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Steele EJ, Franklin A, Lindley RA. Somatic mutation patterns at Ig and Non-Ig Loci. DNA Repair (Amst) 2024; 133:103607. [PMID: 38056368 DOI: 10.1016/j.dnarep.2023.103607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023]
Abstract
The reverse transcriptase (RT) model of immunoglobulin (Ig) somatic hypermutation (SHM) has received insufficient scientific attention. This is understandable given that DNA deamination mediated by activation-induced deaminase (AID), the initiating step of Ig SHM, has dominated experiments since 2002. We summarise some key history of the RT Ig SHM model dating to 1987. For example, it is now established that DNA polymerase η, the sole DNA repair polymerase involved in post-replication short-patch repair, is an efficient cellular RT. This implies that it is potentially able to initiate target site reverse transcription by RNA-directed DNA repair at AID-induced lesions. Recently, DNA polymerase θ has also been shown to be an efficient cellular RT. Since DNA polymerase θ plays no significant role in Ig SHM, it could serve a similar RNA-dependent DNA polymerase role as DNA polymerase η at non-Ig loci in the putative RNA-templated nucleotide excision repair of bulky adducts and other mutagenic lesions on the transcribed strand. A major yet still poorly recognised consequence of the proposed RT process in Ig SHM is the generation of significant and characteristic strand-biased mutation signatures at both deoxyadenosine/deoxythymidine and deoxyguanosine/deoxycytidine base pairs. In this historical perspective, we highlight how diagnostic strand-biased mutation signatures are detected in vivo during SHM at both Ig loci in germinal centre B lymphocytes and non-Ig loci in cancer genomes. These strand-biased signatures have been significantly obscured by technical issues created by improper use of the polymerase chain reaction technique. A heightened awareness of this fact should contribute to better data interpretation and somatic mutation pattern recognition both at Ig and non-Ig loci.
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Affiliation(s)
- Edward J Steele
- Melville Analytics Pty Ltd, 2/102 Duke St, Kangaroo Point, Brisbane 4169, Qld, Australia.
| | - Andrew Franklin
- Novartis Pharmaceuticals UK Limited, The WestWorks Building, White City Place, 195 Wood Lane, W12 7FQ London, United Kingdom
| | - Robyn A Lindley
- GMDxgenomics, Suite 201, 697 Burke Rd, Camberwell, Melbourne 3124, Vic, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, Vic, Australia
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2
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Mamrot J, Hall NE, Lindley RA. Predicting clinical outcomes using cancer progression associated signatures. Oncotarget 2021; 12:845-858. [PMID: 33889305 PMCID: PMC8057277 DOI: 10.18632/oncotarget.27934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/22/2021] [Indexed: 12/09/2022] Open
Abstract
Somatic mutation signatures are an informative facet of cancer aetiology, however they are rarely useful for predicting patient outcome. The aim of this study is to evaluate the utility of a panel of 142 mutation-signature–associated metrics (P142) for predicting cancer progression in patients from a ‘TCGA PanCancer Atlas’ cohort. The P142 metrics are comprised of AID/APOBEC and ADAR deaminase associated SNVs analyzed for codon context, strand bias, and transitions/transversions. TCGA tumor-normal mutation data was obtained for 10,437 patients, representing 31 of the most prevalent forms of cancer. Stratified random sampling was used to split patients into training, tuning and validation cohorts for each cancer type. Cancer specific machine learning (XGBoost) models were built using the output from the P142 panel to predict patient Progression Free Survival (PFS) status as either “High PFS” or “Low PFS”. Predictive performance of each model was evaluated using the validation cohort. Models accurately predicted PFS status for several cancer types, including adrenocortical carcinoma, glioma, mesothelioma, and sarcoma. In conclusion, the P142 panel of metrics successfully predicted cancer progression status in patients with some, but not all cancer types analyzed. These results pave the way for future studies on cancer progression associated signatures.
