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Read JF, Serralha M, Armitage JD, Iqbal MM, Cruickshank MN, Saxena A, Strickland DH, Waithman J, Holt PG, Bosco A. Single cell transcriptomics reveals cell type specific features of developmentally regulated responses to lipopolysaccharide between birth and 5 years. Front Immunol 2023; 14:1275937. [PMID: 37920467 PMCID: PMC10619903 DOI: 10.3389/fimmu.2023.1275937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
Background Human perinatal life is characterized by a period of extraordinary change during which newborns encounter abundant environmental stimuli and exposure to potential pathogens. To meet such challenges, the neonatal immune system is equipped with unique functional characteristics that adapt to changing conditions as development progresses across the early years of life, but the molecular characteristics of such adaptations remain poorly understood. The application of single cell genomics to birth cohorts provides an opportunity to investigate changes in gene expression programs elicited downstream of innate immune activation across early life at unprecedented resolution. Methods In this study, we performed single cell RNA-sequencing of mononuclear cells collected from matched birth cord blood and 5-year peripheral blood samples following stimulation (18hrs) with two well-characterized innate stimuli; lipopolysaccharide (LPS) and Polyinosinic:polycytidylic acid (Poly(I:C)). Results We found that the transcriptional response to LPS was constrained at birth and predominantly partitioned into classical proinflammatory gene upregulation primarily by monocytes and Interferon (IFN)-signaling gene upregulation by lymphocytes. Moreover, these responses featured substantial cell-to-cell communication which appeared markedly strengthened between birth and 5 years. In contrast, stimulation with Poly(I:C) induced a robust IFN-signalling response across all cell types identified at birth and 5 years. Analysis of gene regulatory networks revealed IRF1 and STAT1 were key drivers of the LPS-induced IFN-signaling response in lymphocytes with a potential developmental role for IRF7 regulation. Conclusion Additionally, we observed distinct activation trajectory endpoints for monocytes derived from LPS-treated cord and 5-year blood, which was not apparent among Poly(I:C)-induced monocytes. Taken together, our findings provide new insight into the gene regulatory landscape of immune cell function between birth and 5 years and point to regulatory mechanisms relevant to future investigation of infection susceptibility in early life.
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Affiliation(s)
- James F. Read
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Michael Serralha
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Jesse D. Armitage
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Muhammad Munir Iqbal
- Genomics WA, Joint Initiative of Telethon Kids Institute, Harry Perkins Institute of Medical Research and The University of Western Australia, Nedlands, WA, Australia
| | - Mark N. Cruickshank
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Alka Saxena
- Genomics WA, Joint Initiative of Telethon Kids Institute, Harry Perkins Institute of Medical Research and The University of Western Australia, Nedlands, WA, Australia
| | - Deborah H. Strickland
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
- UWA Centre for Child Health Research, The University of Western Australia, Nedlands, WA, Australia
| | - Jason Waithman
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Patrick G. Holt
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
- UWA Centre for Child Health Research, The University of Western Australia, Nedlands, WA, Australia
| | - Anthony Bosco
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
- Department of Immunobiology, The University of Arizona College of Medicine, Tucson, AZ, United States
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2
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Cheung LC, Aya-Bonilla C, Cruickshank MN, Chiu SK, Kuek V, Anderson D, Chua GA, Singh S, Oommen J, Ferrari E, Hughes AM, Ford J, Kunold E, Hesselman MC, Post F, Faulk KE, Breese EH, Guest EM, Brown PA, Loh ML, Lock RB, Kees UR, Jafari R, Malinge S, Kotecha RS. Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy. Leukemia 2023; 37:61-71. [PMID: 36380143 PMCID: PMC9883157 DOI: 10.1038/s41375-022-01746-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 04/30/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022]
Abstract
Infants with KMT2A-rearranged B-cell acute lymphoblastic leukemia (ALL) have a dismal prognosis. Survival outcomes have remained static in recent decades despite treatment intensification and novel therapies are urgently required. KMT2A-rearranged infant ALL cells are characterized by an abundance of promoter hypermethylation and exhibit high BCL-2 expression, highlighting potential for therapeutic targeting. Here, we show that hypomethylating agents exhibit in vitro additivity when combined with most conventional chemotherapeutic agents. However, in a subset of samples an antagonistic effect was seen between several agents. This was most evident when hypomethylating agents were combined with methotrexate, with upregulation of ATP-binding cassette transporters identified as a potential mechanism. Single agent treatment with azacitidine and decitabine significantly prolonged in vivo survival in KMT2A-rearranged infant ALL xenografts. Treatment of KMT2A-rearranged infant ALL cell lines with azacitidine and decitabine led to differential genome-wide DNA methylation, changes in gene expression and thermal proteome profiling revealed the target protein-binding landscape of these agents. The selective BCL-2 inhibitor, venetoclax, exhibited in vitro additivity in combination with hypomethylating or conventional chemotherapeutic agents. The addition of venetoclax to azacitidine resulted in a significant in vivo survival advantage indicating the therapeutic potential of this combination to improve outcome for infants with KMT2A-rearranged ALL.
