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Chabes, Andrei, ProfessorORCID iD iconorcid.org/0000-0003-1708-8259
Biography [swe]

dNTPs and maintenance of genome stability

The four dNTPs (dATP, dTTP, dCTP, and dGTP) are the building blocks of DNA. A balanced supply and a correct overall concentration of dNTPs are key prerequisites for faithful genome replication. These requirements, along with the fact that the concentrations of dNTPs fluctuate during the cell cycle, mean that the production of dNTPs must be tightly regulated through multiple mechanisms.

We are investigating (i) how the genome integrity checkpoint regulates the concentration of dNTPs and how dNTPs regulate the activation of the genome integrity checkpoint, and (ii) how imbalanced dNTP pools affect the fidelity of replication and genome stability and how different replication errors are recognized and repaired. We hope to understand how metabolic changes in the dNTP pool balance affect aging, the development of cancer, and other genetic disorders.

Publications (10 of 85) Show all publications
van der Horst, S. C., Kollenstart, L., Batté, A., Keizer, S., Vreeken, K., Pandey, P., . . . van Attikum, H. (2025). Replication-IDentifier links epigenetic and metabolic pathways to the replication stress response. Nature Communications, 16(1), Article ID 1416.
Open this publication in new window or tab >>Replication-IDentifier links epigenetic and metabolic pathways to the replication stress response
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2025 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 16, no 1, article id 1416Article in journal (Refereed) Published
Abstract [en]

Perturbation of DNA replication, for instance by hydroxyurea-dependent dNTP exhaustion, often leads to stalling or collapse of replication forks. This triggers a replication stress response that stabilizes these forks, activates cell cycle checkpoints, and induces expression of DNA damage response genes. While several factors are known to act in this response, the full repertoire of proteins involved remains largely elusive. Here, we develop Replication-IDentifier (Repli-ID), which allows for genome-wide identification of regulators of DNA replication in Saccharomyces cerevisiae. During Repli-ID, the replicative polymerase epsilon (Pol ε) is tracked at a barcoded origin of replication by chromatin immunoprecipitation (ChIP) coupled to next-generation sequencing of the barcode in thousands of hydroxyurea-treated yeast mutants. Using this approach, 423 genes that promote Pol ε binding at replication forks were uncovered, including LGE1 and ROX1. Mechanistically, we show that Lge1 affects replication initiation and/or fork stability by promoting Bre1-dependent H2B mono-ubiquitylation. Rox1 affects replication fork progression by regulating S-phase entry and checkpoint activation, hinging on cellular ceramide levels via transcriptional repression of SUR2. Thus, Repli-ID provides a unique resource for the identification and further characterization of factors and pathways involved in the cellular response to DNA replication perturbation.

Place, publisher, year, edition, pages
Springer Nature, 2025
National Category
Medical Biotechnology (Focus on Cell Biology, (incl. Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Biochemistry Molecular Biology
Identifiers
urn:nbn:se:umu:diva-236035 (URN)10.1038/s41467-025-56561-y (DOI)001416001300011 ()39915438 (PubMedID)2-s2.0-85218225870 (Scopus ID)
Funder
Swedish Cancer Society, 22 2377Swedish Research Council, 2022–00675
Available from: 2025-03-05 Created: 2025-03-05 Last updated: 2025-03-05Bibliographically approved
Awoyomi, O. F., Gorospe, C. M., Das, B., Mishra, P., Sharma, S., Diachenko, O., . . . Chabes, A. (2025). RRM2B deficiency causes dATP and dGTP depletion through enhanced degradation and slower synthesis. Proceedings of the National Academy of Sciences of the United States of America, 122(16), Article ID e2503531122.
Open this publication in new window or tab >>RRM2B deficiency causes dATP and dGTP depletion through enhanced degradation and slower synthesis
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2025 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 122, no 16, article id e2503531122Article in journal (Refereed) Published
Abstract [en]

Mitochondrial DNA (mtDNA) replication requires a steady supply of deoxyribonucleotides (dNTPs), synthesized de novo by ribonucleotide reductase (RNR). In nondividing cells, RNR consists of RRM1 and RRM2B subunits. Mutations in RRM2B cause mtDNA depletion syndrome, linked to muscle weakness, neurological decline, and early mortality. The impact of RRM2B deficiency on dNTP pools in nondividing tissues remains unclear. Using a mouse knockout model, we demonstrate that RRM2B deficiency selectively depletes dATP and dGTP, while dCTP and dTTP levels remain stable or increase. This depletion pattern resembles the effects of hydroxyurea, an inhibitor that reduces overall RNR activity. Mechanistically, we propose that the depletion of dATP and dGTP arises from their preferred degradation by the dNTPase SAMHD1 and the lower production rate of dATP by RNR. Identifying dATP and dGTP depletion as a hallmark of RRM2B deficiency provides insights for developing nucleoside bypass therapies to alleviate the effects of RRM2B mutations.