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Affiliation(s)
- Jared Mamrot
- GMDx Group Ltd, Melbourne, Victoria, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, Australia
| | | | - Robyn A Lindley
- GMDx Group Ltd, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The Victorian Comprehensive Cancer Centre, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, VIC, Australia
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3
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Steele EJ, Gorczynski RM, Lindley RA, Liu Y, Temple R, Tokoro G, Wickramasinghe DT, Wickramasinghe NC. The efficient Lamarckian spread of life in the cosmos. ADVANCES IN GENETICS 2020; 106:21-43. [PMID: 33081924 PMCID: PMC7340397 DOI: 10.1016/bs.adgen.2020.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this Chapter we discuss the various mechanisms that are available for the possible transfer of cosmic microbial living systems from one cosmic habitat to another. With the 100 or so habitable planets that are now known to exist in our galaxy alone transfers of cometary dust carrying life including fragments of icy planetoids/asteroids would be expected to occur on a routine basis. It is thus easy to view the galaxy as a single connected "biosphere" of which our planet Earth is a minor component. The Hoyle-Wickramasinghe Panspermia paradigm provides a cogent biological rationale for the actual widespread existence of Lamarckian modes of inheritance in terrestrial systems (which we review here). Thus the Panspermia paradigm provides the raison d'etre for Lamarckian Inheritance. Under a terrestrially confined neoDarwinian viewpoint such an association may have been thought spurious in the past. Our aim here is to outline the main evidence for rapid terrestrial-based Lamarckian-based evolutionary hypermutation processes dependent on reverse transcription-coupled mechanisms among others. Such rapid adaptation mechanisms would be consistent with the effective cosmic spread of living systems. For example, a viable, or cryo-preserved, living system traveling through space in a protective matrix will of necessity need to adapt rapidly and proliferate on landing in a new cosmic niche. Lamarckian mechanisms thus come to the fore and supersede the slow (blind and random) genetic processes expected under neoDarwinian Earth centred theories.
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Affiliation(s)
- Edward J Steele
- C.Y.O'Connor ERADE Village Foundation, Piara Waters, Perth, WA, Australia; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Melville Analytics Pty Ltd, Melbourne, VIC, Australia.
| | | | - Robyn A Lindley
- Department of Clinical Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, Melbourne, VIC, Australia; GMDx Group Ltd, Melbourne, VIC, Australia
| | - Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Robert Temple
- The History of Chinese Science and Culture Foundation, Conway Hall, London, United Kingdom
| | - Gensuke Tokoro
- Institute for the Study of Panspermia and Astroeconomics, Gifu, Japan
| | - Dayal T Wickramasinghe
- College of Physical and Mathematical Sciences, Australian National University, Canberra, ACT, Australia
| | - N Chandra Wickramasinghe
- Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Institute for the Study of Panspermia and Astroeconomics, Gifu, Japan; University of Buckingham, Buckingham, United Kingdom; National Institute of Fundamental Studies, Kandy, Sri Lanka.
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4
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Franklin A, Steele EJ, Lindley RA. A proposed reverse transcription mechanism for (CAG)n and similar expandable repeats that cause neurological and other diseases. Heliyon 2020; 6:e03258. [PMID: 32140575 PMCID: PMC7044655 DOI: 10.1016/j.heliyon.2020.e03258] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/26/2019] [Accepted: 01/15/2020] [Indexed: 12/12/2022] Open
Abstract
The mechanism of (CAG)n repeat generation, and related expandable repeat diseases in non-dividing cells, is currently understood in terms of a DNA template-based DNA repair synthesis process involving hairpin stabilized slippage, local error-prone repair via MutSβ (MSH2-MSH3) hairpin protective stabilization, then nascent strand extension by DNA polymerases-β and -δ. We advance a very similar slipped hairpin-stabilized model involving MSH2-MSH3 with two key differences: the copying template may also be the nascent pre-mRNA with the repair pathway being mediated by the Y-family error-prone enzymes DNA polymerase-η and DNA polymerase-κ acting as reverse transcriptases. We argue that both DNA-based and RNA-based mechanisms could well be activated in affected non-dividing brain cells in vivo. Here, we compare the advantages of the RNA/RT-based model proposed by us as an adjunct to previously proposed models. In brief, our model depends upon dysregulated innate and adaptive immunity cascades involving AID/APOBEC and ADAR deaminases that are known to be involved in normal locus-specific immunoglobulin somatic hypermutation, cancer progression and somatic mutations at many off-target non-immunoglobulin sites across the genome: we explain how these processes could also play an active role in repeat expansion diseases at RNA polymerase II-transcribed genes.