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Affiliation(s)
- Laurence C Cheung
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Carlos Aya-Bonilla
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | | | - Sung K Chiu
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Vincent Kuek
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Denise Anderson
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Grace-Alyssa Chua
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Sajla Singh
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Joyce Oommen
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Emanuela Ferrari
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Anastasia M Hughes
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Jette Ford
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Elena Kunold
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Maria C Hesselman
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Frederik Post
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Kelly E Faulk
- University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO, USA
| | - Erin H Breese
- Cancer and Blood Diseases Institute, Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Erin M Guest
- Division of Hematology, Oncology, Blood and Marrow Transplantation, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Patrick A Brown
- Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD, USA
| | - Mignon L Loh
- Division of Pediatric Hematology, Oncology, Bone Marrow Transplant and Cellular Therapy, Seattle Children's Hospital, Seattle, WA, USA
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre/School of Women's and Children's Health/UNSW Centre for Childhood Cancer Research, UNSW Sydney, Kensington, NSW, Australia
| | - Ursula R Kees
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Rozbeh Jafari
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Sébastien Malinge
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Rishi S Kotecha
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia.
- Curtin Medical School, Curtin University, Perth, WA, Australia.
- The University of Western Australia, Perth, WA, Australia.
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children's Hospital, Perth, WA, Australia.
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3
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Ng HL, Quail E, Cruickshank MN, Ulgiati D. To Be, or Notch to Be: Mediating Cell Fate from Embryogenesis to Lymphopoiesis. Biomolecules 2021; 11:biom11060849. [PMID: 34200313 PMCID: PMC8227657 DOI: 10.3390/biom11060849] [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] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/29/2021] [Accepted: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
Notch signaling forms an evolutionarily conserved juxtacrine pathway crucial for cellular development. Initially identified in Drosophila wing morphogenesis, Notch signaling has since been demonstrated to play pivotal roles in governing mammalian cellular development in a large variety of cell types. Indeed, abolishing Notch constituents in mouse models result in embryonic lethality, demonstrating that Notch signaling is critical for development and differentiation. In this review, we focus on the crucial role of Notch signaling in governing embryogenesis and differentiation of multiple progenitor cell types. Using hematopoiesis as a diverse cellular model, we highlight the role of Notch in regulating the cell fate of common lymphoid progenitors. Additionally, the influence of Notch through microenvironment interplay with lymphoid cells and how dysregulation influences disease processes is explored. Furthermore, bi-directional and lateral Notch signaling between ligand expressing source cells and target cells are investigated, indicating potentially novel therapeutic options for treatment of Notch-mediated diseases. Finally, we discuss the role of cis-inhibition in regulating Notch signaling in mammalian development.
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Affiliation(s)
- Han Leng Ng
- Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK;
- School of Biomedical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (E.Q.); (M.N.C.)
| | - Elizabeth Quail
- School of Biomedical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (E.Q.); (M.N.C.)
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Mark N. Cruickshank
- School of Biomedical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (E.Q.); (M.N.C.)
| | - Daniela Ulgiati
- School of Biomedical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; (E.Q.); (M.N.C.)
- Correspondence: ; Tel.: +61-8-6457-1076
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4
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Ng HL, Taylor RL, Cheng J, Abraham LJ, Quail E, Cruickshank MN, Ulgiati D. Notch signaling induces a transcriptionally permissive state at the Complement C3d Receptor 2 (CR2) promoter in a pre-B cell model. Mol Immunol 2020; 128:150-164. [PMID: 33129017 DOI: 10.1016/j.molimm.2020.10.001] [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: 05/25/2020] [Revised: 09/11/2020] [Accepted: 10/02/2020] [Indexed: 01/08/2023]
Abstract
During mammalian lymphoid development, Notch signaling is necessary at multiple stages of T lymphopoiesis, including lineage commitment, and later stages of T cell effector differentiation. In contrast, outside of a defined role in the development of splenic marginal zone B cells, there is conflicting evidence regarding whether Notch signaling plays functional roles in other B cell sub-populations. Complement receptor 2 (CR2) modulates BCR-signaling and is tightly regulated throughout differentiation. During B lymphopoiesis, CR2 is detected on immature and mature B cells with high surface expression on marginal zone B cells. Here, we have explored the possibility that Notch regulates human CR2 transcriptional activity using in vitro models including a co-culture system, co-transfection gene reporters and chromatin accessibility assays. We provide evidence that Notch signaling regulates CR2 promoter activity in a mature B cell line, as well as the induction of endogenous CR2 mRNA in a non-expressing pre-B cell line. The dynamics of endogenous gene activation suggests additional unidentified factors are required to mediate surface CR2 expression on immature and mature B lineage cells.
