cell cycle progression at G2/M, followed by apoptosis. Thus, licochalcone A has potential for further development as a therapeutic agent against breast cancer.
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Affiliation(s)
- Shuai Gong
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, China
| | - Shinji Maegawa
- Departments of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, U.S.A
| | - Yanwen Yang
- Departments of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, U.S.A
| | - Vidya Gopalakrishnan
- Departments of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, U.S.A
- Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, U.S.A
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, U.S.A
| | - Donghang Cheng
- Departments of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, U.S.A
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16
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Shaik S, Maegawa S, Sharma A, Haltom A, Dobson T, Yang Y, Schadler K, Gopalakrishnan V. TAMI-58. A NOVEL ROLE FOR REST IN THE CONTROL OF THE MEDULLOBLASTOMA MICROENVIRONMENT. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
The REI Silensing Transcription Factor (REST) is a transcriptional repressor and a canonical regulator of neurogenesis. Its expression is elevated in human sonic hedgehog (SHH) subgroup of medulloblastomas (MBs), where functional studies shown its elevated expression to promote proliferation and block neuronal specification. A role for REST in the control of the MB tumor microenvironment (TME) has not been described previously. Here, we demonstrate that REST also controls the MB-TME, and specifically vascular remodeling. Using our unique RESTTG mouse model, we show that conditional expression of human REST transgene in cerebellar granule neuron progenitors (CGNPs), the cell of origin of a subset of SHH MBs, promoted increased vascular growth. In the context of constitutive activation of SHH signaling, a key driver of SHH-MB development, REST elevation drove tumor progression by altering the tumor vasculature. These findings were validated in mouse orthotopic models of human MB cell lines and through analyses of publicly available transcriptomic database of human MB samples. A strong positive correlation between REST and that of endothelial genes CD31/VEGFR1/ETS1 was seen in samples from patients with SHH-MBs subtypes that are associated with the worst prognosis. Proteomic analyses identified increased secretion of a number of pro-angiogenic factors in the context of upregulated REST expression in MB cells. Unexpectedly, in vitro and in vivo studies showed that MB cells expressed these endothelial markers and co-localized with endothelial cells suggesting that REST elevation may have altered the fate of cells that were destined to become neurons. Finally, ETS1 knockdown in MB cell lines not only downregulated VEGFR1 levels in these cells, and blocked tube formation in vitro, but also caused a reduction in tumor cell co-localization with endothelial cells. Collectively, these data suggest that REST elevation remodels MB vasculature through cell-intrinsic and cell-extrinsic mechanisms.
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17
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Haltom AR, Toll SA, Cheng D, Maegawa S, Gopalakrishnan V, Khatua S. Medulloblastoma epigenetics and the path to clinical innovation. J Neurooncol 2020; 150:35-46. [PMID: 32816225 DOI: 10.1007/s11060-020-03591-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/06/2020] [Indexed: 12/30/2022]
Abstract
INTRODUCTION In the last decade, a number of genomic and pharmacological studies have demonstrated the importance of epigenetic dysregulation in medulloblastoma initiation and progression. High throughput approaches including gene expression array, next-generation sequencing (NGS), and methylation profiling have now clearly identified at least four molecular subgroups within medulloblastoma, each with distinct clinical and prognostic characteristics. These studies have clearly shown that despite the overall paucity of mutations, clinically relevant events do occur within the cellular epigenetic machinery. Thus, this review aims to provide an overview of our current understanding of the spectrum of epi-oncogenetic perturbations in medulloblastoma. METHODS Comprehensive review of epigenetic profiles of different subgroups of medulloblastoma in the context of molecular features. Epigenetic regulation is mediated mainly by DNA methylation, histone modifications and microRNAs (miRNA). Importantly, epigenetic mis-events are reversible and have immense therapeutic potential. CONCLUSION The widespread epigenetic alterations present in these tumors has generated intense interest in their use as therapeutic targets. We provide an assessment of the progress that has been made towards the development of molecular subtypes-targeted therapies and the current status of clinical trials that have leveraged these recent advances.
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Affiliation(s)
- Amanda R Haltom
- Division of Pediatrics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie A Toll
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Children's Hospital of Michigan, Detroit, USA
| | - Donghang Cheng
- Division of Pediatrics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Shinji Maegawa
- Division of Pediatrics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.,Center for Cancer Epigenetics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Vidya Gopalakrishnan
- Division of Pediatrics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA. .,Department of Molecular and Cellular Oncology, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA. .,Center for Cancer Epigenetics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA. .,Brain Tumor Center, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
| | - Soumen Khatua
- Division of Pediatrics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA. .,Brain Tumor Center, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
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18
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Kennis BA, Michel KA, Brugmann WB, Laureano A, Tao RH, Somanchi SS, Einstein SA, Bravo-Alegria JB, Maegawa S, Wahba A, Kiany S, Gordon N, Silla L, Schellingerhout D, Khatua S, Zaky W, Sandberg D, Cooper L, Lee DA, Bankson JA, Gopalakrishnan V. Correction to: Monitoring of intracerebellarly-administered natural killer cells with fluorine-19 MRI. J Neurooncol 2019; 142:409. [DOI: 10.1007/s11060-019-03162-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Kennis BA, Michel KA, Brugmann WB, Laureano A, Tao RH, Somanchi SS, Einstein SA, Bravo-Alegria JB, Maegawa S, Wahba A, Kiany S, Gordon N, Silla L, Schellingerhout D, Khatua S, Zaky W, Sandberg D, Cooper L, Lee DA, Bankson JA, Gopalakrishnan V. Monitoring of intracerebellarly-administered natural killer cells with fluorine-19 MRI. J Neurooncol 2019; 142:395-407. [DOI: 10.1007/s11060-019-03091-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/05/2019] [Indexed: 01/13/2023]
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20
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Tao Y, Kang B, Petkovich DA, Bhandari YR, In J, Stein-O'Brien G, Kong X, Xie W, Zachos N, Maegawa S, Vaidya H, Brown S, Chiu Yen RW, Shao X, Thakor J, Lu Z, Cai Y, Zhang Y, Mallona I, Peinado MA, Zahnow CA, Ahuja N, Fertig E, Issa JP, Baylin SB, Easwaran H. Aging-like Spontaneous Epigenetic Silencing Facilitates Wnt Activation, Stemness, and Braf V600E-Induced Tumorigenesis. Cancer Cell 2019; 35:315-328.e6. [PMID: 30753828 PMCID: PMC6636642 DOI: 10.1016/j.ccell.2019.01.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/25/2018] [Accepted: 01/07/2019] [Indexed: 11/22/2022]
Abstract
We addressed the precursor role of aging-like spontaneous promoter DNA hypermethylation in initiating tumorigenesis. Using mouse colon-derived organoids, we show that promoter hypermethylation spontaneously arises in cells mimicking the human aging-like phenotype. The silenced genes activate the Wnt pathway, causing a stem-like state and differentiation defects. These changes render aged organoids profoundly more sensitive than young ones to transformation by BrafV600E, producing the typical human proximal BRAFV600E-driven colon adenocarcinomas characterized by extensive, abnormal gene-promoter CpG-island methylation, or the methylator phenotype (CIMP). Conversely, CRISPR-mediated simultaneous inactivation of a panel of the silenced genes markedly sensitizes to BrafV600E-induced transformation. Our studies tightly link aging-like epigenetic abnormalities to intestinal cell fate changes and predisposition to oncogene-driven colon tumorigenesis.
