1
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Cheung K, Amos TG, Shine R, DeVore JL, Ducatez S, Edwards RJ, Rollins LA. Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory. Ecol Evol 2024; 14:e11115. [PMID: 38435005 PMCID: PMC10909579 DOI: 10.1002/ece3.11115] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/05/2024] Open
Abstract
Invasive species offer insights into rapid adaptation to novel environments. The iconic cane toad (Rhinella marina) is an excellent model for studying rapid adaptation during invasion. Previous research using the mitochondrial NADH dehydrogenase 3 (ND3) gene in Hawai'ian and Australian invasive populations found a single haplotype, indicating an extreme genetic bottleneck following introduction. Nuclear genetic diversity also exhibited reductions across the genome in these two populations. Here, we investigated the mitochondrial genomics of cane toads across this invasion trajectory. We created the first reference mitochondrial genome for this species using long-read sequence data. We combined whole-genome resequencing data of 15 toads with published transcriptomic data of 125 individuals to construct nearly complete mitochondrial genomes from the native (French Guiana) and introduced (Hawai'i and Australia) ranges for population genomic analyses. In agreement with previous investigations of these populations, we identified genetic bottlenecks in both Hawai'ian and Australian introduced populations, alongside evidence of population expansion in the invasive ranges. Although mitochondrial genetic diversity in introduced populations was reduced, our results revealed that it had been underestimated: we identified 45 mitochondrial haplotypes in Hawai'ian and Australian samples, none of which were found in the native range. Additionally, we identified two distinct groups of haplotypes from the native range, separated by a minimum of 110 base pairs (0.6%). These findings enhance our understanding of how invasion has shaped the genetic landscape of this species.
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Affiliation(s)
- Kelton Cheung
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Timothy G. Amos
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Rick Shine
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Jayna L. DeVore
- Univ. Polynésie FrancaiseUMR 241 EIO (UPF, IRD, IFREMER, ILM) BP 6570 Faa'aTahitiFrench Polynesia
| | - Simon Ducatez
- Institut de Recherche pour le Développement (IRD)UMR 241 EIO (UPF, IRD, IFREMER, ILM) BP 6570 Faa'aTahitiFrench Polynesia
| | - Richard J. Edwards
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Minderoo OceanOmics Centre at UWA, Oceans InstituteThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Lee Ann Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
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2
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Louie RHY, Cai C, Samir J, Singh M, Deveson IW, Ferguson JM, Amos TG, McGuire HM, Gowrishankar K, Adikari T, Balderas R, Bonomi M, Ruella M, Bishop D, Gottlieb D, Blyth E, Micklethwaite K, Luciani F. CAR + and CAR - T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies. Nat Commun 2023; 14:7767. [PMID: 38012187 PMCID: PMC10682404 DOI: 10.1038/s41467-023-43656-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy is effective in treating B cell malignancies, but factors influencing the persistence of functional CAR+ T cells, such as product composition, patients' lymphodepletion, and immune reconstitution, are not well understood. To shed light on this issue, here we conduct a single-cell multi-omics analysis of transcriptional, clonal, and phenotypic profiles from pre- to 1-month post-infusion of CAR+ and CAR- T cells from patients from a CARTELL study (ACTRN12617001579381) who received a donor-derived 4-1BB CAR product targeting CD19. Following infusion, CAR+ T cells and CAR- T cells shows similar differentiation profiles with clonally expanded populations across heterogeneous phenotypes, demonstrating clonal lineages and phenotypic plasticity. We validate these findings in 31 patients with large B cell lymphoma treated with CD19 CAR T therapy. For these patients, we identify using longitudinal mass-cytometry data an association between NK-like subsets and clinical outcomes at 6 months with both CAR+ and CAR- T cells. These results suggest that non-CAR-derived signals can provide information about patients' immune recovery and be used as correlate of clinically relevant parameters.