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Affiliation(s)
- Han Leng Ng
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Australia
| | - Rhonda L Taylor
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Australia
| | - Jessica Cheng
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Australia
| | - Lawrence J Abraham
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Australia
| | - Elizabeth Quail
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Australia; School of Molecular Sciences, Faculty of Science, The University of Western Australia, Australia
| | - Mark N Cruickshank
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Australia
| | - Daniela Ulgiati
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Australia.
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5
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Chee J, Wilson C, Buzzai A, Wylie B, Forbes CA, Booth M, Principe N, Foley B, Cruickshank MN, Waithman J. Impaired T cell proliferation by ex vivo BET-inhibition impedes adoptive immunotherapy in a murine melanoma model. Epigenetics 2020; 15:134-144. [PMID: 31423932 PMCID: PMC6961692 DOI: 10.1080/15592294.2019.1656156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/25/2019] [Accepted: 08/08/2019] [Indexed: 01/26/2023] Open
Abstract
Activation of naïve CD8+ T cells stimulates proliferation and differentiation into cytotoxic T-lymphocytes (CTLs). Adoptive T Cell Therapy (ACT) involves multiple rounds of ex vivo activation to generate enough CTLs for reinfusion into patients, but this drives differentiation into terminal effector T cells. Less differentiated CTL populations, such as stem cell memory T cells, are more ideal candidates for ACT because of increased self-renewal and persistent properties. Ex vivo targeting of T cell differentiation with epigenetic modifiers is a potential strategy to improve cytotoxic T-lymphocyte (CTL) generation for ACT. We established a pipeline to assess the effects of epigenetic modifiers on CD8+ T cell proliferation, differentiation, and efficacy in a preclinical melanoma model. Single treatment with epigenetic modifiers inhibited T cell proliferation in vitro, producing CD44hiCD62Lhi effector-like T cells rather than a stem cell memory T cell phenotype. Most epigenetic modifying agents had no significant effect on ACT efficacy with the notable exception of the bromodomain and extraterminal (BET)-inhibitor JQ1 which was associated with a decrease in efficacy compared to unmodified T cells. These findings reveal the complexity of epigenetic targeting of T cell differentiation, highlighting the need to precisely define the epigenetic targeting strategies to improve CTL generation for ACT.
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Affiliation(s)
- Jonathan Chee
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, West Perth, WA, Australia
- National Centre for Asbestos Related Diseases, School of Biomedical Sciences, University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Chelsea Wilson
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, West Perth, WA, Australia
| | - Anthony Buzzai
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, West Perth, WA, Australia
| | - Ben Wylie
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, West Perth, WA, Australia
| | - Catherine A Forbes
- National Centre for Asbestos Related Diseases, School of Biomedical Sciences, University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Mitchell Booth
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, West Perth, WA, Australia
| | - Nicola Principe
- National Centre for Asbestos Related Diseases, School of Biomedical Sciences, University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Bree Foley
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, West Perth, WA, Australia
| | - Mark N Cruickshank
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, West Perth, WA, Australia
| | - Jason Waithman
- Telethon Kids Institute, Centre for Child Health Research, The University of Western Australia, West Perth, WA, Australia
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6
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Wylie B, Chee J, Forbes CA, Booth M, Stone SR, Buzzai A, Abad A, Foley B, Cruickshank MN, Waithman J. Acquired resistance during adoptive cell therapy by transcriptional silencing of immunogenic antigens. Oncoimmunology 2019; 8:1609874. [PMID: 31413920 PMCID: PMC6682399 DOI: 10.1080/2162402x.2019.1609874] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 11/08/2018] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/23/2022] Open
Abstract
Immunotherapies such as adoptive cell therapy (ACT) are promising treatments for solid cancers. However, relapsing disease remains a problem and the molecular mechanisms underlying resistance are poorly defined. We postulated that the deregulated epigenetic landscape in cancer cells could underpin the acquisition of resistance to immunotherapy. To address this question, two preclinical models of ACT were employed to study transcriptional and epigenetic regulatory processes within ACT-treated cancer cells. In these models ACT consistently causes robust tumor regression, but resistance develops and tumors relapse. We identified down-regulated expression of immunogenic antigens at the mRNA level correlated with escape from immune control. To determine whether this down-regulation was under epigenetic control, we treated escaped tumor cells with DNA demethylating agents, azacytidine (AZA) and decitabine (DEC). AZA or DEC treatment restored antigen expression in a proportion of the tumor population. To explore the importance of other epigenetic modifications we isolated tumor cells refractory to DNA demethylation and screened clones against a panel of 19 different epigenetic modifying agents (EMAs). The library of EMAs included inhibitors of a range of chromosomal and transcription regulatory protein complexes, however, when tested as single agents none restored further antigen expression. These findings suggest that tumor cells employ multiple epigenetic and genetic mechanisms to evade immune control, and a combinatorial approach employing several EMAs targeting transcription and genome stability may be required to overcome tumor resistance to immunotherapy.
