Close
Close

preLights is supported by…

Related posts

Related preLists

Mutational signatures are jointly shaped by DNA damage and repair

Nadezda V Volkova, Bettina Meier, Víctor González-Huici, Simone Bertolini, Santiago Gonzalez, Harald Voeringer, Federico Abascal, Iñigo Martincorena, Peter J Campbell, Anton Gartner, Moritz Gerstung

Preprint posted on 11 February 2020 https://www.biorxiv.org/content/10.1101/686295v2

Article now published in Nature Communications at http://dx.doi.org/10.1038/s41467-020-15912-7

A combinatory mutational screen in C. elegans, combining 54 DNA repair mutants and 12 genotoxins, demonstrates that mutations are a result of both DNA damage and failed repair.

Selected by Kerryn Elliott

Categories: cancer biology, cell biology, genetics, genomics

Background

The DNA of a given cell is constantly altered by DNA replication errors and genotoxic stresses. An assemblage of repair pathways specifically designed to keep mutations at bay usually efficiently repairs these alterations. Occasionally this process fails, and DNA lesions escape detection, or are repaired by error-prone pathways, leading to diseases such as cancer.

With the recent advances in whole genome sequencing, the mutational spectra of human cancers have been dissected into individual mutagenic processes using computational pattern recognition programs that correlate genotoxic exposures, such as UV light, or DNA repair deficiencies, such as defects in mismatch repair (MMR), with certain mutational signatures. There are now more than 50 mutational signatures identified computationally, and approximately one third of these have no known etiology (Alexandrov et. al., 2020). It is possible that these unknown signatures represent combinations of mutagens and repair pathway defects. In this paper the authors perform a combinatorial mutagenesis screen with 12 genotoxic agents on 53 different DNA repair mutants in C. elegans to show that mutations are a result of both DNA damage AND failed repair.

Figure 1. Experimental setup and representative mutational spectra in the study made available under a CC-BY-NC-ND 4.0 International license

 

Main findings

The combination of using genotoxin treatment in backgrounds of DNA repair deficiency was a clever approach to understand whether the genotoxins themselves, or the failed repair contributed more to the mutational signature. The authors found that over 40% of the combination treatments demonstrated unique mutational signatures or altered mutation rates, but unexpectedly there were also combinations where the loss of translesion synthesis enzymes (TLS) led to a decrease in mutagenesis. This suggests that the majority of mutations induced by genotoxins are caused by error-prone translesion synthesis. By comparing to the genotoxin treatments on a wild type background, the authors were able to attribute the mutations to either the genotoxin itself (54%), DNA repair deficiencies themselves (26%), and to positive (23%) and negative (3%) genotoxin-repair interactions. Notably, nucleotide excision repair (NER) was found to be responsible for the majority of the repair following genotoxin exposure, as the loss of NER proteins increased the mutational load substantially.

Interestingly, while the interactions between genotoxins and DNA repair deficiencies usually retained a similar mutation spectrum with an increased mutation rate, around 10% of the interactions resulted in a change in the mutational spectrum. The authors found lesion-specific mutations for alkylating agents under different DNA repair deficiency backgrounds. The alkylating agent MMS was highlighted, as MMS can alkylate A and G nucleotides to generate different modifications, mainly N3-methyladenine and O6-methylguanine. These modifications are processed by different repair pathways, and therefore blocking one or the other pathway led to a different mutational outcome. Using the specific mutants, the authors were able to link the translesion synthesis enzyme Pol κ to the repair of specific adenine lesions (N3-methyladenine), and the alkyl-transferase AGT-1 to the repair of guanine modifications (O6-methylguanine). They also proposed that the error-prone TLS enzyme Pol ζ was responsible for a large proportion of the additional mutations occurring in the knockouts, as the Pol ζ deficient strain showed a decrease in single base mutations, and instead showed an increase in large deletions, possibly due to fork-stalling. It is this combination of DNA repair deficiency alongside genotoxin exposure which makes this paper a very interesting read!

Why I chose this paper:

Mutational signatures, particularly those driven by the combination of damage and repair are a main research interest of mine. The use of C. elegans as a model organism allowed the combination of treatments to be studied in detail, leading to the ability to dissect out the cause of the mutational signature, be it the mutagen itself or the associated repair process.

This work is important for the field to understand the heterogeneity of mutagenesis and the importance of the combination of damage and failed repair in generating mutations.

Questions to the authors:

Are these results directly relatable to human cancers, given the treatment was on C. elegans? You mention an organism-specific spectrum in Cisplatin, but are there additional complexities (transcription factor families, orthologs, levels of mutagen exposure in human life etc.) that are missing in the model organism that may influence mutations in human cells?