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Affiliation(s)
- Andrew Franklin
- Medical Department, Novartis Pharmaceuticals UK Limited, 200 Frimley Business Park, Frimley, Surrey, GU16 7SR, United Kingdom
| | - Edward J. Steele
- Melville Analytics Pty Ltd, Melbourne, Vic, 3004, Australia
- CYO’Connor ERADE Village Foundation, Perth, WA, Australia
| | - Robyn A. Lindley
- GMDxgenomics, Melbourne, Vic, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, Vic, Australia
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5
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Steele EJ, Lindley RA. Regulatory T cells and co-evolution of allele-specific MHC recognition by the TCR. Scand J Immunol 2019; 91:e12853. [PMID: 31793005 PMCID: PMC7064991 DOI: 10.1111/sji.12853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/27/2019] [Indexed: 12/13/2022]
Abstract
What is the evolutionary mechanism for the TCR-MHC-conserved interaction? We extend Dembic's model (Dembic Z. In, Scand J Immunol e12806, 2019) of thymus positive selection for high-avidity anti-self-MHC Tregs among double (CD4 + CD8+)-positive (DP) developing thymocytes. This model is based on competition for self-MHC (+ Pep) complexes presented on cortical epithelium. Such T cells exit as CD4 + CD25+FoxP3 + thymic-derived Tregs (tTregs). The other positively selected DP T cells are then negatively selected on medulla epithelium removing high-avidity anti-self-MHC + Pep as T cells commit to CD4 + or CD8 + lineages. The process is likened to the competitive selection and affinity maturation in Germinal Centre for the somatic hypermutation (SHM) of rearranged immunoglobulin (Ig) variable region (V[D]Js) of centrocytes bearing antigen-specific B cell receptors (BCR). We now argue that the same direct SHM processes for TCRs occur in post-antigenic Germinal Centres, but now occurring in peripheral pTregs. This model provides a potential solution to a long-standing problem previously recognized by Cohn and others (Cohn M, Anderson CC, Dembic Z. In, Scand J Immunol e12790, 2019) of how co-evolution occurs of species-specific MHC alleles with the repertoire of their germline TCR V counterparts. We suggest this is not by 'blind', slow, and random Darwinian natural selection events, but a rapid structured somatic selection vertical transmission process. The pTregs bearing somatic TCR V mutant genes then, on arrival in reproductive tissues, can donate their TCR V sequences via soma-to-germline feedback as discussed in this journal earlier. (Steele EJ, Lindley RA. In, Scand J Immunol e12670, 2018) The high-avidity tTregs also participate in the same process to maintain a biased, high-avidity anti-self-MHC germline V repertoire.
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Affiliation(s)
- Edward J Steele
- Melville Analytics Pty Ltd, Melbourne, Vic, Australia.,CYO'Connor ERADE Village Foundation, Perth, WA, Australia
| | - Robyn A Lindley
- GMDxCo Pty Ltd, Melbourne, Vic, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, Melbourne, Vic, Australia
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6
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Steele EJ, Gorczynski RM, Lindley RA, Liu Y, Temple R, Tokoro G, Wickramasinghe DT, Wickramasinghe NC. Lamarck and Panspermia - On the Efficient Spread of Living Systems Throughout the Cosmos. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 149:10-32. [PMID: 31445944 DOI: 10.1016/j.pbiomolbio.2019.08.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 08/14/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
We review the main lines of evidence (molecular, cellular and whole organism) published since the 1970s demonstrating Lamarckian Inheritance in animals, plants and microorganisms viz. the transgenerational inheritance of environmentally-induced acquired characteristics. The studies in animals demonstrate the genetic permeability of the soma-germline Weismann Barrier. The widespread nature of environmentally-directed inheritance phenomena reviewed here contradicts a key pillar of neo-Darwinism which affirms the rigidity of the Weismann Barrier. These developments suggest that neo-Darwinian evolutionary theory is in need of significant revision. We argue that Lamarckian inheritance strategies involving environmentally-induced rapid directional genetic adaptations make biological sense in the context of cosmic Panspermia allowing the efficient spread of living systems and genetic innovation throughout the Universe. The Hoyle-Wickramasinghe Panspermia paradigm also developed since the 1970s, unlike strictly geocentric neo-Darwinism provides a cogent biological rationale for the actual widespread existence of Lamarckian modes of inheritance - it provides its raison d'être. Under a terrestrially confined neo-Darwinian viewpoint such an association may have been thought spurious in the past. Our aim is to outline the conceptual links between rapid Lamarckian-based evolutionary hypermutation processes dependent on reverse transcription-coupled mechanisms among others and the effective cosmic spread of living systems. For example, a viable, or cryo-preserved, living system travelling through space in a protective matrix will need of necessity to rapidly adapt and proliferate on landing in a new cosmic niche. Lamarckian mechanisms thus come to the fore and supersede the slow (blind and random) genetic processes expected under a traditional neo-Darwinian evolutionary paradigm.