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Affiliation(s)
- Ben Wylie
- Phylogica, Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands, Australia
| | - Jonathan Chee
- National Centre for Asbestos Related Diseases, School of Biomedical Sciences, University of Western Australia, QEII Medical Centre, Nedlands, Australia
| | - Catherine A Forbes
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Mitchell Booth
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Shane R Stone
- Phylogica, Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands, Australia
| | - Anthony Buzzai
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Ana Abad
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Bree Foley
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Mark N Cruickshank
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
| | - Jason Waithman
- Telethon Kids Institute, University of Western Australia, Northern Entrance, Perth Children's Hospital, Nedlands, Australia
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7
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Cheung LC, Cruickshank MN, Hughes AM, Singh S, Chua GA, Ford J, Ferrari E, Oommen J, Malinge S, Lock RB, Kees UR, Kotecha RS. Romidepsin enhances the efficacy of cytarabine in vivo, revealing histone deacetylase inhibition as a promising therapeutic strategy for KMT2A-rearranged infant acute lymphoblastic leukemia. Haematologica 2019; 104:e300-e303. [PMID: 30679330 DOI: 10.3324/haematol.2018.192906] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Laurence C Cheung
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth.,School of Pharmacy and Biomedical Sciences, Curtin University, Perth
| | - Mark N Cruickshank
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Anastasia M Hughes
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Sajla Singh
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Grace-Alyssa Chua
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Jette Ford
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Emanuela Ferrari
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Joyce Oommen
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Sébastien Malinge
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney
| | - Ursula R Kees
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth
| | - Rishi S Kotecha
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth .,School of Pharmacy and Biomedical Sciences, Curtin University, Perth.,Department of Haematology and Oncology, Perth Children's Hospital, Perth.,Division of Paediatrics, School of Medicine, University of Western Australia, Perth, Australia
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8
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Wylie B, Read J, Buzzai AC, Wagner T, Troy N, Syn G, Stone SR, Foley B, Bosco A, Cruickshank MN, Waithman J. CD8 +XCR1 neg Dendritic Cells Express High Levels of Toll-Like Receptor 5 and a Unique Complement of Endocytic Receptors. Front Immunol 2019; 9:2990. [PMID: 30700986 PMCID: PMC6343586 DOI: 10.3389/fimmu.2018.02990] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 12/04/2018] [Indexed: 01/21/2023] Open
Abstract
Conventional dendritic cells (cDC) resident in the lymphoid organs of mice have been classically divided into CD8+ and CD8neg subsets. It is well-established that CD8+ dendritic cells (DCs) and their migratory counterparts in the periphery comprise the cross-presenting cDC1 subset. In contrast, CD8neg DCs are grouped together in the heterogeneous cDC2 subset. CD8neg DCs are relatively poor cross-presenters and drive more prominent CD4+ T cell responses against exogenous antigens. The discovery of the X-C motif chemokine receptor 1 (XCR1) as a specific marker of cross-presenting DCs, has led to the identification of a divergent subset of CD8+ DCs that lacks the ability to cross-present. Here, we report that these poorly characterized CD8+XCR1neg DCs have a gene expression profile that is consistent with both plasmacytoid DCs (pDCs) and cDC2. Our data demonstrate that CD8+XCR1neg DCs possess a unique pattern of endocytic receptors and a restricted toll-like receptor (TLR) profile that is particularly enriched for TLR5, giving them a unique position within the DC immunosurveillance network.
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Affiliation(s)
- Ben Wylie
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - James Read
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Anthony C Buzzai
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Teagan Wagner
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Niamh Troy
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Genevieve Syn
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Shane R Stone
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Bree Foley
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Anthony Bosco
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Mark N Cruickshank
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Jason Waithman
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
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9
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Wang E, Sorolla A, Cunningham PT, Bogdawa HM, Beck S, Golden E, Dewhurst RE, Florez L, Cruickshank MN, Hoffmann K, Hopkins RM, Kim J, Woo AJ, Watt PM, Blancafort P. Tumor penetrating peptides inhibiting MYC as a potent targeted therapeutic strategy for triple-negative breast cancers. Oncogene 2018; 38:140-150. [PMID: 30076412 PMCID: PMC6318000 DOI: 10.1038/s41388-018-0421-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 05/24/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022]
Abstract
Overexpression of MYC oncogene is highly prevalent in many malignancies such as aggressive triple-negative breast cancers (TNBCs) and it is associated with very poor outcome. Despite decades of research, attempts to effectively inhibit MYC, particularly with small molecules, still remain challenging due to the featureless nature of its protein structure. Herein, we describe the engineering of the dominant-negative MYC peptide (OmoMYC) linked to a functional penetrating 'Phylomer' peptide (FPPa) as a therapeutic strategy to inhibit MYC in TNBC. We found FPPa-OmoMYC to be a potent inducer of apoptosis (with IC50 from 1-2 µM) in TNBC cells with negligible effects in non-tumorigenic cells. Transcriptome analysis of FPPa-OmoMYC-treated cells indicated that the fusion protein inhibited MYC-dependent networks, inducing dynamic changes in transcriptional, metabolic, and apoptotic processes. We demonstrated the efficacy of FPPa-OmoMYC in inhibiting breast cancer growth when injected orthotopically in TNBC allografts. Lastly, we identified strong pharmacological synergisms between FPPa-OmoMYC and chemotherapeutic agents. This study highlights a novel therapeutic approach to target highly aggressive and chemoresistant MYC-activated cancers.