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Affiliation(s)
- Yong Tao
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Byunghak Kang
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Daniel A Petkovich
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Yuba R Bhandari
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Julie In
- Hopkins Conte Digestive Disease, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Genevieve Stein-O'Brien
- Division of Biostatistics & Bioinformatics, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Xiangqian Kong
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Wenbing Xie
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Nicholas Zachos
- Hopkins Conte Digestive Disease, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Unit 853, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Himani Vaidya
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Stephen Brown
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Ray-Whay Chiu Yen
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Xiaojian Shao
- Department of Human Genetics, Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
| | - Jai Thakor
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Zhihao Lu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yi Cai
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Yuezheng Zhang
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Izaskun Mallona
- Germans Trias i Pujol Health Science Research Institute (IGTP), Program for Personalized Medicine of Cancer, Badalona, 08916 Catalonia, Spain
| | - Miguel Angel Peinado
- Germans Trias i Pujol Health Science Research Institute (IGTP), Program for Personalized Medicine of Cancer, Badalona, 08916 Catalonia, Spain
| | - Cynthia A Zahnow
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Nita Ahuja
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA
| | - Elana Fertig
- Division of Biostatistics & Bioinformatics, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jean-Pierre Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Stephen B Baylin
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA.
| | - Hariharan Easwaran
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD 21287, USA.
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Dobson THW, Tao RH, Swaminathan J, Maegawa S, Shaik S, Bravo-Alegria J, Sharma A, Kennis B, Yang Y, Callegari K, Haltom AR, Taylor P, Kogiso M, Qi L, Khatua S, Goldman S, Lulla RR, Fangusaro J, MacDonald TJ, Li XN, Hawkins C, Rajaram V, Gopalakrishnan V. Transcriptional repressor REST drives lineage stage-specific chromatin compaction at Ptch1 and increases AKT activation in a mouse model of medulloblastoma. Sci Signal 2019; 12:12/565/eaan8680. [PMID: 30670636 DOI: 10.1126/scisignal.aan8680] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In medulloblastomas (MBs), the expression and activity of RE1-silencing transcription factor (REST) is increased in tumors driven by the sonic hedgehog (SHH) pathway, specifically the SHH-α (children 3 to 16 years) and SHH-β (infants) subgroups. Neuronal maturation is greater in SHH-β than SHH-α tumors, but both correlate with poor overall patient survival. We studied the contribution of REST to MB using a transgenic mouse model (RESTTG ) wherein conditional NeuroD2-controlled REST transgene expression in lineage-committed Ptch1 +/- cerebellar granule neuron progenitors (CGNPs) accelerated tumorigenesis and increased penetrance and infiltrative disease. This model revealed a neuronal maturation context-specific antagonistic interplay between the transcriptional repressor REST and the activator GLI1 at Ptch1 Expression of Arrb1, which encodes β-arrestin1 (a GLI1 inhibitor), was substantially reduced in proliferating and, to a lesser extent, lineage-committed RESTTG cells compared with wild-type proliferating CGNPs. Lineage-committed RESTTG cells also had decreased GLI1 activity and increased histone H3K9 methylation at the Ptch1 locus, which correlated with premature silencing of Ptch1 These cells also had decreased expression of Pten, which encodes a negative regulator of the kinase AKT. Expression of PTCH1 and GLI1 were less, and ARRB1 was somewhat greater, in patient SHH-β than SHH-α MBs, whereas that of PTEN was similarly lower in both subtypes than in others. Inhibition of histone modifiers or AKT reduced proliferation and induced apoptosis, respectively, in cultured REST-high MB cells. Our findings linking REST to differentiation-specific chromatin remodeling, PTCH1 silencing, and AKT activation in MB tissues reveal potential subgroup-specific therapeutic targets for MB patients.
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Affiliation(s)
- Tara H W Dobson
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rong-Hua Tao
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shavali Shaik
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Javiera Bravo-Alegria
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ajay Sharma
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bridget Kennis
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yanwen Yang
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Keri Callegari
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amanda R Haltom
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pete Taylor
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mari Kogiso
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lin Qi
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Soumen Khatua
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stewart Goldman
- Department of Pediatrics, Northwestern University, Chicago, IL 60611, USA
| | - Rishi R Lulla
- Department of Pediatrics, Northwestern University, Chicago, IL 60611, USA
| | - Jason Fangusaro
- Department of Pediatrics, Northwestern University, Chicago, IL 60611, USA
| | | | - Xiao-Nan Li
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pediatrics, Northwestern University, Chicago, IL 60611, USA
| | - Cynthia Hawkins
- Department of Pathology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Veena Rajaram
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA. .,Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA.,Brain Tumor Center, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for Cancer Epigenetics, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA.,The University of Texas MD Anderson Cancer Center-University of Texas Health Science Center at Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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Callegari K, Maegawa S, Bravo-Alegria J, Gopalakrishnan V. Pharmacological inhibition of LSD1 activity blocks REST-dependent medulloblastoma cell migration. Cell Commun Signal 2018; 16:60. [PMID: 30227871 PMCID: PMC6145331 DOI: 10.1186/s12964-018-0275-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Medulloblastoma (MB) is the most common malignant brain tumor in children. Current problems in the clinic include metastasis, recurrence, and treatment-related sequelae that highlight the need for targeted therapies. Epigenetic perturbations are an established hallmark of human MB and expression of Lysine Specific Demethylase 1 (LSD1) is elevated in MBs compared to normal tissue, suggesting that LSD1 inhibitors may have efficacy against human MB tumors. METHODS Expression of LSD1 was examined across a publicly-available database and correlated with patient outcomes. Sonic Hedgehog (SHH) MB samples were clustered based on expression of LSD1 and LSD1-associated RE-1 silencing transcription factor (REST) target genes as well as genes involved in metastasis. Resulting clusters were examined for patient outcomes associated with LSD1 and REST expression. Human SHH MB cell lines were transduced with a REST-transgene to create isogenic cell pairs. In vitro viability and cell migration assays were used to examine the effect of LSD1 knockdown or inhibition on these parameters. RESULTS We demonstrate that subsets of SHH MB tumors have elevated LSD1 expression coincident with increased expression of its deubiquitylase, USP7, and REST. Patients with co-elevation of USP7, REST, and LSD1 have poorer outcomes compared to those with lower expression of these genes. In SHH MB cell lines, REST elevation increased cell growth and LSD1 protein levels. Surprisingly, while genetic loss of LSD1 reduced cell viability, pharmacological targeting of its activity using LSD1 inhibitors did not affect cell viability. However, a reduction in REST-dependent cell migration was seen in wound healing, suggesting that REST-LSD1 interaction regulates cell migration. Ingenuity pathway analyses validated these findings and identified Hypoxia Inducible Factor 1 alpha (HIF1A) as a potential target. In line with this, ectopic expression of HIF1A rescued the loss of migration seen following LSD1 inhibition. CONCLUSIONS A subset of SHH patients display increased levels of LSD1 and REST, which is associated with poor outcomes. REST elevation in MB in conjunction with elevated LSD1 promotes MB cell migration. LSD1 inhibition blocks REST-dependent cell migration of MB cells in a HIF1A-dependent manner.