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Affiliation(s)
- Edward J Steele
- C.Y.O'Connor ERADE Village Foundation, Piara Waters, Perth, 6112, WA, Australia; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Melville Analytics Pty Ltd, Melbourne, Vic, Australia.
| | | | - Robyn A Lindley
- Department of Clinical Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of MelbourneVic, Australia; GMDx Group Ltd, Melbourne, Vic, Australia
| | - Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Robert Temple
- The History of Chinese Science and Culture Foundation, Conway Hall, London, UK
| | - Gensuke Tokoro
- Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Dayal T Wickramasinghe
- Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; College of Physical and Mathematical Sciences, Australian National University, Canberra, Australia
| | - N Chandra Wickramasinghe
- Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Institute for the Study of Panspermia and Astrobiology, Gifu, Japan; Buckingham Centre for Astrobiology, University of Buckingham, UK
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7
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Yamazaki H, Shirakawa K, Matsumoto T, Hirabayashi S, Murakawa Y, Kobayashi M, Sarca AD, Kazuma Y, Matsui H, Maruyama W, Fukuda H, Shirakawa R, Shindo K, Ri M, Iida S, Takaori-Kondo A. Endogenous APOBEC3B Overexpression Constitutively Generates DNA Substitutions and Deletions in Myeloma Cells. Sci Rep 2019; 9:7122. [PMID: 31073151 PMCID: PMC6509214 DOI: 10.1038/s41598-019-43575-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/26/2019] [Indexed: 02/07/2023] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) DNA cytosine deaminases have emerged as potential genomic mutators in various cancers. Multiple myeloma accumulates APOBEC signature mutations as it progresses; however, the mechanisms underlying APOBEC signature acquisition and its consequences remain elusive. In this study, we examined the significance and clinical impact of APOBEC3B (A3B) activity in multiple myeloma. Among APOBECs, only highly expressed A3B was associated with poor prognosis in myeloma patients, independent of other known poor prognostic factors. Quantitative PCR revealed that CD138-positive primary myeloma cells and myeloma cell lines exhibited remarkably high A3B expression levels. Interestingly, lentiviral A3B knockdown prevented the generation of deletion and loss-of-function mutations in exogenous DNA, whereas in control cells, these mutations accumulated with time. A3B knockdown also decreased the basal levels of γ-H2AX foci, suggesting that A3B promotes constitutive DNA double-strand breaks in myeloma cells. Importantly, among control shRNA-transduced cells, we observed the generation of clones that harboured diverse mutations in exogenous genes and several endogenous genes frequently mutated in myeloma, including TP53. Taken together, the results suggest that A3B constitutively mutates the tumour genome beyond the protection of the DNA repair system, which may lead to clonal evolution and genomic instability in myeloma.
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Affiliation(s)
- Hiroyuki Yamazaki
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Tadahiko Matsumoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Shigeki Hirabayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.,RIKEN-HMC Clinical Omics Unit, RIKEN Baton Zone Program, Kanagawa, 230-0045, Japan
| | - Yasuhiro Murakawa
- RIKEN-HMC Clinical Omics Unit, RIKEN Baton Zone Program, Kanagawa, 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Kanagawa, 230-0045, Japan
| | - Masayuki Kobayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Anamaria Daniela Sarca
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Hiroyuki Matsui
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Wataru Maruyama
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Hirofumi Fukuda
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Ryutaro Shirakawa
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Keisuke Shindo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Masaki Ri
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Shinsuke Iida
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.