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Affiliation(s)
- Raymond Hall Yip Louie
- School of Computer Science and Engineering, UNSW Sydney, Sydney, NSW, Australia
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Curtis Cai
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Jerome Samir
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Mandeep Singh
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | - Ira W Deveson
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | | | - Timothy G Amos
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | - Helen Marie McGuire
- Ramaciotti Facility for Human Systems Biology, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Infection, Immunity and Inflammation Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Kavitha Gowrishankar
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Thiruni Adikari
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | | | - Martina Bonomi
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- Department of Physics, University of Bologna, Bologna, Italy
| | - Marco Ruella
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - David Bishop
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - David Gottlieb
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Emily Blyth
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Kenneth Micklethwaite
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
- NSW Health Pathology Blood Transplant and Cell Therapies Laboratory - ICPMR Westmead, Sydney, NSW, Australia
| | - Fabio Luciani
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia.
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia.
- Garvan Institute for Medical Research, Sydney, NSW, Australia.
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3
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Samarakoon H, Ferguson JM, Jenner SP, Amos TG, Parameswaran S, Gamaarachchi H, Deveson IW. Flexible and efficient handling of nanopore sequencing signal data with slow5tools. Genome Biol 2023; 24:69. [PMID: 37024927 PMCID: PMC10080837 DOI: 10.1186/s13059-023-02910-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow5tools enables lossless data conversion and a range of tools for interacting with SLOW5 files. Slow5tools uses multi-threading, multi-processing, and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We provide examples and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its performance.
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Affiliation(s)
- Hiruna Samarakoon
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - James M Ferguson
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Sasha P Jenner
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Timothy G Amos
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Sri Parameswaran
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Hasindu Gamaarachchi
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia.
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia.
| | - Ira W Deveson
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia.
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
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4
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Galbraith JD, Ludington AJ, Sanders KL, Amos TG, Thomson VA, Enosi Tuipulotu D, Dunstan N, Edwards RJ, Suh A, Adelson DL. Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes. Genes (Basel) 2022; 13:genes13020217. [PMID: 35205262 PMCID: PMC8872380 DOI: 10.3390/genes13020217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/23/2022] [Accepted: 01/23/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~30 Mya and have since rapidly diversified into six amphibious, ~60 marine and ~100 terrestrial species that fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.
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Affiliation(s)
- James D. Galbraith
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Alastair J. Ludington
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Kate L. Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Timothy G. Amos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Vicki A. Thomson
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Division of Immunity, Inflammation and Infection, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | | | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology-Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
| | - David L. Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
- South Australian Museum, Adelaide, SA 5000, Australia
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
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5
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Chen SH, Rossetto M, van der Merwe M, Lu-Irving P, Yap JYS, Sauquet H, Bourke G, Amos TG, Bragg JG, Edwards RJ. Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C. Mol Ecol Resour 2022; 22:1836-1854. [PMID: 35016262 DOI: 10.1111/1755-0998.13574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/31/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022]
Abstract
Telopea speciosissima, the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8% of Embryophyta BUSCOs "Complete". We present a new method in Diploidocus (https://github.com/slimsuite/diploidocus) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome size estimation from the read depth of single-copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1% of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA (CYC) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 "Duplicated" BUSCO genes using a new tool, DepthKopy (https://github.com/slimsuite/depthkopy), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level T. speciosissima reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.
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Affiliation(s)
- Stephanie H Chen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales, Australia.,Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia
| | - Marlien van der Merwe
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Patricia Lu-Irving
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia
| | - Jia-Yee S Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia.,School of Biological, Earth and Environmental Sciences, UNSW Sydney, New South Wales, Australia
| | - Greg Bourke
- Blue Mountains Botanic Garden, Mount Tomah, New South Wales, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales, Australia
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, New South Wales, Australia.,School of Biological, Earth and Environmental Sciences, UNSW Sydney, New South Wales, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales, Australia
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6
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Gamaarachchi H, Samarakoon H, Jenner SP, Ferguson JM, Amos TG, Hammond JM, Saadat H, Smith MA, Parameswaran S, Deveson IW. Fast nanopore sequencing data analysis with SLOW5. Nat Biotechnol 2022; 40:1026-1029. [PMID: 34980914 PMCID: PMC9287168 DOI: 10.1038/s41587-021-01147-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 06/29/2021] [Accepted: 11/02/2021] [Indexed: 12/19/2022]
Abstract
Nanopore sequencing depends on the FAST5 file format, which does not allow efficient parallel analysis. Here we introduce SLOW5, an alternative format engineered for efficient parallelization and acceleration of nanopore data analysis. Using the example of DNA methylation profiling of a human genome, analysis runtime is reduced from more than two weeks to approximately 10.5 h on a typical high-performance computer. SLOW5 is approximately 25% smaller than FAST5 and delivers consistent improvements on different computer architectures. Nanopore sequencing data are rapidly analyzed with parallel data access.