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Affiliation(s)
- Keri Callegari
- Department of Pediatrics, University of Texas M.D. Anderson Cancer Center, Unit 853, 1515 Holcombe Blvd, Houston, TX, 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Austin, USA
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas M.D. Anderson Cancer Center, Unit 853, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Javiera Bravo-Alegria
- Department of Pediatrics, University of Texas M.D. Anderson Cancer Center, Unit 853, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas M.D. Anderson Cancer Center, Unit 853, 1515 Holcombe Blvd, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Brain Tumor Center, University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. .,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Austin, USA.
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23
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Shaik S, Kennis B, Maegawa S, Schadler K, Yanwen Y, Callegari K, Lulla R, Goldman S, Nazarian J, Rajaram V, Fangusaro J, Gopalakrishnan V. DIPG-64. REST MODULATES NEOVASCULATURE VIA REGULATION OF GREMLIN EXPRESSION IN DIFFUSE INTRINSIC PONTINE GLIOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | | | - Yang Yanwen
- M.D. Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - Javad Nazarian
- George Washington University School of Medicine, Washington, DC, USA
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Bravo-Alegria J, Maegawa S, Callegari K, Kennis B, Ma W, Brugmann W, Rao A, Lee DA, Khatua S, Zaky W, Sandberg D, Goldman S, Gopalakrishnan V. IMMU-22. NATURAL KILLER CELL IMMUNOTHERAPY FOR DIFFUSE INTRINSIC PONTINE GLIOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Shinji Maegawa
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keri Callegari
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bridget Kennis
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wencai Ma
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Arvind Rao
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dean Anthony Lee
- Nationwide Children’s Hospital and The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Soumen Khatua
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wafik Zaky
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Sandberg
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stewart Goldman
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
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25
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Tao RH, Dobson T, Maegawa S, Swaminathan J, Shaik S, Taylor P, Kennis B, Qi L, Khatua S, Goldman S, Lulla R, Fangusaro J, MacDonald T, Li XN, Hawkins C, Rajaram V, Gopalakrishnan V. MBRS-62. REPRESSIVE CHROMATIN REMODELERS IN SHH-DRIVEN MEDULLOBLASTOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Tara Dobson
- UT MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - Pete Taylor
- UT MD Anderson Cancer Center, Houston, TX, USA
| | | | - Lin Qi
- Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | | | - Xiao-Nan Li
- Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX, USA
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26
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Shaik S, Kennis B, Maegawa S, Schadler K, Yanwen Y, Callegari K, Lulla RR, Goldman S, Nazarian J, Rajaram V, Fangusaro J, Gopalakrishnan V. REST upregulates gremlin to modulate diffuse intrinsic pontine glioma vasculature. Oncotarget 2018; 9:5233-5250. [PMID: 29435175 PMCID: PMC5797046 DOI: 10.18632/oncotarget.23750] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/16/2017] [Indexed: 12/30/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive glial tumor that occurs in children. The extremely poor median and 5-year survival in children afflicted with DIPG highlights the need for novel biology-driven therapeutics. Here, we have implicated the chromatin remodeler and regulator of brain development called RE1 Silencing Transcription Factor (REST), in DIPG pathology. We show that REST protein is aberrantly elevated in at least 21% of DIPG tumors compared to normal controls. Its knockdown in DIPG cell lines diminished cell growth and decreased their tumorigenicity in mouse intracranial models. DIPGs are vascularized tumors and interestingly, REST loss in DIPG cells also caused a substantial decline in tumor vasculature as measured by a decrease in CD31 and VEGFR2 staining. These observations were validated in vitro, where a significant decline in tube formation by human umbilical vein endothelial cells (HUVEC) was seen following REST-loss in DIPG cells. Mechanistically, REST controlled the secretion of a pro-angiogenic molecule and ligand for VEGFR2 called Gremlin-1 (GREM-1), and was associated with enhanced AKT activation. Importantly, the decline in tube formation caused by REST loss could be rescued by addition of recombinant GREM-1, which also caused AKT activation in HUVECs and human brain microvascular endothelial cells (HBMECs). In summary, our study is the first to demonstrate autocrine and paracrine functions for REST in DIPG development. It also provides the foundation for future investigations on anti-angiogenic therapies targeting GREM-1 in combination with drugs that target REST-associated chromatin remodeling activities.
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Affiliation(s)
- Shavali Shaik
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Bridget Kennis
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Keri Schadler
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Yang Yanwen
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Keri Callegari
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Rishi R. Lulla
- Department of Pediatrics, Northwestern Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Stewart Goldman
- Department of Pediatrics, Northwestern Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Javad Nazarian
- Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Veena Rajaram
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jason Fangusaro
- Department of Pediatrics, Northwestern Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
- Department of Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
- Center for Cancer Epigenetics, University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
- Brain Tumor Center, University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
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27
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Good CR, Madzo J, Patel B, Maegawa S, Engel N, Jelinek J, Issa JPJ. A novel isoform of TET1 that lacks a CXXC domain is overexpressed in cancer. Nucleic Acids Res 2017; 45:8269-8281. [PMID: 28531272 PMCID: PMC5737541 DOI: 10.1093/nar/gkx435] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/14/2017] [Accepted: 05/03/2017] [Indexed: 02/07/2023] Open
Abstract
TET1 oxidizes methylated cytosine into 5-hydroxymethylcytosine (5hmC), resulting in regulation of DNA methylation and gene expression. Full length TET1 (TET1FL) has a CXXC domain that binds to unmethylated CpG islands (CGIs). This CXXC domain allows TET1 to protect CGIs from aberrant methylation, but it also limits its ability to regulate genes outside of CGIs. Here, we report a novel isoform of TET1 (TET1ALT) that has a unique transcription start site from an alternate promoter in intron 2, yielding a protein with a unique translation start site. Importantly, TET1ALT lacks the CXXC domain but retains the catalytic domain. TET1ALT is repressed in embryonic stem cells (ESCs) but becomes activated in embryonic and adult tissues while TET1FL is expressed in ESCs, but repressed in adult tissues. Overexpression of TET1ALT shows production of 5hmC with distinct (and weaker) effects on DNA methylation or gene expression when compared to TET1FL. TET1ALT is aberrantly activated in multiple cancer types including breast, uterine and glioblastoma, and TET1 activation is associated with a worse overall survival in breast, uterine and ovarian cancers. Our data suggest that the predominantly activated isoform of TET1 in cancer cells does not protect from CGI methylation and likely mediates dynamic site-specific demethylation outside of CGIs.