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8
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Lindley RA, Hall NE. APOBEC and ADAR deaminases may cause many single nucleotide polymorphisms curated in the OMIM database. Mutat Res 2018; 810:33-38. [PMID: 29957488 DOI: 10.1016/j.mrfmmm.2018.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/11/2018] [Accepted: 03/28/2018] [Indexed: 11/28/2022]
Abstract
Cytosine and adenosine deamination events (DNA, RNA substrates) account for most codon-context Targeted Somatic Mutation (TSM) patterns observed in immunoglobulin (Ig) somatic hypermutation (SHM), and in cancer exomes following Ig-SHM-like responses. TSM refers to the process of somatic mutagenesis involving deamination events that results on a dominant type of mutation (e.g., C-to-T), and co-incident at a particular motif (e.g., WRC), and preferentially targeting the first, second or third nucleotide position within the mutated codon (e.g. MC1, MC2 or MC3, read 5-prime to 3-prime). It is now widely accepted that if left uncorrected, the accumulation of uncorrected TSMs involving the deaminases, may lead to a diagnosis of cancer or other degenerative disease. Our hypothesis is that many missense, nonsense and synonymous single nucleotide polymorphisms (SNPs) associated with clinically significant diseases may have arisen in the population by similar highly targeted deamination events. The OMIM database was searched for disease-associated SNPs on the X chromosome, and for all chromosomes. The nucleotide substitution patterns for disease-associated SNPs were analyzed by the TSM method to identify the likely deaminase source for C-to-U (C-to-T/G-to-A) and A-to-I (A-to-G/T-to-C) derived gene mutations preferentially targeting known sequence motifs associated with the deaminases: AID, APOBEC3G, APOBEC3B and ADAR 1/2. Of the 789 OMIM SNPs analysed. In both data sets, the mutation targeting preferences within the mutated codon reveal a statistically significant bias (p < 0.001). The results imply that a deamination of C-site and A-site targets are written into the human germline for the chromosome wide exomic SNPs analysed. This is consistent with previously observed mutation patterns arising in cancer genomes and hypermutated Ig genes during SHM. The results imply that similar types of deaminase-mediated molecular processes that occur in somatic hypermutation and cancer, may be contributing causative drivers of human exomic SNPs.
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Affiliation(s)
- Robyn A Lindley
- GMDxCo Pty Ltd, Melbourne Vic, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne Vic, Australia.
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9
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Steele EJ, Al-Mufti S, Augustyn KA, Chandrajith R, Coghlan JP, Coulson SG, Ghosh S, Gillman M, Gorczynski RM, Klyce B, Louis G, Mahanama K, Oliver KR, Padron J, Qu J, Schuster JA, Smith WE, Snyder DP, Steele JA, Stewart BJ, Temple R, Tokoro G, Tout CA, Unzicker A, Wainwright M, Wallis J, Wallis DH, Wallis MK, Wetherall J, Wickramasinghe DT, Wickramasinghe JT, Wickramasinghe NC, Liu Y. Cause of Cambrian Explosion - Terrestrial or Cosmic? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 136:3-23. [PMID: 29544820 DOI: 10.1016/j.pbiomolbio.2018.03.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We review the salient evidence consistent with or predicted by the Hoyle-Wickramasinghe (H-W) thesis of Cometary (Cosmic) Biology. Much of this physical and biological evidence is multifactorial. One particular focus are the recent studies which date the emergence of the complex retroviruses of vertebrate lines at or just before the Cambrian Explosion of ∼500 Ma. Such viruses are known to be plausibly associated with major evolutionary genomic processes. We believe this coincidence is not fortuitous but is consistent with a key prediction of H-W theory whereby major extinction-diversification evolutionary boundaries coincide with virus-bearing cometary-bolide bombardment events. A second focus is the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus. A third focus concerns the micro-organism fossil evidence contained within meteorites as well as the detection in the upper atmosphere of apparent incoming life-bearing particles from space. In our view the totality of the multifactorial data and critical analyses assembled by Fred Hoyle, Chandra Wickramasinghe and their many colleagues since the 1960s leads to a very plausible conclusion - life may have been seeded here on Earth by life-bearing comets as soon as conditions on Earth allowed it to flourish (about or just before 4.1 Billion years ago); and living organisms such as space-resistant and space-hardy bacteria, viruses, more complex eukaryotic cells, fertilised ova and seeds have been continuously delivered ever since to Earth so being one important driver of further terrestrial evolution which has resulted in considerable genetic diversity and which has led to the emergence of mankind.
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Affiliation(s)
- Edward J Steele
- CY O'Connor ERADE Village Foundation, Piara Waters, WA, Australia; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka.