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Affiliation(s)
- Hasindu Gamaarachchi
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia. .,School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia.
| | - Hiruna Samarakoon
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Sasha P Jenner
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - James M Ferguson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Timothy G Amos
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Jillian M Hammond
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Hassaan Saadat
- School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Martin A Smith
- CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada.,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Sri Parameswaran
- School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia. .,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.
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7
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Van Thillo Q, De Bie J, Seneviratne JA, Demeyer S, Omari S, Balachandran A, Zhai V, Tam WL, Sweron B, Geerdens E, Gielen O, Provost S, Segers H, Boeckx N, Marshall GM, Cheung BB, Isobe K, Kato I, Takita J, Amos TG, Deveson IW, McCalmont H, Lock RB, Oxley EP, Garwood MM, Dickins RA, Uyttebroeck A, Carter DR, Cools J, de Bock CE. Oncogenic cooperation between TCF7-SPI1 and NRAS(G12D) requires β-catenin activity to drive T-cell acute lymphoblastic leukemia. Nat Commun 2021; 12:4164. [PMID: 34230493 PMCID: PMC8260768 DOI: 10.1038/s41467-021-24442-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Spi-1 Proto-Oncogene (SPI1) fusion genes are recurrently found in T-cell acute lymphoblastic leukemia (T-ALL) cases but are insufficient to drive leukemogenesis. Here we show that SPI1 fusions in combination with activating NRAS mutations drive an immature T-ALL in vivo using a conditional bone marrow transplant mouse model. Addition of the oncogenic fusion to the NRAS mutation also results in a higher leukemic stem cell frequency. Mechanistically, genetic deletion of the β-catenin binding domain within Transcription factor 7 (TCF7)-SPI1 or use of a TCF/β-catenin interaction antagonist abolishes the oncogenic activity of the fusion. Targeting the TCF7-SPI1 fusion in vivo with a doxycycline-inducible knockdown results in increased differentiation. Moreover, both pharmacological and genetic inhibition lead to down-regulation of SPI1 targets. Together, our results reveal an example where TCF7-SPI1 leukemia is vulnerable to pharmacological targeting of the TCF/β-catenin interaction.
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Affiliation(s)
- Quentin Van Thillo
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Jolien De Bie
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, UZ Leuven, Leuven, Belgium
| | - Janith A Seneviratne
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Sofie Demeyer
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Sofia Omari
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Anushree Balachandran
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Vicki Zhai
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Wai L Tam
- Technology Innovation Lab, VIB, Gent, Belgium
| | - Bram Sweron
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Ellen Geerdens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Olga Gielen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Sarah Provost
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Heidi Segers
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pediatric Hemato-Oncology, UZ Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Laboratory Medicine, UZ Leuven, Leuven, Belgium
| | - Glenn M Marshall
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Belamy B Cheung
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Kiyotaka Isobe
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Timothy G Amos
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Hannah McCalmont
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B Lock
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Ethan P Oxley
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Maximilian M Garwood
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Anne Uyttebroeck
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pediatric Hemato-Oncology, UZ Leuven, Leuven, Belgium
| | - Daniel R Carter
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
- School of Biomedical Engineering, University of Technology, Sydney, NSW, Australia
| | - Jan Cools
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium.
| | - Charles E de Bock
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia.