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Affiliation(s)
- Charly R. Good
- 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
| | - Bela Patel
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Shinji Maegawa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Nora Engel
- 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
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Sun A, Jelinek J, Maegawa S, Jobin C, Issa JP. Abstract 4441: Non-pathogenic bacteria change host DNA methylation in vivo. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: More than a thousand species of bacteria live in a normal person's gastrointestinal tract. Epigenetic effects on the colon directly caused by the commensal bacteria remain elusive. In the current study, we explore the bacterial effects on DNA methylation of the host colon. Methods: Eight non-pathogenic bacterial species were introduced to the gut of germ-free (GF) mice to make specific-pathogen free (SPF) mice. Our study consisted of the following groups (n = 6 for each): wildtype (WT) GF, WT SPF, IL-10 knockout (KO) GF, IL-10 KO SPF, and IL-10 KO GF or SPF treated with azoxymethane (AOM). We analyzed DNA methylation in genomic DNA extracted from the proximal colon using Digital Restriction Enzyme Analysis of Methylation (DREAM) and compared methylation levels at CpG sites among different groups. Results: 1) Principal component analysis (PCA) performed on methylomes of all the samples separated the mouse samples based on presence or absence of bacteria, IL-10 KO status or AOM treatment into 6 distinct groups. 2) We analyzed CpG sites differentially methylated between GF and SPF mice at p<0.05 significance level. In WT mice, there were 1871 CpG sites (11% out of 17475 analyzed sites), in IL10 KO mice, there were 5986 CpG sites (33% out of 18254 analyzed sites) and in IL10 KO AOM-treated mice there were 6755 CpG sites (31% out of 21697 analyzed sites) differentially methylated. 3) There were 756 common CpG sites differentially methylated in all SPF vs GF comparisons. Interestingly, these sites were enriched 2.6-fold for aging-related CpG sites. 4) WT SPF mice showed increased methylation at CpG sites hypomethylated in WT GF mice and, conversely, decreased methylation at CpG sites hypermethylated in WT GF mice. This pattern of DNA methylation change was also observed by comparing GF with SPF in IL-10 KO mice with or without AOM treatment. 5) Both in GF and SPF mice the DNA methylation changes were more pronounced in IL10 KO while AOM had little additional effect. 6) IL10 KO resulted in genome-wide increase of methylation. However, the introduction of bacteria in SPF mice resulted in the methylation change mainly at CpG islands. Conclusions: Non-pathogenic bacteria introduced in the colon cause methylation gains at CpG sites with low DNA methylation and methylation losses at sites with high DNA methylation in a pattern similar to the changes observed in aging and cancer.
Citation Format: Ang Sun, Jaroslav Jelinek, Shinji Maegawa, Christian Jobin, Jean-Pierre Issa. Non-pathogenic bacteria change host DNA methylation in vivo. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4441.
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Affiliation(s)
- Ang Sun
- 1Fels Institute for Cancer Research and Molecular Biology,School of Medicine, Temple University, Philadelphia, PA
| | - Jaroslav Jelinek
- 1Fels Institute for Cancer Research and Molecular Biology,School of Medicine, Temple University, Philadelphia, PA
| | - Shinji Maegawa
- 1Fels Institute for Cancer Research and Molecular Biology,School of Medicine, Temple University, Philadelphia, PA
| | - Christian Jobin
- 2Department of Medicine, Division of Gastroenterology, College of Medicine, University of Florida, Gainesville, FL
| | - Jean-Pierre Issa
- 1Fels Institute for Cancer Research and Molecular Biology,School of Medicine, Temple University, Philadelphia, PA
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Abstract
Abstract
TET1 is a DNA demethylase that regulates DNA methylation, hydroxymethylation and gene expression patterns. It has a catalytic domain that oxidizes methylated cytosine into 5-hydroxymethylcytosine and can then be further oxidized or converted to un-methylated cytosine. TET1 has a CXXC domain that allows it to recognize and bind to long stretches of CpG dinucleotides, known as CpG islands (CGIs). Our previous work found TET1 to protect CGIs from aberrant methylation and that the CXXC domain limits its ability to regulate genes outside of CGIs. However, many of the methylation changes in cancer are outside CGIs. To determine if TET1 could possibly play a role in this hypomethylation, we searched for alternatively spliced forms of the protein. We identified a novel isoform of TET1 (TET1ALT) that lacks the CXXC domain but retains the demethylase domain. TET1ALT has a unique transcription start site from a strong alternate promoter upstream of exon 3, yielding a protein with a unique translation start site. We confirmed promoter activity using Luciferase constructs, and confirmed TET1ALT translation and function through overexpression experiments. Gene expression analyses by qPCR found that TET1ALT is silenced in mESCs but becomes activated in select embryonic and adult tissues while full length TET1 is favored in mESCs, but is repressed in adult tissues. Thus, there is an isoform switch during differentiation and TET1ALT is the major isoform expressed in adult cells. TET1ALT is over expressed in several cancer cell lines, including breast cancer. In conclusion, we have identified a novel isoform of TET1 that has the potential to regulate DNA methylation outside of CGIs and is the predominant isoform expressed in adult cells. We are investigating the hypothesis that TET1ALT may contribute to the methylation changes observed in cancer outside of CGIs, such as in gene bodies and in enhancers.
Citation Format: Charly R. Good, Jozef Madzo, Shinji Maegawa, Nora Engel, Jaroslav Jelinek, Jean-Pierre Issa. A novel isoform of TET1 that lacks a CXXC domain is overexpressed in cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2659.
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Affiliation(s)
- Charly R. Good
- Fels Institute at Temple University School of Medicine, Philadelphia, PA
| | - Jozef Madzo
- Fels Institute at Temple University School of Medicine, Philadelphia, PA
| | - Shinji Maegawa
- Fels Institute at Temple University School of Medicine, Philadelphia, PA
| | - Nora Engel
- Fels Institute at Temple University School of Medicine, Philadelphia, PA
| | - Jaroslav Jelinek
- Fels Institute at Temple University School of Medicine, Philadelphia, PA
| | - Jean-Pierre Issa
- Fels Institute at Temple University School of Medicine, Philadelphia, PA
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Kang B, In J, Zachos N, Huso D, Maegawa S, Issa JP, Easwaran H, Baylin SB. Abstract 4273: Oncogenic BRAFV600E drives stem cell niche factors-independent growth and tumorigenic transformation in colon organoids. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Herein, we report a model for how BRAF mutations, in contrast to KRAS mutations, specifically associate with and induce, in mouse colon organoids without a microenvironment, the phenotype of human sporadic right-sided colon adenocarcinomas (COAD). The human BRAF mutant COAD are particularly distinguished by having an increased incidence of promoter CpG island methylation, termed CpG island methylator phenotype (CIMP)-High. This latter phenotype contrasts with the majority of the COAD which are classified in the CIMP-low to intermediate groups and have mostly KRAS mutations. To understand how these mutations influence tumor evolution and the methylation landscape, we modeled the early carcinogenesis of colorectal cancer by inducing BRAFV600E and KRASG12D mutations individually in 3D organoids prepared from mouse proximal colon. The induction of BRAFV600E mutation, but not KRASG12D mutation, showed various features of progressive transformation. In vitro induction of BRAFV600E drove the organoids to derive cystic changes in morphology and promoted adoption of a stem cell niche independency characterized by growth in the absence of added stem cell niche factors including Wnt3a, R-Spondin, and Noggin. This independency is not due to increased secretion of niche factors by the Paneth-like cells in BRAFV600E mutant organoids. In addition, BRAFV600E organoids showed dysplastic changes such as high nuclear to cytoplasmic ratio and abnormal budding. The most exciting finding is that induction of BRAFV600E mutation, but not KRASG12D mutation, induced complete transformation of the organoids forming xenograft tumors in NOD/SCID mice. The tumors exhibit histological characteristics of human mucinous adenocarcinoma, which is the tumor type highly associated with BRAFV600E mutation in human COAD. Gene expression analyses revealed up-regulation of intestinal stem cell signature genes and down-regulation of genes related to intestinal differentiation in BRAFV600E organoids. In addition, BRAFV600E organoids showed increased expression levels of Wnt pathway target genes indicating an enhanced and sustained Wnt-signaling. Analyses of CpG-island methylation in a panel of genes showed increased CpG-island methylation only in the BRAFV600E mutant organoids. In conclusion, in mouse colon organoids, BRAFV600E drives a human right-sided COAD phenotype with adoption of a stem cell niche independency, activation of the Wnt pathway, and induction of CpG island methylation.