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Affiliation(s)
- Edina Wang
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Anabel Sorolla
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Paula T Cunningham
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia.,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | - Heique M Bogdawa
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia.,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | - Samuel Beck
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,MDI Biological Laboratory, Kathryn W. Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, 04672, USA
| | - Emily Golden
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Robert E Dewhurst
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia.,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | - Laura Florez
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia.,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | - Mark N Cruickshank
- Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | - Katrin Hoffmann
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia.,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | | | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrew J Woo
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Paul M Watt
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia. .,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia.
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia. .,School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia.
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10
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Cruickshank MN, Ford J, Cheung LC, Heng J, Singh S, Wells J, Failes TW, Arndt GM, Smithers N, Prinjha RK, Anderson D, Carter KW, Gout AM, Lassmann T, O'Reilly J, Cole CH, Kotecha RS, Kees UR. Systematic chemical and molecular profiling of MLL-rearranged infant acute lymphoblastic leukemia reveals efficacy of romidepsin. Leukemia 2016; 31:40-50. [PMID: 27443263 PMCID: PMC5220136 DOI: 10.1038/leu.2016.165] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 05/05/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022]
Abstract
To address the poor prognosis of mixed lineage leukemia (MLL)-rearranged infant acute lymphoblastic leukemia (iALL), we generated a panel of cell lines from primary patient samples and investigated cytotoxic responses to contemporary and novel Food and Drug Administration-approved chemotherapeutics. To characterize representation of primary disease within cell lines, molecular features were compared using RNA-sequencing and cytogenetics. High-throughput screening revealed variable efficacy of currently used drugs, however identified consistent efficacy of three novel drug classes: proteasome inhibitors, histone deacetylase inhibitors and cyclin-dependent kinase inhibitors. Gene expression of drug targets was highly reproducible comparing iALL cell lines to matched primary specimens. Histone deacetylase inhibitors, including romidepsin (ROM), enhanced the activity of a key component of iALL therapy, cytarabine (ARAC) in vitro and combined administration of ROM and ARAC to xenografted mice further reduced leukemia burden. Molecular studies showed that ROM reduces expression of cytidine deaminase, an enzyme involved in ARAC deactivation, and enhances the DNA damage-response to ARAC. In conclusion, we present a valuable resource for drug discovery, including the first systematic analysis of transcriptome reproducibility in vitro, and have identified ROM as a promising therapeutic for MLL-rearranged iALL.
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Affiliation(s)
- M N Cruickshank
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - J Ford
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - L C Cheung
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - J Heng
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - S Singh
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - J Wells
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - T W Failes
- ACRF Drug Discovery Centre for Childhood Cancer, Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - G M Arndt
- ACRF Drug Discovery Centre for Childhood Cancer, Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | - N Smithers
- GlaxoSmithKline, Medicines Research Centre, Stevenage, UK
| | - R K Prinjha
- GlaxoSmithKline, Medicines Research Centre, Stevenage, UK
| | - D Anderson
- Centre for Biostatistics, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - K W Carter
- McCusker Charitable Foundation Bioinformatics Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - A M Gout
- McCusker Charitable Foundation Bioinformatics Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - T Lassmann
- McCusker Charitable Foundation Bioinformatics Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - J O'Reilly
- Department of Haematology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Perth, Australia.,School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - C H Cole
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Australia.,Department of Haematology and Oncology, Princess Margaret Hospital for Children, Perth, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
| | - R S Kotecha
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Australia.,Department of Haematology and Oncology, Princess Margaret Hospital for Children, Perth, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Australia
| | - U R Kees
- Division of Children's Leukaemia and Cancer Research, Telethon Kids Institute, University of Western Australia, Perth, Australia
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11
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Taylor RL, Cruickshank MN, Karimi M, Ng HL, Quail E, Kaufman KM, Harley JB, Abraham LJ, Tsao BP, Boackle SA, Ulgiati D. Focused transcription from the human CR2/CD21 core promoter is regulated by synergistic activity of TATA and Initiator elements in mature B cells. Cell Mol Immunol 2016; 13:119-31. [PMID: 25640655 PMCID: PMC4711682 DOI: 10.1038/cmi.2014.138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/05/2014] [Accepted: 12/27/2014] [Indexed: 12/13/2022] Open
Abstract
Complement receptor 2 (CR2/CD21) is predominantly expressed on the surface of mature B cells where it forms part of a coreceptor complex that functions, in part, to modulate B-cell receptor signal strength. CR2/CD21 expression is tightly regulated throughout B-cell development such that CR2/CD21 cannot be detected on pre-B or terminally differentiated plasma cells. CR2/CD21 expression is upregulated at B-cell maturation and can be induced by IL-4 and CD40 signaling pathways. We have previously characterized elements in the proximal promoter and first intron of CR2/CD21 that are involved in regulating basal and tissue-specific expression. We now extend these analyses to the CR2/CD21 core promoter. We show that in mature B cells, CR2/CD21 transcription proceeds from a focused TSS regulated by a non-consensus TATA box, an initiator element and a downstream promoter element. Furthermore, occupancy of the general transcriptional machinery in pre-B versus mature B-cell lines correlate with CR2/CD21 expression level and indicate that promoter accessibility must switch from inactive to active during the transitional B-cell window.