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8
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Benaud N, Edwards RJ, Amos TG, D'Agostino PM, Gutiérrez-Chávez C, Montgomery K, Nicetic I, Ferrari BC. Antarctic desert soil bacteria exhibit high novel natural product potential, evaluated through long-read genome sequencing and comparative genomics. Environ Microbiol 2020; 23:3646-3664. [PMID: 33140504 DOI: 10.1111/1462-2920.15300] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 11/30/2022]
Abstract
Actinobacteria and Proteobacteria are important producers of bioactive natural products (NP), and these phyla dominate in the arid soils of Antarctica, where metabolic adaptations influence survival under harsh conditions. Biosynthetic gene clusters (BGCs) which encode NPs, are typically long and repetitious high G + C regions difficult to sequence with short-read technologies. We sequenced 17 Antarctic soil bacteria from multi-genome libraries, employing the long-read PacBio platform, to optimize capture of BGCs and to facilitate a comprehensive analysis of their NP capacity. We report 13 complete bacterial genomes of high quality and contiguity, representing 10 different cold-adapted genera including novel species. Antarctic BGCs exhibited low similarity to known compound BGCs (av. 31%), with an abundance of terpene, non-ribosomal peptide and polyketide-encoding clusters. Comparative genome analysis was used to map BGC variation between closely related strains from geographically distant environments. Results showed the greatest biosynthetic differences to be in a psychrotolerant Streptomyces strain, as well as a rare Actinobacteria genus, Kribbella, while two other Streptomyces spp. were surprisingly similar to known genomes. Streptomyces and Kribbella BGCs were predicted to encode antitumour, antifungal, antibacterial and biosurfactant-like compounds, and the synthesis of NPs with antibacterial, antifungal and surfactant properties was confirmed through bioactivity assays.
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Affiliation(s)
- Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Paul M D'Agostino
- Technische Universität Dresden, Chair of Technical Biochemistry, Bergstraße 66, 01602 Dresden, Germany
| | | | - Kate Montgomery
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Iskra Nicetic
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
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9
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Edwards RJ, Tuipulotu DE, Amos TG, O'Meally D, Richardson MF, Russell TL, Vallinoto M, Carneiro M, Ferrand N, Wilkins MR, Sequeira F, Rollins LA, Holmes EC, Shine R, White PA. Draft genome assembly of the invasive cane toad, Rhinella marina. Gigascience 2018; 7:5096832. [PMID: 30101298 PMCID: PMC6145236 DOI: 10.1093/gigascience/giy095] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 03/22/2018] [Accepted: 07/22/2018] [Indexed: 12/28/2022] Open
Abstract
Background The cane toad (Rhinella marina formerly Bufo marinus) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding of cane toad genetics. The availability of a genome would help to close these gaps and accelerate cane toad research. Findings We report a draft genome assembly for R. marina, the first of its kind for the Bufonidae family. We used a combination of long-read Pacific Biosciences RS II and short-read Illumina HiSeq X sequencing to generate 359.5 Gb of raw sequence data. The final hybrid assembly of 31,392 scaffolds was 2.55 Gb in length with a scaffold N50 of 168 kb. BUSCO analysis revealed that the assembly included full length or partial fragments of 90.6% of tetrapod universal single-copy orthologs (n = 3950), illustrating that the gene-containing regions have been well assembled. Annotation predicted 25,846 protein coding genes with similarity to known proteins in Swiss-Prot. Repeat sequences were estimated to account for 63.9% of the assembly. Conclusions The R. marina draft genome assembly will be an invaluable resource that can be used to further probe the biology of this invasive species. Future analysis of the genome will provide insights into cane toad evolution and enrich our understanding of their interplay with the ecosystem at large.