Citation Format: Byunghak Kang, Julie In, Nicholas Zachos, David Huso, Shinji Maegawa, Jean-Pierre Issa, Hariharan Easwaran, Stephen B. Baylin. Oncogenic BRAFV600E drives stem cell niche factors-independent growth and tumorigenic transformation in colon organoids. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4273.
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Affiliation(s)
| | - Julie In
- 1Johns Hopkins University, Baltimore, MD
| | | | - David Huso
- 1Johns Hopkins University, Baltimore, MD
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Tahara T, Maegawa S, Chung W, Garriga J, Jelinek J, Estécio MRH, Shibata T, Hirata I, Arisawa T, Issa JPJ. Examination of whole blood DNA methylation as a potential risk marker for gastric cancer. Cancer Prev Res (Phila) 2013; 6:1093-100. [PMID: 23943784 DOI: 10.1158/1940-6207.capr-13-0034] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Whole blood DNA methylation analysis has been proposed to be a risk marker for cancer that can be used to target patients for preventive interventions. To test this, we examined whole blood DNA methylation of 16 CpG island promoters and LINE1 repetitive element in patients with gastric cancer and control subjects. Bisulfite pyrosequencing was used to quantify the methylation of 14 CpG island promoters (MINT25, RORA, GDNF, CDH1, RARAB2, ER, CDH13, MYOD1, SFRP1, P2RX7, SLC16A12, IGF2, DPYS, and N33) and LINE1 from 72 patients with gastric cancer, 67 control, and 52 healthy young individuals. Quantitative methylation-specific real-time PCR was also conducted for 3 CpG island promoters (MINT25, MYO3A, and SOX11). Among all sites tested, only a marginal increase in the methylation of the SFRP1 promoter was observed in the blood of patients with gastric cancer when compared with the control group (11.3 % vs 10.5%; age-adjusted P value: P = 0.009), and this association was also seen in a validation set of 91 patients with gastric cancer (11.5% vs 10.5%; age-adjusted P value: P = 0.001). The methylation of 9 sites (GDNF, CDH1, RARAB2, CDH13, MYOD1, SFRP1, SLC16A12, DPYS, N33, and LINE1) and their mean Z score was correlated with higher age (R = 0.41, P < 0.0001) and marginally with telomere shortening (R = -0.18, P = 0.01) but not with gastric cancer risk (other than SFRP1 methylation). Variability in whole blood DNA methylation of cancer markers is primarily associated with aging, reflecting turnover of white blood cells, and has no direct link to gastric cancer predisposition. SFRP1 methylation in whole blood may be associated with gastric cancer risk.
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Affiliation(s)
- Tomomitsu Tahara
- Temple University School of Medicine, 3307 N. Broad Street, Room 154 PAHB, Philadelphia, PA 19140.
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Burzurí E, Luis F, Montero O, Barbara B, Ballou R, Maegawa S. Quantum interference oscillations of the superparamagnetic blocking in an Fe8 molecular nanomagnet. Phys Rev Lett 2013; 111:057201. [PMID: 23952438 DOI: 10.1103/physrevlett.111.057201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 05/17/2013] [Indexed: 06/02/2023]
Abstract
We show that the dynamic magnetic susceptibility and the superparamagnetic blocking temperature of an Fe(8) single molecule magnet oscillate as a function of the magnetic field H(x) applied along its hard magnetic axis. These oscillations are associated with quantum interferences, tuned by H(x), between different spin tunneling paths linking two excited magnetic states. The oscillation period is determined by the quantum mixing between the ground S=10 and excited multiplets. These experiments enable us to quantify such mixing. We find that the weight of excited multiplets in the magnetic ground state of Fe(8) amounts to approximately 11.6%.
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Affiliation(s)
- E Burzurí
- Instituto de Ciencia de Materiales de Aragón, CSIC-Universidad de Zaragoza, E-50009 Zaragoza, Spain
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Tashiro H, Nishiyama M, Oyamada A, Itou T, Maegawa S, Yano M, Ono T, Tanaka H. Effect of DM interaction in a quantum antiferromagnet on a deformed kagome lattice, Rb2Cu3SnF12. ACTA ACUST UNITED AC 2011. [DOI: 10.1088/1742-6596/320/1/012052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Burzurí E, Luis F, Barbara B, Ballou R, Ressouche E, Montero O, Campo J, Maegawa S. Magnetic dipolar ordering and quantum phase transition in an Fe8 molecular magnet. Phys Rev Lett 2011; 107:097203. [PMID: 21929265 DOI: 10.1103/physrevlett.107.097203] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Indexed: 05/31/2023]
Abstract
We show that a crystal of mesoscopic Fe(8) single-molecule magnets is an experimental realization of the quantum Ising model in a transverse field, with dipolar interactions. Quantum annealing has enabled us to explore the quantum and classical phase transitions between the paramagnetic and ferromagnetic phases, at thermodynamical equilibrium. The phase diagram and critical exponents that we obtain agree with expectations for the mean-field universality class.
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Affiliation(s)
- E Burzurí
- Instituto de Ciencia de Materiales de Aragón, C.S.I.C.-Universidad de Zaragoza, and Departamento de Física de la Materia Condensada, Universidad de Zaragoza, E-50009 Zaragoza, Spain
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Fini L, Piazzi G, Daoud Y, Selgrad M, Maegawa S, Garcia M, Fogliano V, Romano M, Graziani G, Vitaglione P, Carmack SW, Gasbarrini A, Genta RM, Issa JP, Boland CR, Ricciardiello L. Chemoprevention of intestinal polyps in ApcMin/+ mice fed with western or balanced diets by drinking annurca apple polyphenol extract. Cancer Prev Res (Phila) 2011; 4:907-15. [PMID: 21383028 DOI: 10.1158/1940-6207.capr-10-0359] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Western diet (WD) is associated with a higher incidence of colorectal cancer (CRC) than the Mediterranean diet. Polyphenols extracted from Annurca apple showed chemopreventive properties in CRC cells. A multifactorial, four-arm study by using wild-type (wt) and Apc(Min/+) mice was carried out to evaluate the effect on polyp number and growth of APE treatment (60 μmol/L) ad libitum in drinking water combined with a WD or a balanced diet (BD) for 12 weeks. Compared with APE treatment, we found a significant drop in body weight (P < 0.0001), severe rectal bleeding (P = 0.0076), presence of extraintestinal tumors, and poorer activity status (P = 0.0034) in water-drinking Apc(Min/+) mice, more remarkably in the WD arm. In the BD and WD groups, APE reduced polyp number (35% and 42%, respectively, P < 0.001) and growth (60% and 52%, respectively, P < 0.0001) in both colon and small intestine. Increased antioxidant activity was found in wt animals fed both diets and in Apc(Min/+) mice fed WD and drinking APE. Reduced lipid peroxidation was found in Apc(Min/+) mice drinking APE fed both diets and in wt mice fed WD. In normal mucosa, mice drinking water had lower global levels of DNA methylation than mice drinking APE. APE treatment is highly effective in reducing polyps in Apc(Min/+) mice and supports the concept that a mixture of phytochemicals, as they are naturally present in foods, represent a plausible chemopreventive agent for CRC, particularly in populations at high risk for colorectal neoplasia.