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Affiliation(s)
- Rhonda L Taylor
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
- Biochemistry and Molecular Biology, School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, Australia
| | - Mark N Cruickshank
- Telethon Kids Institute, The University of Western Australia, Crawley, WA, Australia
| | - Mahdad Karimi
- Biochemistry and Molecular Biology, School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, Australia
| | - Han Leng Ng
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
| | - Elizabeth Quail
- Biochemistry and Molecular Biology, School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, Australia
| | - Kenneth M Kaufman
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - John B Harley
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Lawrence J Abraham
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
| | - Betty P Tsao
- Division of Rheumatology, Department of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Susan A Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Daniela Ulgiati
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
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12
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Cruickshank MN, Oshlack A, Theda C, Davis PG, Martino D, Sheehan P, Dai Y, Saffery R, Doyle LW, Craig JM. Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy. Genome Med 2013; 5:96. [PMID: 24134860 PMCID: PMC3978871 DOI: 10.1186/gm500] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 09/26/2013] [Indexed: 02/08/2023] Open
Abstract
Background Preterm birth confers a high risk of adverse long term health outcomes for survivors, yet the underlying molecular mechanisms are unclear. We hypothesized that effects of preterm birth can be mediated through measurable epigenomic changes throughout development. We therefore used a longitudinal birth cohort to measure the epigenetic mark of DNA methylation at birth and 18 years comparing survivors of extremely preterm birth with infants born at term. Methods Using 12 extreme preterm birth cases and 12 matched, term controls, we extracted DNA from archived neonatal blood spots and blood collected in a similar way at 18 years of age. DNA methylation was measured at 347,789 autosomal locations throughout the genome using Infinium HM450 arrays. Representative methylation differences were confirmed by Sequenom MassArray EpiTYPER. Results At birth we found 1,555 sites with significant differences in methylation between term and preterm babies. At 18 years of age, these differences had largely resolved, suggesting that DNA methylation differences at birth are mainly driven by factors relating to gestational age, such as cell composition and/or maturity. Using matched longitudinal samples, we found evidence for an epigenetic legacy associated with preterm birth, identifying persistent methylation differences at ten genomic loci. Longitudinal comparisons of DNA methylation at birth and 18 years uncovered a significant overlap between sites that were differentially-methylated at birth and those that changed with age. However, we note that overlapping sites may either differ in the same (300/1,555) or opposite (431/1,555) direction during gestation and aging respectively. Conclusions We present evidence for widespread methylation differences between extreme preterm and term infants at birth that are largely resolved by 18 years of age. These results are consistent with methylation changes associated with blood cell development, cellular composition, immune induction and age at these time points. Finally, we identified ten probes significantly associated with preterm individuals and with greater than 5% methylation discordance at birth and 18 years that may reflect a long term epigenetic legacy of preterm birth.