| | - Shirwan Al-Mufti
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Kenneth A Augustyn
- Center for the Physics of Living Organisms, Department of Physics, Michigan Technological University, Michigan, United States
| | | | - John P Coghlan
- University of Melbourne, Office of the Dean, Faculty Medicine, Dentistry and Health Sciences, 3rd Level, Alan Gilbert Building, Australia
| | - S G Coulson
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Sudipto Ghosh
- Metallurgical & Materials Engineering IIT, Kanpur, India
| | - Mark Gillman
- South African Brain Research Institute, 6 Campbell Street, Waverly, Johannesburg, South Africa
| | - Reginald M Gorczynski
- University Toronto Health Network, Toronto General Hospital, University of Toronto, Canada
| | - Brig Klyce
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Godfrey Louis
- Department of Physics, Cochin University of Science and Technology Cochin, India
| | | | - Keith R Oliver
- School of Veterinary and Life Sciences Murdoch University, Perth, WA, Australia
| | - Julio Padron
- Studio Eutropi, Clinical Pathology and Nutrition, Via Pompei 46, Ardea, 00040, Rome, Italy
| | - Jiangwen Qu
- Department of Infectious Disease Control, Tianjin Center for Disease Control and Prevention, China
| | - John A Schuster
- School of History and Philosophy of Science, Faculty of Science, University of Sydney, Sydney, Australia
| | - W E Smith
- Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Duane P Snyder
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Julian A Steele
- Centre for Surface Chemistry and Catalysis, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
| | - Brent J Stewart
- CY O'Connor ERADE Village Foundation, Piara Waters, WA, Australia
| | - Robert Temple
- The History of Chinese Culture Foundation, Conway Hall, London, UK
| | - Gensuke Tokoro
- Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Christopher A Tout
- Institute of Astronomy, The Observatories, Madingley Road, Cambridge, CB3 0HA, UK
| | | | - Milton Wainwright
- Buckingham Centre for Astrobiology, University of Buckingham, UK; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka
| | - Jamie Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Daryl H Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - Max K Wallis
- Buckingham Centre for Astrobiology, University of Buckingham, UK
| | - John Wetherall
- School of Biomedical Sciences, Perth, Curtin University, WA, Australia
| | - D T Wickramasinghe
- College of Physical and Mathematical Sciences, Australian National University, Canberra, Australia
| | | | - N Chandra Wickramasinghe
- Buckingham Centre for Astrobiology, University of Buckingham, UK; Centre for Astrobiology, University of Ruhuna, Matara, Sri Lanka; Institute for the Study of Panspermia and Astrobiology, Gifu, Japan
| | - Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, 453003, China; Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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10
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Steele EJ. Reverse Transcriptase Mechanism of Somatic Hypermutation: 60 Years of Clonal Selection Theory. Front Immunol 2017; 8:1611. [PMID: 29218047 PMCID: PMC5704389 DOI: 10.3389/fimmu.2017.01611] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/07/2017] [Indexed: 01/24/2023] Open
Abstract
The evidence for the reverse transcriptase mechanism of somatic hypermutation is substantial and multifactorial. In this 60th anniversary year of the publication of Sir MacFarlane Burnet's Clonal Selection Theory, the evidence is briefly reviewed and updated.
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Affiliation(s)
- Edward J. Steele
- CYO’Connor ERADE Village Foundation Inc., Piara Waters, WA, Australia
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11
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Gleber-Netto FO, Zhao M, Trivedi S, Wang J, Jasser S, McDowell C, Kadara H, Zhang J, Wang J, William WN, Lee JJ, Nguyen ML, Pai SI, Walline HM, Shin DM, Ferris RL, Carey TE, Myers JN, Pickering CR. Distinct pattern of TP53 mutations in human immunodeficiency virus-related head and neck squamous cell carcinoma. Cancer 2017; 124:84-94. [PMID: 29053175 DOI: 10.1002/cncr.31063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/12/2017] [Accepted: 07/25/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Human immunodeficiency virus-infected individuals (HIVIIs) have a higher incidence of head and neck squamous cell carcinoma (HNSCC), and clinical and histopathological differences have been observed in their tumors in comparison with those of HNSCC patients without a human immunodeficiency virus (HIV) infection. The reasons for these differences are not clear, and molecular differences between HIV-related HNSCC and non-HIV-related HNSCC may exist. This study compared the mutational patterns of HIV-related HNSCC and non-HIV-related HNSCC. METHODS The DNA of 20 samples of HIV-related HNSCCs and 32 samples of non-HIV-related HNSCCs was sequenced. DNA libraries covering exons of 18 genes frequently mutated in HNSCC (AJUBA, CASP8, CCND1, CDKN2A, EGFR, FAT1, FBXW7, HLA-A, HRAS, KEAP1, NFE2L2, NOTCH1, NOTCH2, NSD1, PIK3CA, TGFBR2, TP53, and TP63) were prepared and sequenced on an Ion Personal Genome Machine sequencer. DNA sequencing data were analyzed with Ion Reporter software. The human papillomavirus (HPV) status of the tumor samples was assessed with in situ hybridization, the MassARRAY HPV multiplex polymerase chain reaction assay, and p16 immunostaining. Mutation calls were compared among the studied groups. RESULTS HIV-related HNSCC revealed a distinct pattern of mutations in comparison with non-HIV-related HNSCC. TP53 mutation frequencies were significantly lower in HIV-related HNSCC. Mutations in HIV+ patients tended to be TpC>T nucleotide changes for all mutated genes but especially for TP53. CONCLUSIONS HNSCC in HIVIIs presents a distinct pattern of genetic mutations, particularly in the TP53 gene. HIV-related HNSCC may have a distinct biology, and an effect of the HIV virus on the pathogenesis of these tumors should not be ruled out. Cancer 2018;124:84-94. © 2017 American Cancer Society.