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Affiliation(s)
- Lucia Fini
- Department of Internal Medicine, Baylor Research Institute, Sammons Cancer Center, USA
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Hayashi S, Yoshida M, Fujiwara T, Maegawa S, Fukusaki E. Single-Embryo Metabolomics and Systematic Prediction of Developmental Stage in Zebrafish. Z NATURFORSCH C 2011. [DOI: 10.5560/znc.2011.66c0191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Estécio MR, Gallegos J, Vallot C, Castoro RJ, Chung W, Maegawa S, Oki Y, Kondo Y, Jelinek J, Shen L, Hartung H, Aplan PD, Czerniak BA, Liang S, Issa JPJ. Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. Genome Res 2010; 20:1369-82. [DOI: 10.1101/gr.107318.110] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epigenetic silencing plays an important role in cancer development. An attractive hypothesis is that local DNA features may participate in differential predisposition to gene hypermethylation. We found that, compared with methylation-resistant genes, methylation-prone genes have a lower frequency of SINE and LINE retrotransposons near their transcription start site. In several large testing sets, this distribution was highly predictive of promoter methylation. Genome-wide analysis showed that 22% of human genes were predicted to be methylation-prone in cancer; these tended to be genes that are down-regulated in cancer and that function in developmental processes. Moreover, retrotransposon distribution marks a larger fraction of methylation-prone genes compared to Polycomb group protein (PcG) marking in embryonic stem cells; indeed, PcG marking and our predictive model based on retrotransposon frequency appear to be correlated but also complementary. In summary, our data indicate that retrotransposon elements, which are widespread in our genome, are strongly associated with gene promoter DNA methylation in cancer and may in fact play a role in influencing epigenetic regulation in normal and abnormal physiological states.
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Maegawa S, Hinkal G, Kim HS, Shen L, Zhang L, Zhang J, Zhang N, Liang S, Donehower LA, Issa JPJ. Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res 2010; 20:332-40. [PMID: 20107151 DOI: 10.1101/gr.096826.109] [Citation(s) in RCA: 379] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aberrant methylation of promoter CpG islands in cancer is associated with silencing of tumor-suppressor genes, and age-dependent hypermethylation in normal appearing mucosa may be a risk factor for human colon cancer. It is not known whether this age-related DNA methylation phenomenon is specific to human tissues. We performed comprehensive DNA methylation profiling of promoter regions in aging mouse intestine using methylated CpG island amplification in combination with microarray analysis. By comparing C57BL/6 mice at 3-mo-old versus 35-mo-old for 3627 detectable autosomal genes, we found 774 (21%) that showed increased methylation and 466 (13%) that showed decreased methylation. We used pyrosequencing to quantitatively validate the microarray data and confirmed linear age-related methylation changes for all 12 genomic regions examined. We then examined 11 changed genomic loci for age-related methylation in other tissues. Of these, three of 11 showed similar changes in lung, seven of 11 changed in liver, and six of 11 changed in spleen, though to a lower degree than the changes seen in colon. There was partial conservation between age-related hypermethylation in human and mouse intestines, and Polycomb targets in embryonic stem cells were enriched among the hypermethylated genes. Our findings demonstrate a surprisingly high rate of hyper- and hypomethylation as a function of age in normal mouse small intestine tissues and a strong tissue-specificity to the process. We conclude that epigenetic deregulation is a common feature of aging in mammals.
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Affiliation(s)
- Shinji Maegawa
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
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Itou T, Oyamada A, Maegawa S, Tamura M, Kato R. 13C NMR study of the spin-liquid state in the triangular quantum antiferromagnet EtMe3Sb[Pd(dmit)2]2. ACTA ACUST UNITED AC 2009. [DOI: 10.1088/1742-6596/145/1/012039] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Otsuka S, Maegawa S, Takamura A, Kamitani H, Watanabe T, Oshimura M, Nanba E. Aberrant promoter methylation and expression of the imprinted PEG3 gene in glioma. Proc Jpn Acad Ser B Phys Biol Sci 2009; 85:157-165. [PMID: 19367087 PMCID: PMC3524298 DOI: 10.2183/pjab.85.157] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 03/04/2009] [Indexed: 05/27/2023]
Abstract
Glioma includes astrocytoma, oligodendroglioma, ependymoma and glioblastoma. We previously reported the epigenetic silencing of paternally expressed gene 3 (PEG3) in glioma cell lines. In this study, we investigated methylation of an exonic CpG island in the promoter region and the expression of PEG3 gene in 20 glioma and 5 non-tumor tissue samples. We found wide variations in the methylation level. Hypomethylaiton and hypermethylation was found in 3 and 4 glioma tissue samples, respectively. Monoallelic expression, which is an evidence of an imprinted gene, was maintained in eight out of nine informative cases which have T/C polymorphisms in PEG3. The lower gene expression, which suggested epigenetic silencing of PEG3, was confirmed statistically in glioblastoma using quantitative reverse-transcription polymerase chain reaction. Interestingly, we found higher expression of PEG3 in two out of three oligodendrogliomas. A negative correlation between the methylation level and gene expression was shown by regression analysis. These results suggest that the abnormal regulation of PEG3 is associated with several glioma subtypes and that it plays an important role in tumorigenesis.
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Affiliation(s)
- Susumu Otsuka
- Division of Functional Genomics, Research Center for Bioscience and Technology, Tottori University, Tottori, Japan
- Department of Biomedical Science, Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori, Japan
| | - Shinji Maegawa
- Division of Functional Genomics, Research Center for Bioscience and Technology, Tottori University, Tottori, Japan
| | - Ayumi Takamura
- Division of Functional Genomics, Research Center for Bioscience and Technology, Tottori University, Tottori, Japan
| | - Hideki Kamitani
- Department of Neurosurgery, Institute of Neurological Science, Tottori University, Tottori, Japan
| | - Takashi Watanabe
- Department of Neurosurgery, Institute of Neurological Science, Tottori University, Tottori, Japan
| | - Mitsuo Oshimura
- Department of Biomedical Science, Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori, Japan
| | - Eiji Nanba
- Division of Functional Genomics, Research Center for Bioscience and Technology, Tottori University, Tottori, Japan
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Francks C, Maegawa S, Laurén J, Abrahams BS, Velayos-Baeza A, Medland SE, Colella S, Groszer M, McAuley EZ, Caffrey TM, Timmusk T, Pruunsild P, Koppel I, Lind PA, Matsumoto-Itaba N, Nicod J, Xiong L, Joober R, Enard W, Krinsky B, Nanba E, Richardson AJ, Riley BP, Martin NG, Strittmatter SM, Möller HJ, Rujescu D, St Clair D, Muglia P, Roos JL, Fisher SE, Wade-Martins R, Rouleau GA, Stein JF, Karayiorgou M, Geschwind DH, Ragoussis J, Kendler KS, Airaksinen MS, Oshimura M, DeLisi LE, Monaco AP. LRRTM1 on chromosome 2p12 is a maternally suppressed gene that is associated paternally with handedness and schizophrenia. Mol Psychiatry 2007; 12:1129-39, 1057. [PMID: 17667961 PMCID: PMC2990633 DOI: 10.1038/sj.mp.4002053] [Citation(s) in RCA: 226] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Left-right asymmetrical brain function underlies much of human cognition, behavior and emotion. Abnormalities of cerebral asymmetry are associated with schizophrenia and other neuropsychiatric disorders. The molecular, developmental and evolutionary origins of human brain asymmetry are unknown. We found significant association of a haplotype upstream of the gene LRRTM1 (Leucine-rich repeat transmembrane neuronal 1) with a quantitative measure of human handedness in a set of dyslexic siblings, when the haplotype was inherited paternally (P=0.00002). While we were unable to find this effect in an epidemiological set of twin-based sibships, we did find that the same haplotype is overtransmitted paternally to individuals with schizophrenia/schizoaffective disorder in a study of 1002 affected families (P=0.0014). We then found direct confirmatory evidence that LRRTM1 is an imprinted gene in humans that shows a variable pattern of maternal downregulation. We also showed that LRRTM1 is expressed during the development of specific forebrain structures, and thus could influence neuronal differentiation and connectivity. This is the first potential genetic influence on human handedness to be identified, and the first putative genetic effect on variability in human brain asymmetry. LRRTM1 is a candidate gene for involvement in several common neurodevelopmental disorders, and may have played a role in human cognitive and behavioral evolution.