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Affiliation(s)
- Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Denis O'Meally
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camperdown, NSW, 2052, Australia
| | - Mark F Richardson
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3216, Australia.,Bioinformatics Core Research Group, Deakin University, Geelong, VIC, 3216, Australia
| | - Tonia L Russell
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Marcelo Vallinoto
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Laboratório de Evolução, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, South Africa
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,Ramaciotti Centre for Genomics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Fernando Sequeira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Lee A Rollins
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3216, Australia.,Evolution and Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Richard Shine
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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10
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Glenn WK, Ngan CC, Amos TG, Edwards RJ, Swift J, Lutze-Mann L, Shang F, Whitaker NJ, Lawson JS. High risk human papilloma viruses (HPVs) are present in benign prostate tissues before development of HPV associated prostate cancer. Infect Agent Cancer 2017; 12:46. [PMID: 28811834 PMCID: PMC5553674 DOI: 10.1186/s13027-017-0157-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [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: 03/21/2017] [Accepted: 08/05/2017] [Indexed: 12/31/2022] Open
Abstract
Background Although high risk HPVs are associated with an increased risk of prostate cancer it is not known if they have a causal role. The purpose of this study is to investigate the potential role of human papilloma viruses (HPVs) in prostate cancer. The aims are (i) to investigate the presence and confirm the identity of high risk HPVs in benign prostate tissues prior to the development of HPV positive prostate cancer in the same patients, and (ii) to determine if HPVs are biologically active. Methods We used polymerase chain reaction (PCR) to identify HPVs in specimens from 52 Australian men with benign prostate biopsies who 1 to 10 years later developed prostate cancer. Immunohistochemistry (IHC) was used to assess the expression of HPV E7 oncoproteins, cytokeratin and prostate specific antigen (PSA). We used RNASeq data from The Cancer Genome Atlas (TCGA) to identify possible HPV RNA sequences in prostate cancer. Results HPV screening using standard PCR was conducted on 28 of the 52 sets of benign and later prostate cancers. HPV L1 genes were identified in 13 (46%) benign and 8 (29%) of 28 later prostate cancers in the same patients. HPV E7 genes were identified in 23 (82%) benign and 19 (68%) of 28 subsequent prostate cancers in the same patients. The same HPV types were present in both the benign and subsequent prostate cancers in 9 sets of specimens. HPV type 16 was identified in 15% of benign and 3% of prostate cancers. HPV type 18 was identified in 26% of benign and 16% of prostate cancers. Small numbers of HPV types 45, 47, 76 and 115 were also identified. High confidence RNA-Seq evidence for high risk HPV types 16 and 18 was identified in 12 (2%) of the 502 TCGA prostate cancer transcriptomes. High risk HPV E7 oncoprotein was positively expressed in 23 (82%) of 28 benign prostate specimens but only in 8 (29%) of 28 of the later prostate cancer specimens. This difference is statistically significant (p = 0.001). Prostate specific antigen (PSA) was more highly expressed in 26 (50%) of 52 prostate cancer specimens as compared to prior benign prostate specimens in the same patients. Conclusions High risk HPVs are present in benign prostate tissues prior to the development of HPV positive prostate cancer. There is a significantly higher expression of HPV E7 oncoproteins in benign prostate tissues as compared to late prostate cancer that subsequently developed in the same patients. This observation suggests that HPV oncogenic activity is an early phenomenon in a majority of prostate oncogenesis. TCGA RNA-Seq data suggests that HPV is biologically active in some prostate tumour samples. Electronic supplementary material The online version of this article (doi:10.1186/s13027-017-0157-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wendy K Glenn
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Christopher C Ngan
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Joshua Swift
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Louise Lutze-Mann
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Fei Shang
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - Noel J Whitaker
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
| | - James S Lawson
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW Australia
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11
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Waters SA, McAteer SP, Kudla G, Pang I, Deshpande NP, Amos TG, Leong KW, Wilkins MR, Strugnell R, Gally DL, Tollervey D, Tree JJ. Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E. EMBO J 2016; 36:374-387. [PMID: 27836995 PMCID: PMC5286369 DOI: 10.15252/embj.201694639] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [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: 04/26/2016] [Revised: 10/06/2016] [Accepted: 10/11/2016] [Indexed: 02/04/2023] Open
Abstract
RNA sequencing studies have identified hundreds of non‐coding RNAs in bacteria, including regulatory small RNA (sRNA). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high‐throughput analysis of RNA–RNA interactions in bacteria. Here we demonstrate that in vivo sRNA–mRNA duplexes can be recovered using UV‐crosslinking, ligation and sequencing of hybrids (CLASH). Many sRNAs recruit the endoribonuclease, RNase E, to facilitate processing of mRNAs. We were able to recover base‐paired sRNA–mRNA duplexes in association with RNase E, allowing proximity‐dependent ligation and sequencing of cognate sRNA–mRNA pairs as chimeric reads. We verified that this approach captures bona fide sRNA–mRNA interactions. Clustering analyses identified novel sRNA seed regions and sets of potentially co‐regulated target mRNAs. We identified multiple mRNA targets for the pathotype‐specific sRNA Esr41, which was shown to regulate colicin sensitivity and iron transport in E. coli. Numerous sRNA interactions were also identified with non‐coding RNAs, including sRNAs and tRNAs, demonstrating the high complexity of the sRNA interactome.
