Experimental constraints on Li isotope fractionation during clay formation

Knowledge of the lithium (Li) isotope fractionation factor during clay mineral formation is a key parameter for Earth sys-tem models. This study refines our understanding of isotope fractionation during clay formation with essential implicationsfor the interpretation of field data and the global geochemical cycle of Li. We synthesised Mg-rich layer silicates (stevensiteand saponite) at temperatures relevant for Earth surface processes. The resultant solids were characterised by X-ray diffrac-tion (XRD) and Fourier-transform infrared spectroscopy (FT-IR) to confirm the mineralogy and crystallinity of the product.Bulk solid samples were treated with ammonium chloride to remove exchangeable Li in order to distinguish the Li isotopicfractionation between these sites and structural (octahedral) sites. Bulk solids, residual solids and exchangeable solutions wereall enriched in6Li compared to the initial solution. On average, the exchangeable solutions hadd7Li values 7?lower than theinitial solution. The average difference between the residual solid and initial solutiond7Li values (D7Liresidue-solution) for the syn-thesised layer silicates was?16.6 $\pm$ 1.7?at 20?C, in agreement with modelling studies, extrapolations from high tempera-ture experimental data and field observations. Three bonding environments were identified from7Li-NMR spectra which werepresent in both bulk and residual solid7Li-NMR spectra, implying that some exchangeable Li remains after treatment withammonium chloride. The7Li-NMR peaks were assigned to octahedral, outer-sphere (interlayer and adsorbed) and pseudo-hexagonal (ditrigonal cavity) Li. By combining the7Li-NMR data with mass balance constraints we calculated a fractionationfactor, based on a Monte Carlo minimum misfit method, for each bonding environment. The calculated values are?21.5$\pm$ 1.1?,?0.2 $\pm$ 1.9?and 15.0 $\pm$ 12.3?for octahedral, outer-sphere and pseudo-hexagonal sites respectively (errors 1r).The bulk fractionation factor (D7Libulk-solution) is dependent on the chemistry of the initial solution. The higher the Na concen-tration in the initial solution the lower the bulkd7Li value. We suggest this is due to Na outcompeting Li for interlayer sitesand as interlayer Li has a highd7Li value relative to octahedral Li, increased Na serves to lower the bulkd7Li value. Threeexperiments conducted at higher pH exhibited lowerd7Li values in the residual solid. This could either be a kinetic effect,resulting from the higher reaction rate at high pH, or an equilibrium effect resulting from reduced Li incorporation in theresidual solid and/or a change in Li speciation in solution.This study highlights the power of7Li-NMR in experimental studies of clay synthesis to target site specific Li isotope frac-tionation factors which can then be used to provide much needed constraints on field processes

Experimental constraints on Li isotope fractionation during clay formation

Knowledge of the lithium (Li) isotope fractionation factor during clay mineral formation is a key parameter for Earth sys-tem models. This study refines our understanding of isotope fractionation during clay formation with essential implicationsfor the interpretation of field data and the global geochemical cycle of Li. We synthesised Mg-rich layer silicates (stevensiteand saponite) at temperatures relevant for Earth surface processes. The resultant solids were characterised by X-ray diffrac-tion (XRD) and Fourier-transform infrared spectroscopy (FT-IR) to confirm the mineralogy and crystallinity of the product.Bulk solid samples were treated with ammonium chloride to remove exchangeable Li in order to distinguish the Li isotopicfractionation between these sites and structural (octahedral) sites. Bulk solids, residual solids and exchangeable solutions wereall enriched in6Li compared to the initial solution. On average, the exchangeable solutions hadd7Li values 7‰lower than theinitial solution. The average difference between the residual solid and initial solutiond7Li values (D7Liresidue-solution) for the syn-thesised layer silicates was�16.6 ± 1.7‰at 20�C, in agreement with modelling studies, extrapolations from high tempera-ture experimental data and field observations. Three bonding environments were identified from7Li-NMR spectra which werepresent in both bulk and residual solid7Li-NMR spectra, implying that some exchangeable Li remains after treatment withammonium chloride. The7Li-NMR peaks were assigned to octahedral, outer-sphere (interlayer and adsorbed) and pseudo-hexagonal (ditrigonal cavity) Li. By combining the7Li-NMR data with mass balance constraints we calculated a fractionationfactor, based on a Monte Carlo minimum misfit method, for each bonding environment. The calculated values are�21.5± 1.1‰,�0.2 ± 1.9‰and 15.0 ± 12.3‰for octahedral, outer-sphere and pseudo-hexagonal sites respectively (errors 1r).The bulk fractionation factor (D7Libulk-solution) is dependent on the chemistry of the initial solution. The higher the Na concen-tration in the initial solution the lower the bulkd7Li value. We suggest this is due to Na outcompeting Li for interlayer sitesand as interlayer Li has a highd7Li value relative to octahedral Li, increased Na serves to lower the bulkd7Li value. Threeexperiments conducted at higher pH exhibited lowerd7Li values in the residual solid. This could either be a kinetic effect,resulting from the higher reaction rate at high pH, or an equilibrium effect resulting from reduced Li incorporation in theresidual solid and/or a change in Li speciation in solution.This study highlights the power of7Li-NMR in experimental studies of clay synthesis to target site specific Li isotope frac-tionation factors which can then be used to provide much needed constraints on field processes