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Affiliation(s)
- Mark N Cruickshank
- Early Life Epigenetics Group, Murdoch Childrens Research Institute (MCRI), Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia ; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia ; Present address: Telethon Institute for Child Health Research, University of Western Australia, 100 Roberts Road, Subiaco, WA 6008, Australia
| | - Alicia Oshlack
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia ; Bioinformatics Group, MCRI, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
| | - Christiane Theda
- Early Life Epigenetics Group, Murdoch Childrens Research Institute (MCRI), Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia ; Neonatal Services, Royal Women's Hospital, Parkville, Victoria 3052, Australia ; Department of Obstetrics and Gynaecology, University of Melbourne, Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - Peter G Davis
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia ; Neonatal Services, Royal Women's Hospital, Parkville, Victoria 3052, Australia ; Department of Obstetrics and Gynaecology, University of Melbourne, Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - David Martino
- Cancer and Developmental Epigenetics Group, MCRI, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
| | - Penelope Sheehan
- Department of Obstetrics and Gynaecology, University of Melbourne, Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - Yun Dai
- Early Life Epigenetics Group, Murdoch Childrens Research Institute (MCRI), Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
| | - Richard Saffery
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia ; Cancer and Developmental Epigenetics Group, MCRI, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
| | - Lex W Doyle
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia ; Neonatal Services, Royal Women's Hospital, Parkville, Victoria 3052, Australia ; Department of Obstetrics and Gynaecology, University of Melbourne, Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - Jeffrey M Craig
- Early Life Epigenetics Group, Murdoch Childrens Research Institute (MCRI), Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia ; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
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13
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Martino D, Loke YJ, Gordon L, Ollikainen M, Cruickshank MN, Saffery R, Craig JM. Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance. Genome Biol 2013; 14:R42. [PMID: 23697701 PMCID: PMC4054827 DOI: 10.1186/gb-2013-14-5-r42] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 05/22/2013] [Indexed: 02/02/2023] Open
Abstract
Background The extent to which development- and age-associated epigenetic changes are influenced by genetic, environmental and stochastic factors remains to be discovered. Twins provide an ideal model with which to investigate these influences but previous cross-sectional twin studies provide contradictory evidence of within-pair epigenetic drift over time. Longitudinal twin studies can potentially address this discrepancy. Results In a pilot, genome-scale study of DNA from buccal epithelium, a relatively homogeneous tissue, we show that one-third of the CpGs assayed show dynamic methylation between birth and 18 months. Although all classes of annotated genomic regions assessed show an increase in DNA methylation over time, probes located in intragenic regions, enhancers and low-density CpG promoters are significantly over-represented, while CpG islands and high-CpG density promoters are depleted among the most dynamic probes. Comparison of co-twins demonstrated that within-pair drift in DNA methylation in our cohort is specific to a subset of pairs, who show more differences at 18 months. The rest of the pairs show either minimal change in methylation discordance, or more similar, converging methylation profiles at 18 months. As with age-associated regions, sites that change in their level of within-pair discordance between birth and 18 months are enriched in genes involved in development, but the average magnitude of change is smaller than for longitudinal change. Conclusions Our findings suggest that DNA methylation in buccal epithelium is influenced by non-shared stochastic and environmental factors that could reflect a degree of epigenetic plasticity within an otherwise constrained developmental program.
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14
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Abstract
Epigenome-wide association studies (EWAS) can be used to investigate links between early life environment, epigenetics and disease. However, such studies raise the question of which came first: the mark or the malady? A recent study has demonstrated that EWAS can be performed on neonatal 'Guthrie' heel-prick blood spots. As Guthrie cards are collected from all newborn infants and stored indefinitely in many countries, they represent an important timepoint to compare with later disease-associated epigenetic marks.
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Affiliation(s)
- Mark N Cruickshank
- Division of Leukaemia and Cancer Research, Telethon Institute for Child Health Research, Centre for Child Health, University of Western Australia, WA, Australia
| | - James Pitt
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, VIC, Australia
| | - Jeffrey M Craig
- Early Life Epigenetics Group, Murdoch Childrens Research Institute and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC, Australia
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15
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Gordon L, Joo JE, Powell JE, Ollikainen M, Novakovic B, Li X, Andronikos R, Cruickshank MN, Conneely KN, Smith AK, Alisch RS, Morley R, Visscher PM, Craig JM, Saffery R. Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence. Genome Res 2012; 22:1395-406. [PMID: 22800725 PMCID: PMC3409253 DOI: 10.1101/gr.136598.111] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Comparison between groups of monozygotic (MZ) and dizygotic (DZ) twins enables an estimation of the relative contribution of genetic and shared and nonshared environmental factors to phenotypic variability. Using DNA methylation profiling of ∼20,000 CpG sites as a phenotype, we have examined discordance levels in three neonatal tissues from 22 MZ and 12 DZ twin pairs. MZ twins exhibit a wide range of within-pair differences at birth, but show discordance levels generally lower than DZ pairs. Within-pair methylation discordance was lowest in CpG islands in all twins and increased as a function of distance from islands. Variance component decomposition analysis of DNA methylation in MZ and DZ pairs revealed a low mean heritability across all tissues, although a wide range of heritabilities was detected for specific genomic CpG sites. The largest component of variation was attributed to the combined effects of nonshared intrauterine environment and stochastic factors. Regression analysis of methylation on birth weight revealed a general association between methylation of genes involved in metabolism and biosynthesis, providing further support for epigenetic change in the previously described link between low birth weight and increasing risk for cardiovascular, metabolic, and other complex diseases. Finally, comparison of our data with that of several older twins revealed little evidence for genome-wide epigenetic drift with increasing age. This is the first study to analyze DNA methylation on a genome scale in twins at birth, further highlighting the importance of the intrauterine environment on shaping the neonatal epigenome.