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Affiliation(s)
- Shafagh A Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sean P McAteer
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Grzegorz Kudla
- MRC Human Genetic Unit, University of Edinburgh, Edinburgh, UK
| | - Ignatius Pang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Systems Biology Initiative, University of New South Wales, Sydney, NSW, Australia
| | - Nandan P Deshpande
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Systems Biology Initiative, University of New South Wales, Sydney, NSW, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Kai Wen Leong
- Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Systems Biology Initiative, University of New South Wales, Sydney, NSW, Australia
| | - Richard Strugnell
- Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - David L Gally
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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12
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Venturi V, Nzingha K, Amos TG, Charles WC, Dekhtiarenko I, Cicin-Sain L, Davenport MP, Rudd BD. The Neonatal CD8+ T Cell Repertoire Rapidly Diversifies during Persistent Viral Infection. J Immunol 2016; 196:1604-16. [PMID: 26764033 DOI: 10.4049/jimmunol.1501867] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/05/2015] [Indexed: 01/22/2023]
Abstract
CMV is the most common congenital infection in the United States. The major target of congenital CMV is the brain, with clinical manifestations including mental retardation, vision impairment, and sensorineural hearing loss. Previous reports have shown that CD8(+) T cells are required to control viral replication and significant numbers of CMV-specific CD8(+) T cells persist in the brain even after the initial infection has been cleared. However, the dynamics of CD8(+) T cells in the brain during latency remain largely undefined. In this report, we used TCR sequencing to track the development and maintenance of neonatal clonotypes in the brain and spleen of mice during chronic infection. Given the discontinuous nature of tissue-resident memory CD8(+) T cells, we hypothesized that neonatal TCR clonotypes would be locked in the brain and persist into adulthood. Surprisingly, we found that the Ag-specific T cell repertoire in neonatal-infected mice diversified during persistent infection in both the brain and spleen, while maintaining substantial similarity between the CD8(+) T cell populations in the brain and spleen in both early and late infection. However, despite the diversification of, and potential interchange between, the spleen and brain Ag-specific T cell repertoires, we observed that germline-encoded TCR clonotypes, characteristic of neonatal infection, persisted in the brain, albeit sometimes in low abundance. These results provide valuable insights into the evolution of CD8(+) T cell repertoires following neonatal CMV infection and thus have important implications for the development of therapeutic strategies to control CMV in early life.