Signatures of TOP1 transcription-associated mutagenesis in cancer and germline

The mutational landscape is shaped by many processes. Genic regions are vulnerable to mutation but are preferentially protected by transcription-coupled repair1. In microorganisms, transcription has been demonstrated to be mutagenic2,3; however, the impact of transcription-associated mutagenesis remains to be established in higher eukaryotes4. Here we show that ID4—a cancer insertion–deletion (indel) mutation signature of unknown aetiology5 characterized by short (2 to 5 base pair) deletions —is due to a transcription-associated mutagenesis process. We demonstrate that defective ribonucleotide excision repair in mammals is associated with the ID4 signature, with mutations occurring at a TNT sequence motif, implicating topoisomerase 1 (TOP1) activity at sites of genome-embedded ribonucleotides as a mechanistic basis. Such TOP1-mediated deletions occur somatically in cancer, and the ID-TOP1 signature is also found in physiological settings, contributing to genic de novo indel mutations in the germline. Thus, although topoisomerases protect against genome instability by relieving topological stress6, their activity may also be an important source of mutations in the human genome

Signatures of TOP1 transcription-associated mutagenesis in cancer and germline

The mutational landscape is shaped by many processes. Genic regions are vulnerable to mutation but are preferentially protected by transcription-coupled repair1. In microorganisms, transcription has been demonstrated to be mutagenic2,3; however, the impact of transcription-associated mutagenesis remains to be established in higher eukaryotes4. Here we show that ID4—a cancer insertion–deletion (indel) mutation signature of unknown aetiology5 characterized by short (2 to 5 base pair) deletions —is due to a transcription-associated mutagenesis process. We demonstrate that defective ribonucleotide excision repair in mammals is associated with the ID4 signature, with mutations occurring at a TNT sequence motif, implicating topoisomerase 1 (TOP1) activity at sites of genome-embedded ribonucleotides as a mechanistic basis. Such TOP1-mediated deletions occur somatically in cancer, and the ID-TOP1 signature is also found in physiological settings, contributing to genic de novo indel mutations in the germline. Thus, although topoisomerases protect against genome instability by relieving topological stress6, their activity may also be an important source of mutations in the human genome.We thank S. Jinks-Robertson for suggesting the traffic light reporter approach; H. Klein for guidance on fluctuation assays; R. van Boxtel for sharing sequencing data for MLH1-KO organoids; A. Bretherick, O. B. Reina and G. Kudla for advice on HygroR re-coding; staff at the IGC core services (L. Murphy, C. Nicol, C. Warnock, E. Freyer, S. Brown and J. Joseph), C. Logan, A. Fluteau, A. Robertson and the staff at Edinburgh Genomics for technical assistance; staff at Liverpool CLL Biobank (funded by Blood Cancer UK) for samples used to generate GEL WGS data; A. Ewing, C.-A. Martin, N. Hastie and W. Bickmore for discussions. Funding for this work: UK Medical Research Council Human Genetics Unit core grants (MC_UU_00007/5 to A.P.J., MC_UU_00007/11 to M.S.T.); Edinburgh Clinical Academic Track PhD programme (Wellcome Trust 204802/Z/16/Z) to T.C.W.; 2021 AACR-Amgen Fellowship in Clinical/Translational Cancer Research (grant number 21-40-11-NADE) to F.N.; a CRUK Brain Tumour Centre of Excellence Award (C157/A27589) to M.D.N.; EKFS research grant (2019_A09), Wilhelm Sander-Stiftung (2019.046.1) to K.A., CRUK programme grant (C20807/A2864) to T.S.; La Caixa Foundation (CLLEvolution-LCF/PR/HR17/52150017, Health Research 2017 Program HR17-00221) to E.C.; E.C. is an Academia Researcher of the Institució Catalana de Recerca i Estudis Avançats of the Generalitat de Catalunya. Edinburgh Genomics is partly supported by NERC (R8/H10/56), MRC (MR/K001744/1) and BBSRC (BB/J004243/1). This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health and Social Care). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support.Peer Reviewed"Article signat per 22 autors/es: Martin A. M. Reijns, David A. Parry, Thomas C. Williams, Ferran Nadeu, Rebecca L. Hindshaw, Diana O. Rios Szwed, Michael D. Nicholson, Paula Carroll, Shelagh Boyle, Romina Royo, Alex J. Cornish, Hang Xiang, Kate Ridout, The Genomics England Research Consortium, Colorectal Cancer Domain UK 100,000 Genomes Project, Anna Schuh, Konrad Aden, Claire Palles, Elias Campo, Tatjana Stankovic, Martin S. Taylor & Andrew P. Jackson "Postprint (published version