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Affiliation(s)
- Frederico O Gleber-Netto
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mei Zhao
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sanchit Trivedi
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiping Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Samar Jasser
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christina McDowell
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - William N William
- Department of Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Minh Ly Nguyen
- Department of Internal Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Sara I Pai
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Heather M Walline
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Dong M Shin
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia
| | - Robert L Ferris
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Thomas E Carey
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey N Myers
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Steele EJ, Lindley RA. ADAR deaminase A-to-I editing of DNA and RNA moieties of RNA:DNA hybrids has implications for the mechanism of Ig somatic hypermutation. DNA Repair (Amst) 2017; 55:1-6. [PMID: 28482199 DOI: 10.1016/j.dnarep.2017.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/14/2017] [Accepted: 04/14/2017] [Indexed: 11/16/2022]
Abstract
The implications are discussed of recently published biochemical studies on ADAR-mediated A-to-I DNA and RNA deamination at RNA:DNA hybrids. The significance of these data are related to previous work on strand-biased and codon-context mutation signatures in B lymphocytes and cancer genomes. Those studies have established that there are two significant strand biases at A:T and G:C base pairs, A-site mutations exceed T-site mutations (A>>T) by 2.9 fold and G-site mutations exceed C-site mutations (G>>C) by 1.7 fold. Both these strand biases are inconsistent with alternative "DNA Deamination" mechanisms, yet are expected consequences of the RNA/RT-based "Reverse Transcriptase" mechanism of immunoglobulin (Ig) somatic hypermutation (SHM). The A-to-I DNA editing component at RNA:DNA hybrids that is likely to occur in Transcription Bubbles, while important, is of far lower A-to-I editing efficiency than in dsRNA substrates. The RNA moiety of RNA:DNA hybrids is also edited at similar lower frequencies relative to the editing rate at dsRNA substrates. Further, if the A-to-I DNA editing at RNA:DNA hybrids were the sole cause of A-to-I (read as A-to-G) mutation events for Ig SHM in vivo then the exact opposite strand biases at A:T base pairs (T>>A) of what is actually observed (A>>T) would be predicted. It is concluded that the strand-biased somatic mutation patterns at both A:T and G:C base pairs in vivo are best interpreted by the sequential steps of the RNA/RT-based mechanism. Further, the direct DNA A-to-I deamination at Transcription Bubbles is expected to contribute to the T-to-C component of the strand-biased Ig SHM spectrum.
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Affiliation(s)
- Edward J Steele
- CYO'Connor ERADE Village Foundation Inc., Piara Waters, WA, Australia.
| | - Robyn A Lindley
- GMDxCo Pty Ltd., Hawthorn Vic, Australia; Department of Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne Vic, Australia
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13
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Kim JI, Tohashi K, Iwai S, Kuraoka I. Inosine-specific ribonuclease activity of natural variants of human endonuclease V. FEBS Lett 2016; 590:4354-4360. [PMID: 27800608 DOI: 10.1002/1873-3468.12470] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/13/2016] [Accepted: 10/17/2016] [Indexed: 12/26/2022]
Abstract
Adenine bases in DNA, RNA, and nucleotides are deaminated during normal metabolism via hydrolytic and nitrosative reactions. In RNA, the deaminated product inosine is resolved by human endonuclease V, and mice deficient in this enzyme are cancer-prone. We have now produced, purified, and characterized naturally occurring variants of human endonuclease V (V29I, R112Q, K114R, H141Y, and D201N). We found that H141Y, but not other variants, is catalytically impaired, suggesting that individuals homozygous for H141Y may be predisposed to disease.