It is interesting that some of these “created” signatures can be detected in human cancers. How do you propose we move forward to understand “combinatory” signatures in humans? How confident are you in the current mutational signature spectra, particularly in assigning etiology?

The increase in large deletions and decrease in SNVs in some TLS mutants was quite interesting to me. Could you expand on your reasoning as to why this might happen, as you suggested this was likely due to replication stalling and fork collapse? Has this been detected in humans, or are there other TLS enzymes that take over this role and prevent large deletions from occurring?

References:

Alexandrov, L.B., Kim, J., Haradhvala, N.J. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).

 

Tags: cancer, mutagen

Posted on: 24 February 2020 , updated on: 25 February 2020

doi: https://doi.org/10.1242/prelights.16938

Read preprint (No Ratings Yet)

Author's response

Nadezda Volkova, Bettina Meier, Anton Gartner and Moritz Gerstung shared

Are these results directly relatable to human cancers, given the treatment was on C. elegans? You mention an organism-specific spectrum in Cisplatin, but are there additional complexities (transcription factor families, orthologs, levels of mutagen exposure in human life etc.) that are missing in the model organism that may influence mutations in human cells?

 

While DNA repair pathways are highly conserved across eukaryotes some differences exist. For cisplatin, the precise reason for discrepancies in the spectrum is yet to discover, but for e.g. UV-induced damage there is evidence that orthologs of the same repair enzymes act at different efficiency leading to differences between organisms and experimental systems (Hartman et al. 1989). Endogenous sources of mutations can also contribute to the divergence of signatures: as we have shown previously, 5-methylcytosines abundant in human cells but absent in C. elegans can undergo deamination and turn into thymines, which contributes the mutational spectra of ageing, but also mismatch repair deficiency in cancer (Meier et al. 2018). Further differences include humans having a more diverse set of translesion synthesis polymerases. Lastly, some compounds are only genotoxic upon metabolic activation, which can explain additional differences between organisms and even experimental systems derived from the same organism.

 

It is interesting that some of these “created” signatures can be detected in human cancers. How do you propose we move forward to understand “combinatory” signatures in humans? How confident are you in the current mutational signature spectra, particularly in assigning etiology?

 

Our data show that the same genotoxin and also the same DNA repair deficiency can produce a multitude of different mutational signatures. This might challenge a unique attribution of observed patterns to underlying mechanisms and more factors need to be accounted for establishing a signature’s etiology. The situation is especially challenging when a repair deficiency removes mutations in which case the breakdown of mutational spectra into positive signature contributions may not provide a correct answer.

 

The increase in large deletions and decrease in SNVs in some TLS mutants was quite interesting to me. Could you expand on your reasoning as to why this might happen, as you suggested this was likely due to replication stalling and fork collapse? Has this been detected in humans, or are there other TLS enzymes that take over this role and prevent large deletions from occurring?

 

It was indeed one of the most fascinating insights derived from our study that the majority of base substitutions appears to be contributed by error-prone TLS seemingly to avoid fewer and possibly more deleterious deletions. This phenomenon has been described in other model systems such as yeast (Lawrence and Hinkle 1996). In mammalian cells, polymerase ζ was shown to prevent replication-dependent DNA breaks (Lange et al. 2012), and also indicated as having a major role in replication of human cells under UV exposure (Gibbs et al. 1998), but its contribution was never assessed at a genome scale across multiple genotoxins. To our knowledge, no human mutational signature of TLS deficiency is known, and TLS deficiency does not appear to be selected for in human cancers, but germline variants in POLH underlie the disorder Xeroderma Pigmentosum Variant that predisposes to skin cancers (Masutani et al. 1999).

 

References:

Alexandrov, L.B., Kim, J., Haradhvala, N.J. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).

Hartman, P. S. et al. Excision repair of UV radiation-induced DNA damage in Caenorhabditis elegans. Genetics 122, 379–385 (1989).

Meier, B., Volkova, N.V., et al. Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers. Genome Res. 28, 666–675 (2018).

Lawrence, C. W. & Hinkle, D. C. DNA polymerase zeta and the control of DNA damage induced mutagenesis in eukaryotes. Cancer Surv. 28, 21–31 (1996).

Lange, S.S, Wittschieben, J.P., and Wood, R.D. DNA polymerase zeta is required for proliferation of normal mammalian cells. Nucleic Acids Res. 40(10), 4473–4482 (2012).

Gibbs, P.E.M. et al. A human homolog of the Saccharomyces cerevisiae REV3 gene, which encodes the catalytic subunit of DNA polymerase ζ. PNAS 95(12), 6876–6880 (1998).