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Affiliation(s)
- C Francks
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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Itaba-Matsumoto N, Maegawa S, Yamagata H, Kondo I, Oshimura M, Nanba E. Imprinting status of paternally imprinted DLX5 gene in Japanese patients with Rett syndrome. Brain Dev 2007; 29:491-5. [PMID: 17363207 DOI: 10.1016/j.braindev.2007.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 01/24/2007] [Accepted: 01/24/2007] [Indexed: 10/23/2022]
Abstract
Rett syndrome (RTT) is an X-linked severe neurodevelopmental disorder mostly affecting female and is mainly caused by mutations of methyl-CpG-binding protein 2 gene (MECP2). MECP2, which has a crucial role for transcriptional repression and chromatin remodeling, consists of methyl-CpG binding domain (MBD) and transcriptional repression domain (TRD). Paternally imprinted distal-less homeobox gene 5 (DLX5), that has an important role for the development of gamma-aminobutyric acid (GABA)-ergic neurons, was identified as a target of MECP2 recently. We selected the 12 samples from the 40 RTT lymphoblast cell lines by a mononucleotide repeat polymorphism within the 3'UTR of DLX5. In 12 samples, 5 and 6 samples have the mutations located in MBD and TRD, respectively. No expression and 25-75% expression of the mutated MECP2 allele were detected in 4 samples with MBD mutation and 4 samples with TRD mutation. In this study, the expression of mutated MECP2 alleles was low especially in the samples with the MBD mutation suggesting the biased frequency of the cells during the culture. However, a sample with high expression of mutated MECP2 in TRD mutation showed bialleic expression of DLX5 suggesting loss of imprinting.
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Affiliation(s)
- Noriko Itaba-Matsumoto
- Division of Functional Genomics, Research Center for Bioscience and Technology, Tottori University, 86 Nishicho, Yonago, Tottori 683-8503, Japan
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Kobayashi D, Ieiri I, Hirota T, Takane H, Maegawa S, Kigawa J, Suzuki H, Nanba E, Oshimura M, Terakawa N, Otsubo K, Mine K, Sugiyama Y. FUNCTIONAL ASSESSMENT OFABCG2(BCRP) GENE POLYMORPHISMS TO PROTEIN EXPRESSION IN HUMAN PLACENTA. Drug Metab Dispos 2004; 33:94-101. [PMID: 15475413 DOI: 10.1124/dmd.104.001628] [Citation(s) in RCA: 233] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The aim of the present study was to assess the contribution of polymorphisms in the breast cancer resistance protein/ATP-binding cassette transporter G2 (BCRP/ABCG2) gene to the placental expression from a new perspective, allelic imbalance. Polymorphisms were screened by polymerase chain reaction (PCR)-single-strand conformation polymorphism analysis followed by sequencing with DNA extracted from 100 placentas. To examine whether polymorphisms of the BCRP gene correlate with the placental BCRP expression, we determined mRNA and protein levels by quantitative real-time PCR and Western blotting, respectively. In placentas, G34A (Val(12)Met) and C421A (Gln(141)Lys) were frequently observed (18-36%), but C376T, which creates a stop codon (Gln(126) stop codon), was found with an allelic frequency of 1%. The mean of the BCRP protein level was significantly lower (p < 0.05) in homozygotes for the A421 allele than in those for the C421 allele, and heterozygotes had an intermediate value. To evaluate whether the C421A polymorphism acts as a cis-element in BCRP transcription, allelic imbalance was determined using informative lymphoblasts and 56 samples of placental cDNA. In most of the placental samples we tested, the difference in expression levels between the two alleles was small, and only two samples indicated a monoallelic expression (i.e., preferential expression of one allele). These results suggest that 1) the predominant allelic expression pattern of BCRP in placental samples is biallelic, and 2) the mutation C421A is not a genetic variant acting in cis, but is considered to influence the translation efficiency.
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Affiliation(s)
- Daisuke Kobayashi
- Department of Hospital Pharmacy, Faculty of Medicine, Tottori University, Nishi-machi 36-1, Yonago, 683-8504, Japan
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Hirota T, Ieiri I, Takane H, Maegawa S, Hosokawa M, Kobayashi K, Chiba K, Nanba E, Oshimura M, Sato T, Higuchi S, Otsubo K. Allelic expression imbalance of the human CYP3A4 gene and individual phenotypic status. Hum Mol Genet 2004; 13:2959-69. [PMID: 15459178 DOI: 10.1093/hmg/ddh313] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The human cytochrome P450 3A4 (CYP3A4) plays a dominant role in the metabolism of numerous clinically useful drugs. Alterations in the activity or expression of this enzyme may account for a major part of the variation in drug responsiveness and toxicity. However, it is generally accepted that most of the known single nucleotide polymorphisms in the coding and 5'-flanking regions are not the main determinants for the large inter-individual variability of CYP3A4 expression and activity. We show that the allelic variation is critically involved in determining the individual total hepatic CYP3A4 mRNA level and metabolic capability. There exists a definite correlation between the total CYP3A4 mRNA level and allelic expression ratio, the relative transcript level ratio derived from the two alleles. Individuals with a low expression ratio, exhibiting a large difference of transcript level between the two alleles, revealed extremely low levels of total hepatic CYP3A4 mRNA, and thus low metabolic capability as assessed by testosterone 6beta-hydroxylation. These results present a new insight into the individualized CYP3A4-dependent pharmacotherapy and the importance of expression imbalance to human phenotypic diversity.