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Affiliation(s)
- Jung In Kim
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Kosuke Tohashi
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Isao Kuraoka
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Osaka, Japan
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Hainaut P, Pfeifer GP. Somatic TP53 Mutations in the Era of Genome Sequencing. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026179. [PMID: 27503997 DOI: 10.1101/cshperspect.a026179] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Amid the complexity of genetic alterations in human cancer, TP53 mutation appears as an almost invariant component, representing by far the most frequent genetic alteration overall. Compared with previous targeted sequencing studies, recent integrated genomics studies offer a less biased view of TP53 mutation patterns, revealing that >20% of mutations occur outside the DNA-binding domain. Among the 12 mutations representing each at least 1% of all mutations, five occur at residues directly involved in specific DNA binding, four affect the tertiary fold of the DNA-binding domain, and three are nonsense mutations, two of them in the carboxyl terminus. Significant mutations also occur in introns, affecting alternative splicing events or generating rearrangements (e.g., in intron 1 in sporadic osteosarcoma). In aggressive cancers, mutation is so common that it may not have prognostic value (all these cancers have impaired p53 function caused by mutation or by other mechanisms). In several other cancers, however, mutation makes a clear difference for prognostication, as, for example, in HER2-enriched breast cancers and in lung adenocarcinoma with EGFR mutations. Thus, the clinical significance of TP53 mutation is dependent on tumor subtype and context. Understanding the clinical impact of mutation will require integrating mutation-specific information (type, frequency, and predicted impact) with data on haplotypes and on loss of heterozygosity.
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Affiliation(s)
- Pierre Hainaut
- University Grenoble Alpes, Institut Albert Bonniot, Institut National de la Santé et de la Recherche Médicale (INSERM), 823 Grenoble, France
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503
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Somatic hypermutation in immunity and cancer: Critical analysis of strand-biased and codon-context mutation signatures. DNA Repair (Amst) 2016; 45:1-24. [DOI: 10.1016/j.dnarep.2016.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023]
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16
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Lindley RA, Humbert P, Larner C, Akmeemana EH, Pendlebury CRR. Association between targeted somatic mutation (TSM) signatures and HGS-OvCa progression. Cancer Med 2016; 5:2629-40. [PMID: 27485054 PMCID: PMC5055158 DOI: 10.1002/cam4.825] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 06/08/2016] [Accepted: 06/13/2016] [Indexed: 12/30/2022] Open
Abstract
Evidence already exists that the activation‐induced cytidine deaminase (AID/APOBEC) and the adenosine deaminase (ADAR) families of enzymes are implicated as powerful mutagens in oncogenic processes in many somatic tissues. Each deaminase is identified by the DNA or RNA nucleotide sequence (“motif”) surrounding the nucleotide targeted for deamination. The primary objective of this study is to develop an in silico approach to identify nucleotide sequence changes of the target motifs of key deaminases during oncogenesis. If successful, a secondary objective is to investigate if such changes are associated with disease progression indicators that include disease stage and progression‐free survival time. Using a discovery cohort of 194 high‐grade serous ovarian adenocarcinoma (HGS‐OvCa) exomes, the results confirm the ability of the novel in silico approach used to identify changes in the preferred target motifs for AID, APOBEC3G, APOBEC3B, and ADAR1 during oncogenesis. Using this approach, a set of new cancer‐progression associated signatures (C‐PASs) were identified. Furthermore, it was found that the C‐PAS identified can be used to differentiate between the cohort of patients that remained progression‐free for longer than 60 months, from those in which disease progressed within 60 months (sensitivity 95%, specificity 90%). The spectrum of outcomes observed here could provide a foundation for future clinical assessment of susceptibility variants in ovarian, and several other cancers as disease progresses. The ability of the in silico methodology used to identify changes in deaminase motifs during oncogenesis also suggests new links between immune system function and tumorigenesis.
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Affiliation(s)
- Robyn A Lindley
- Department of Pathology, University of Melbourne, Parkville, Victoria, 3010, Australia. .,GMDx Pty Ltd, Melbourne, Victoria, 3000, Australia.
| | - Patrick Humbert
- Department of Pathology, University of Melbourne, Parkville, Victoria, 3010, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.,Cell Cycle and Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, 3002, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Cliff Larner
- Swinburne University of Technology, Hawthorn, Victoria, 3132, Australia
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Steele EJ. Commentary: Past, present, and future of epigenetics applied to livestock breeding - Hard versus Soft Lamarckian Inheritance Mechanisms. Front Genet 2016; 7:29. [PMID: 26941780 PMCID: PMC4763540 DOI: 10.3389/fgene.2016.00029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 02/13/2016] [Indexed: 12/24/2022] Open
Affiliation(s)
- Edward J Steele
- CY O'Connor ERADE Village Foundation Piara Waters, WA, Australia
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