Masutani, C., et al. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η. Nature 399(6737), 700–704 (1999).

Have your say

Your email address will not be published.

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Sign up to customise the site to your preferences and to receive alerts

Register here

Also in the cancer biology category:

BRCA1/BARD1 ubiquitinates PCNA in unperturbed conditions to promote replication fork stability and continuous DNA synthesis

Daniel Salas-Lloret, Néstor García-Rodríguez, Lisanne Giebel, et al.



Selected by Pierre Caron

Functional synapses between small cell lung cancer and glutamatergic neurons

Anna Schmitt, Vignesh Sakthivelu, Kristiano Ndoci, et al.



Selected by Jade Chan

Nuclear myosin VI maintains replication fork stability

Jie Shi, Kristine Hauschulte, Ivan Mikicic, et al.



Selected by Pierre Caron

Also in the cell biology category:

BRCA1/BARD1 ubiquitinates PCNA in unperturbed conditions to promote replication fork stability and continuous DNA synthesis

Daniel Salas-Lloret, Néstor García-Rodríguez, Lisanne Giebel, et al.



Selected by Pierre Caron

Quantification of gallium cryo-FIB milling damage in biological lamella

Bronwyn A. Lucas, Nikolaus Grigorieff



Selected by Kanika Khanna

Coordinated growth of linked epithelia is mediated by the Hippo pathway

Sophia Friesen, Iswar K. Hariharan



Selected by Girish Kale

Also in the genetics category:

Unclearing Microscopy

Ons M’Saad, Michael Shribak, Joerg Bewersdorf



Selected by Robert Mahen

Restructuring of an asymmetric neural circuit during associative learning

Leo T.H. Tang, Garrett A. Lee, Steven J. Cook, et al.



Selected by Chee Kiang Ewe

An improved Erk biosensor reveals oscillatory Erk dynamics driven by mitotic erasure during early development

Scott G. Wilcockson, Luca Guglielmi, Pablo Araguas Rodriguez, et al.



Selected by Sakurako Kobayashi

Also in the genomics category:

Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis

Irene Mota-Gómez, Juan Antonio Rodríguez, Shannon Dupont, et al.



Selected by Martin Estermann

Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast

Yue Shen, Feng Gao, Yun Wang, et al.



Selected by Grace Heredge Thomas

Disrupting cellular memory to overcome drug resistance

Guillaume Harmange, Raúl A. Reyes Hueros, Dylan Schaff, et al.



Selected by Nate Mullin

preLists in the cancer biology category:

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

Single Cell Biology 2020

A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.

 



List by Alex Eve

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

Anticancer agents: Discovery and clinical use

Preprints that describe the discovery of anticancer agents and their clinical use. Includes both small molecules and macromolecules like biologics.

 



List by Zhang-He Goh

Biophysical Society Annual Meeting 2019

Few of the preprints that were discussed in the recent BPS annual meeting at Baltimore, USA

 



List by Joseph Jose Thottacherry

Also in the cell biology category:

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

Planar Cell Polarity – PCP

This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.

 



List by Ana Dorrego-Rivas

BioMalPar XVI: Biology and Pathology of the Malaria Parasite

[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria

 



List by Dey Lab, Samantha Seah

1

Cell Polarity

Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.

 



List by Yamini Ravichandran

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

3D Gastruloids

A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.

 



List by Paul Gerald L. Sanchez and Stefano Vianello

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

EMBL Seeing is Believing – Imaging the Molecular Processes of Life

Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019

 



List by Dey Lab

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

Cellular metabolism

A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.

 



List by Pablo Ranea Robles

BSCB/BSDB Annual Meeting 2019

Preprints presented at the BSCB/BSDB Annual Meeting 2019

 



List by Dey Lab

MitoList

This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.

 



List by Sandra Franco Iborra

ASCB/EMBO Annual Meeting 2018

This list relates to preprints that were discussed at the recent ASCB conference.

 



List by Dey Lab, Amanda Haage

Also in the genetics category:

Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University

This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.

 



List by Nándor Lipták

20th “Genetics Workshops in Hungary”, Szeged (25th, September)

In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf

 



List by Nándor Lipták

2nd Conference of the Visegrád Group Society for Developmental Biology

Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)

 



List by Nándor Lipták

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill

Zebrafish immunology

A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.

 



List by Shikha Nayar

Also in the genomics category:

Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University

This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.

 



List by Nándor Lipták

20th “Genetics Workshops in Hungary”, Szeged (25th, September)

In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf

 



List by Nándor Lipták

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.
Close