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Affiliation(s)
- Vanessa Venturi
- Kirby Institute for Infection and Immunity, University of New South Wales Australia, Sydney, New South Wales 2052, Australia;
| | - Kito Nzingha
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850
| | - Timothy G Amos
- Kirby Institute for Infection and Immunity, University of New South Wales Australia, Sydney, New South Wales 2052, Australia
| | - Wisler C Charles
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850
| | - Iryna Dekhtiarenko
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; and
| | - Luka Cicin-Sain
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; and Institute for Virology, Hannover Medical School, 30625 Hannover, Germany
| | - Miles P Davenport
- Kirby Institute for Infection and Immunity, University of New South Wales Australia, Sydney, New South Wales 2052, Australia;
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850;
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13
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Abstract
A bolted galvanized iron silo (21.5 t) was sealed using a polyvinyl resin formulation (1624 White) sprayed onto joints from the inside. Gastightness was assessed by pressure decay and static pressure tests. The silo was loaded with wheat into which cages of insect-infested wheat, thermocouples and gas sampling lines, were introduced. Oxygen levels were reduced to < 1 % by purging with nitrogen, and similar levels were then maintained by a slow nitrogen bleed for 35 days, after which the silo was emptied. All adult insects were dead but, as expected, some immatures survived since the maintenance period was too short to ensure complete kill at the observed grain temperatures (generally < 15�C). The silo was reloaded, resealed and tested again for leaks. Some leaks were found and sealed with silicon rubber. Gastightness was not as good as before, though the silo would still be suitable for fumigation. Further sealing would be required however, if nitrogen were to be used efficiently (maintenance rate of 0.2 m3 t-1 day-1). Sealing achieved was sufficient to permit use of nitrogen or fumigants but sealants cost $132 and labour a minimum of $280, representing an overall cost of $19.1 6 t-1. This would still be cheaper than buying a new silo of suitably gastight construction at a cost of at least $28 t-1.
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14
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Amos TG, Williams P. Insect Growth Regulators: Some Effects of Methoprene and Hydroprene on Productivity of Several Stored Grain Insects. AUST J ZOOL 1977. [DOI: 10.1071/zo9770201] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The effects of two insect growth regulators on the productivity of Rhyzopertha dominica, Sitophilus oryzae and S. granarius were studied by exposing insects to wheat treated with methoprene (isopropyl 11-methoxy-3,7,11-trimethyldodeca-2,4-dienoate) or hydroprene (ethyl 3,7,11-trimethyldodeca-2,4-dienoate) at concentrations of 1, 5, 10 and 20 ppm. Parental adult mortality was generally higher on wheat treated with methoprene than with hydroprene, and this effect was usually enhanced under unventilated conditions. The productivity of the three species was markedly reduced, in some instances suppressed, under unventilated conditions, whereas only R. dominica productivity was depressed under ventilated conditions. When progeny were produced, their productivity was, in general, lower than normal.
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Abstract
The effects were studied of incorporating three synthetic insect juvenile hormones and five analogues
in flour diets for T. castaneum. The synthetic hormones used were: methyl 10,ll-epoxy-7-ethyl-3,ll-dimethyltrideca-
2,6-dienoate (compounds I and II; these had the same structure but consisted of
different isomer ratios), and methyl cis-l0,11-epoxy-3,7,11-trimethyltrideca-trans-2,trans-6-dienoate
(III). The analogues used were: 6',7'-epoxy-3',7'-dimethyloct-trans-2'-enyl 3,4-methylenedioxyphenyl
ether (IV); 3'-methyl-7'-ethylnona-2',6'-dienyl 3,4-methylenedioxyphenyl ether (V); ethyl
3,7,11-trimethyldodeca-2,4-dienoate (VI); isopropyl 11-methoxy-3,7,11-trimethyldodeca-2,4-dienoate
(VII); 6',7'-epoxy-3',7'-dimethyloct-trans-2'-enyl 4-ethylphenyl ether (VIII). Compounds
II-VII were incorporated in flour media at concentrations of 5 and 20 p.p.m. and I and VIII at
5 p.p.m. only.
The number of eggs laid in various treated media did not differ significantly from that in the
control. Egg to adult development was inhibited by VII and VIII at 5 p.p.m. and by II, IV and VI
at 20 p.p.m. Development was completed in other treatments but with a high level of adult morphological
deformity except with V and VI at 5 p.p.m. The compounds tended to increase the developmental
period from egg to adult.
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16
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Amos TG, Waterhouse FL, Chetham NA. Temporal distribution of Tribolium castaneum Herbst and Cadra cautella Walker on temperature gradients. Experientia 1968; 24:86-7. [PMID: 5637630 DOI: 10.1007/bf02136812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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17
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Amos TG. An automated biological recorder. Med Biol Illus 1966; 16:145. [PMID: 5949538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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