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Affiliation(s)
- Takeshi Hirota
- Clinical Pharmacokinetics, Division of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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Maegawa S, Itaba N, Otsuka S, Kamitani H, Watanabe T, Tahimic CGT, Nanba E, Oshimura M. Coordinate Downregulation of a Novel Imprinted Transcript ITUP1 with PEG3 in Glioma Cell Lines. DNA Res 2004; 11:37-49. [PMID: 15141944 DOI: 10.1093/dnares/11.1.37] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The human paternally expressed gene 3 (PEG3) on chromosome 19q13.4 is one of the candidate tumor suppressor genes for glioma. We have previously reported that the epigenetic silencing of PEG3 expression in glioma cell lines is dependent on aberrant DNA methylation of an exonic CpG island. Here, we have identified three expressed sequence tags (ESTs), H80201, H78825 and AW197312, that exhibit paternal allele-specific expression, using human monochromosomal hybrids containing the paternal or maternal origin of PEG3 locus. The EST H80201 was shown to be expressed only from the paternal allele in normal human lymphoblasts by utilizing a single nucleotide polymorphism (SNP). Monoallelic expression of EST H80201 was also detected in non-tumor adult human brain tissues of gliomas. These ESTs were located directly adjacent to PEG3 in a head-to-head orientation. We have named this new transcript, imprinted transcript 1, which is located upstream but oppositely oriented to PEG3 (ITUP1). The ITUP1 showed a similar expression profile with PEG3 in glioma cell lines. Bisulfite genomic sequencing and reverse transcription (RT)-PCR analysis indicated that hypermethylation of the promoter region correlated with the absence of these transcripts. This suggests that ITUP1 and PEG3 are coordinately regulated, and that downregulation of the both genes may be important in the development of glioma.
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Affiliation(s)
- Shinji Maegawa
- Division of Functional Genomics, Research Center for Bioscience and Technology, Tottori University, 86 Nishimachi, Yonago City, Tottori 683-8503, Japan
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Inoue J, Mitsuya K, Maegawa S, Kugoh H, Kadota M, Okamura D, Shinohara T, Nishihara S, Takehara S, Yamauchi K, Schulz TC, Oshimura M. Construction of 700 human/mouse A9 monochromosomal hybrids and analysis of imprinted genes on human chromosome 6. J Hum Genet 2001; 46:137-45. [PMID: 11310581 DOI: 10.1007/s100380170101] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
As an in vitro assay system for the identification of human imprinted genes, a library of human/mouse A9 monochromosomal hybrids containing a single, intact bsr-tagged human chromosome of known parental origin, derived from normal human fibroblasts, has been previously generated by microcell-mediated chromosome transfer (MMCT). To supplement this assay system, we constructed additional 700 A9 monochromosomal hybrids, using a pSTneo or pPGKneo selection marker. To validate the A9 hybrids, we screened them with chromosome-specific polymorphic markers, and identified the hybrids containing either human chromosome 6, 7, 14, 18, or 21 of known parental origin. Matching paternal and maternal chromosome pairs of A9 hybrids were identified for chromosomes 6, 7, 14, and 18. The paternal-specific expression of ZAC (zinc finger protein, which regulates apoptosis and cell cycle arrest) and HYMAI (hydatidiform mole-associated and imprinted transcript), and the maternal-specific methylation of a CpG island within an imprinted domain on human chromosome 6q24, were maintained in A9 hybrids. For an example, we profiled the expression of expressed sequence tags (ESTs) and the methylation of CpG islands in the 300-kb imprinted domain around 6q24, which may be associated with cancers and transient neonatal diabetes mellitus (TNDM). Thus, the 700 A9 hybrids should be useful for various aspects of imprinting studies.
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Affiliation(s)
- J Inoue
- Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Tokyo
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Maegawa S, Yoshioka H, Itaba N, Kubota N, Nishihara S, Shirayoshi Y, Nanba E, Oshimura M. Epigenetic silencing of PEG3 gene expression in human glioma cell lines. Mol Carcinog 2001; 31:1-9. [PMID: 11398192 DOI: 10.1002/mc.1034] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genomic imprinting, the phenomenon in which alleles of genes are expressed differentially depending on their parental origins, has important consequences for mammalian development, and disturbance of normal imprinting leads to abnormal embryogenesis and some inherited diseases and is also associated with various cancers. In the context of screening for novel imprinted genes on human chromosome 19q13.4 with mouse A9 hybrids, we identified a maternal allele-specific methylated CpG island in exon 1 of paternally expressed imprinted gene 3 (PEG3), a gene that exhibits paternal allele-specific expression. Because PEG3 expression is downregulated in some gliomas and glioma cell lines, despite high-level expression in normal brain tissues, we investigated whether the loss of PEG3 expression is related to epigenetic modifications involving DNA methylation. We found monoallelic expression of PEG3 in all normal brain tissues examined and five of nine glioma cell lines that had both unmethylated and methylated alleles; the remaining four glioma cell lines exhibited gain of imprinting with hypermethylated alleles. In addition, treatment of glioma cell lines with the DNA demethylating agent 5-aza-2'-deoxycytidine reversed the silencing of PEG3 biallelically. In this article, we report that the epigenetic silencing of PEG3 expression in glioma cell lines depends on aberrant DNA methylation of an exonic CpG island, suggesting that PEG3 contributes to glioma carcinogenesis in certain cases.
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Affiliation(s)
- S Maegawa
- Gene Research Center, Tottori University, Tottori, Japan
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Pipo JR, Yamamoto T, Takeda H, Maegawa S, Nanba E, Ninomiya H, Ohno K, Takeshita K. Two novel serine repeat length polymorphisms (1043insS and 1043insSS) at exon 23 of the TSC1 gene. Hum Mutat 2000; 16:375. [PMID: 11013456 DOI: 10.1002/1098-1004(200010)16:4<375::aid-humu18>3.0.co;2-t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- J R Pipo
- Division of Child Neurology, Institute of Neurological Sciences, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
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Abstract
Asymmetric distribution of maternal mRNAs has not been well documented in zebrafish. Recently, we have shown that dazl mRNA is localized at the vegetal pole. Here we report a novel zebrafish gene, bruno-like (brul), which provides another example of vegetal mRNA localization. brul encodes an Elav-type RNA-binding protein that belongs to the Bruno-like family that includes mammalian CUG-BP, Xenopus EDEN-BP, and Drosophila Bruno. At 24 hpf, brul mRNA was abundant in lens fiber cells. At the onset of embryogenesis, maternal brul mRNA was detected at the vegetal pole, and it then migrated rapidly toward the blastoderm through yolk cytoplasmic streams. During oogenesis, brul mRNA became localized at the vegetal cortex at stage II, later than dazl mRNA. We found that anchoring of brul mRNA was dependent on microfilaments.
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Affiliation(s)
- H Suzuki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
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Abstract
Members of the DAZ gene family encode RNA-binding proteins and have been shown to play a pivotal role in gametogenesis. In Xenopus, a DAZ-like gene encodes an RNA component of the germ plasm. We have identified a zebrafish DAZ homologue, zDazl. zDazl mRNA was expressed in gonads of both sexes. In ovary, it was localized in the cortex of oocytes. At the onset of embryogenesis, maternal zDazl mRNA was detected at the vegetal pole. It migrated toward blastomeres through cytoplasmic streams as early embryogenesis proceeded. This is the first report showing maternal mRNA localization at the vegetal pole in fish and the existence of mRNA streams in the yolk cytoplasm.
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Affiliation(s)
- S Maegawa
- Graduate School of BioSciences, Nara Institute of Science and Technology, Ikoma 630-0101, Japan
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