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Affiliation(s)
- Lavinia Gordon
- Bioinformatics Unit, Murdoch Childrens Research Institute, Parkville, Victoria 3052, Australia
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16
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Cruickshank MN, Karimi M, Mason RL, Fenwick E, Mercer T, Tsao BP, Boackle SA, Ulgiati D. Transcriptional effects of a lupus-associated polymorphism in the 5' untranslated region (UTR) of human complement receptor 2 (CR2/CD21). Mol Immunol 2012; 52:165-73. [PMID: 22673213 DOI: 10.1016/j.molimm.2012.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 04/24/2012] [Accepted: 04/29/2012] [Indexed: 11/25/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic component that determines risk. A common three single-nucleotide polymorphism (SNP) haplotype of the complement receptor 2 (CR2) gene has been associated with increased risk of SLE (Wu et al., 2007; Douglas et al., 2009), and a less common haplotype consisting of the major allele at SNP1 and minor alleles at SNP2 and 3 confers protection (Douglas et al., 2009). SNP1 (rs3813946), which is located in the 5' untranslated region (UTR) of the CR2 gene, altered transcriptional activity of a CR2 promoter-luciferase reporter gene construct transiently transfected into a B cell line (Wu et al., 2007) and had an independent effect in the protective haplotype (Douglas et al., 2009). In this study, we show that this SNP alters transcriptional activity in a transiently transfected non B-cell line as well as in stably transfected cell lines, supporting its relevance in vivo. Furthermore, the allele at this SNP affects chromatin accessibility of the surrounding sequence and transcription factor binding. These data confirm the effects of rs3813946 on CR2 transcription, identifying the 5' UTR to be a novel regulatory element for the CR2 gene in which variation may alter gene function and modify the development of lupus.
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Affiliation(s)
- Mark N Cruickshank
- Biochemistry and Molecular Biology, School of Chemistry and Biochemistry, The University of Western Australia, Perth, Western Australia, Australia
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17
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Cruickshank MN, Besant P, Ulgiati D. The impact of histone post-translational modifications on developmental gene regulation. Amino Acids 2010; 39:1087-105. [PMID: 20204433 DOI: 10.1007/s00726-010-0530-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 02/12/2010] [Indexed: 02/06/2023]
Abstract
Eukaryotic genomic DNA is orderly compacted to fit into the nucleus and to inhibit accessibility of specific sequences. DNA is manipulated in many different ways by bound RNA and proteins within the composite material known as chromatin. All of the biological processes that require access to genomic DNA (such as replication, recombination and transcription) therefore are dependent on the precise characteristics of chromatin in eukaryotes. This distinction underlies a fundamental property of eukaryotic versus prokaryotic gene regulation such that chromatin structure must be regulated to precisely repress or relieve repression of particular regions of the genome in an appropriate spatio-temporal manner. As well as playing a key role in structuring genomic DNA, histones are subject to site-specific modifications that can influence the organization of chromatin structure. This review examines the molecular processes regulating site-specific histone acetylation, methylation and phosphorylation with an emphasis on how these processes underpin differentiation-regulated transcription.
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Affiliation(s)
- Mark N Cruickshank
- Biochemistry and Molecular Biology, School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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18
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Affiliation(s)
- Mark N Cruickshank
- Department of Biochemistry and Molecular Biology, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia Crawley Western Australia Australia
| | - Daniela Ulgiati
- Department of Biochemistry and Molecular Biology, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia Crawley Western Australia Australia
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19
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Cruickshank MN, Fenwick E, Karimi M, Abraham LJ, Ulgiati D. Cell- and stage-specific chromatin structure across the Complement receptor 2 (CR2/CD21) promoter coincide with CBF1 and C/EBP-beta binding in B cells. Mol Immunol 2009; 46:2613-22. [PMID: 19487031 DOI: 10.1016/j.molimm.2009.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 05/01/2009] [Accepted: 05/02/2009] [Indexed: 01/19/2023]
Abstract
Stringent developmental transcription requires multiple transcription factor (TF) binding sites, cell-specific expression of signaling molecules, TFs and co-regulators and appropriate chromatin structure. During B-lymphopoiesis, human Complement receptor 2 (CR2/CD21) is detected on immature and mature B cells but not on B cell precursors and plasma cells. We examined cell- and stage-specific human CR2 gene regulation using cell lines modeling B-lymphopoiesis. Chromatin accessibility assays revealed a region between -409 and -262 with enhanced accessibility in mature B cells and pre-B cells, compared to either non-lymphoid or plasma cell-types, however, accessibility near the transcription start site (TSS) was elevated only in CR2-expressing B cells. A correlation between histone acetylation and CR2 expression was observed, while histone H3K4 dimethylation was enriched near the TSS in both CR2-expressing B cells and non-expressing pre-B cells. Candidate sites within the CR2 promoter were identified which could regulate chromatin, including a matrix attachment region associated with CDP, SATB1/BRIGHT and CEBP-beta sites as well as two CBF1 sites. ChIP assays verified that both CBF1 and C/EBP-beta bind the CR2 promoter in B cells raising the possibility that these factors facilitate or respond to alterations in chromatin structure to control the timing and/or level of CR2 transcription.
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