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Niavarani A. The role of distinct APOBEC/ADAR mRNA levels in mutational signatures linked to aging and ultraviolet radiation. Sci Rep 2024; 14:15395. [PMID: 38965255 PMCID: PMC11224270 DOI: 10.1038/s41598-024-64986-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/14/2024] [Indexed: 07/06/2024] Open
Abstract
The APOBEC/AID family is known for its mutator activity, and recent evidence also supports the potential impact of ADARs. Furthermore, the mutator impacts of APOBEC/ADAR mutations have not yet been investigated. Assessment of pancancer TCGA exomes identified enriched somatic variants among exomes with nonsynonymous APOBEC1, APOBEC3B, APOBEC3C, ADAR, and ADARB1 mutations, compared to exomes with synonymous ones. Principal component (PC) analysis reduced the number of potential players to eight in cancer exomes/genomes, and to five in cancer types. Multivariate regression analysis was used to assess the impact of the PCs on each COSMIC mutational signature among pancancer exomes/genomes and particular cancers, identifying several novel links, including SBS17b, SBS18, and ID7 mainly determined by APOBEC1 mRNA levels; SBS40, ID1, and ID2 by age; SBS3 and SBS16 by APOBEC3A/APOBEC3B mRNA levels; ID5 and DBS9 by DNA repair/replication (DRR) defects; and SBS7a-d, SBS38, ID4, ID8, ID13, and DBS1 by ultraviolet (UV) radiation/ADARB1 mRNA levels. APOBEC/ADAR mutations appeared to potentiate the impact of DRR defects on several mutational signatures, and some factors seemed to inversely affect certain signatures. These findings potentially implicate certain APOBEC/ADAR mutations/mRNA levels in distinct mutational signatures, particularly APOBEC1 mRNA levels in aging-related signatures and ADARB1 mRNA levels in UV radiation-related signatures.
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Affiliation(s)
- Ahmadreza Niavarani
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
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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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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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Blood and saliva-derived exomes from healthy Caucasian subjects do not display overt evidence of somatic mosaicism. Mutat Res 2020; 821:111705. [PMID: 32569906 DOI: 10.1016/j.mrfmmm.2020.111705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/07/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
Somatic mosaicism is a normal occurrence during development in the tissues and organs. As part of establishing a "healthy population "(HP) background or base-line, we investigated whether such mosaicism can be routinely detected in the circulating DNA secured from a rigorously designed healthy human liquid biopsy clinical trial (saliva, blood). We deployed next generation (NG) whole exome sequencing (WES) at median exome coverage rates of 97.2 % (-to-30x) and 70.0 % (-to-100x). We found that somatic mosaicism is not detectable by such standard bulk WES sequencing assays in saliva and blood DNA in 24 normal healthy Caucasians of both sexes from 18 to 60 years of age. We conclude that for circulating DNA using standard WES no novel somatic mutational variants can be detected in protein-coding regions of normal healthy subjects. This implies that the extent within normal tissues of somatic mosaicism must be at a lower level, below the detection threshold, for these circulating DNA WES read depths.
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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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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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Mamrot J, Balachandran S, Steele EJ, Lindley RA. Molecular model linking Th2 polarized M2 tumour-associated macrophages with deaminase-mediated cancer progression mutation signatures. Scand J Immunol 2019; 89:e12760. [PMID: 30802996 PMCID: PMC6850162 DOI: 10.1111/sji.12760] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
A new and diverse range of somatic mutation signatures are observed in late‐stage cancers, but the underlying reasons are not fully understood. We advance a “combinatorial association model” for deaminase binding domain (DBD) diversification to explain the generation of previously observed cancer‐progression associated mutation signatures. We also propose that changes in the polarization of tumour‐associated macrophages (TAMs) are accompanied by the expression of deaminases with a new and diverse range of DBDs, and thus accounting for the generation of new somatic mutation signatures. The mechanism proposed is molecularly reminiscent of combinatorial association of heavy (H) and light (L) protein chains following V(D)J recombination of immunoglobulin molecules (and similarly for protein chains in heterodimers α/β and γ/δ of V(D)Js of T Cell Receptors) required for pathogen antigen recognition by B cells and T cells, respectively. We also discuss whether extracellular vesicles (EVs) emanating from tumour enhancing M2‐polarized macrophages represent a likely source of the de novo deaminase DBDs. We conclude that M2‐polarized macrophages extruding EVs loaded with deaminase proteins or deaminase‐specific transcription/translation regulatory factors and like information may directly trigger deaminase diversification within cancer cells, and thus account for the many new somatic mutation signatures that are indicative of cancer progression. This hypothesis now has a plausible evidentiary base, and it is worth direct testing in future investigations. A long‐term objective would be to identify molecular biomarkers predicting cancer progression (or metastatic disease) and to support the development of new drug targets before metastatic pathways are activated.
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Affiliation(s)
| | - Siddharth Balachandran
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Edward J Steele
- CYO'Connor ERADE Village Foundation, Perth, Western Australia, Australia.,Melville Analytics Pty Ltd, Melbourne, Victoria, Australia
| | - Robyn A Lindley
- GMDxCo Pty Ltd, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry & Health Sciences, Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
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