Place, publisher, year, edition, pages
Proceedings of the National Academy of Sciences (PNAS), 2025
Keywords
ribonucleotide reductase, dNTP metabolism, mtDNA stability, genome stability
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-238192 (URN)10.1073/pnas.2503531122 (DOI)40244665 (PubMedID)2-s2.0-105003415251 (Scopus ID)
Funder
Swedish Research Council, 2022-00675Swedish Research Council, 2024-03261Swedish Cancer Society, 22 2377 PjSwedish Cancer Society, 22 2381 PjKnut and Alice Wallenberg Foundation, KAW 2021.0053
Available from: 2025-04-26 Created: 2025-04-26 Last updated: 2025-05-26Bibliographically approved
Tran, P., Mishra, P., Williams, L. G., Moskalenko, R., Sharma, S., Nilsson, A. K., . . . Chabes, A. (2024). Altered dNTP pools accelerate tumor formation in mice. Nucleic Acids Research, 52(20), 12475-12486
Open this publication in new window or tab >>Altered dNTP pools accelerate tumor formation in mice
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2024 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 52, no 20, p. 12475-12486Article in journal (Refereed) Published
Abstract [en]

Alterations in deoxyribonucleoside triphosphate (dNTP) pools have been linked to increased mutation rates and genome instability in unicellular organisms and cell cultures. However, the role of dNTP pool changes in tumor development in mammals remains unclear. In this study, we present a mouse model with a point mutation at the allosteric specificity site of ribonucleotide reductase, RRM1-Y285A. This mutation reduced ribonucleotide reductase activity, impairing the synthesis of deoxyadenosine triphosphate (dATP) and deoxyguanosine triphosphate (dGTP). Heterozygous Rrm1+/Y285A mice exhibited distinct alterations in dNTP pools across various organs, shorter lifespans and earlier tumor onset compared with wild-type controls. Mutational spectrum analysis of tumors revealed two distinct signatures, one resembling a signature extracted from a human cancer harboring a mutation of the same amino acid residue in ribonucleotide reductase, RRM1Y285C. Our findings suggest that mutations in enzymes involved in dNTP metabolism can serve as drivers of cancer development.

Place, publisher, year, edition, pages
Oxford University Press, 2024
National Category
Cell and Molecular Biology Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:umu:diva-231911 (URN)10.1093/nar/gkae843 (DOI)001324703500001 ()39360631 (PubMedID)2-s2.0-85208688634 (Scopus ID)
Funder
NIH (National Institutes of Health), R01ES028271Swedish Cancer Society, 22 2377 PjSwedish Research Council, 2022–00675
Available from: 2024-11-20 Created: 2024-11-20 Last updated: 2024-11-20Bibliographically approved
de Jaime-Soguero, A., Hattemer, J., Bufe, A., Haas, A., van den Berg, J., van Batenburg, V., . . . Acebrón, S. P. (2024). Developmental signals control chromosome segregation fidelity during pluripotency and neurogenesis by modulating replicative stress. Nature Communications, 15(1), Article ID 7404.
Open this publication in new window or tab >>Developmental signals control chromosome segregation fidelity during pluripotency and neurogenesis by modulating replicative stress
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2024 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 7404Article in journal (Refereed) Published
Abstract [en]

Human development relies on the correct replication, maintenance and segregation of our genetic blueprints. How these processes are monitored across embryonic lineages, and why genomic mosaicism varies during development remain unknown. Using pluripotent stem cells, we identify that several patterning signals—including WNT, BMP, and FGF—converge into the modulation of DNA replication stress and damage during S-phase, which in turn controls chromosome segregation fidelity in mitosis. We show that the WNT and BMP signals protect from excessive origin firing, DNA damage and chromosome missegregation derived from stalled forks in pluripotency. Cell signalling control of chromosome segregation declines during lineage specification into the three germ layers, but re-emerges in neural progenitors. In particular, we find that the neurogenic factor FGF2 induces DNA replication stress-mediated chromosome missegregation during the onset of neurogenesis, which could provide a rationale for the elevated chromosomal mosaicism of the developing brain. Our results highlight roles for morphogens and cellular identity in genome maintenance that contribute to somatic mosaicism during mammalian development.

Place, publisher, year, edition, pages
Springer Nature, 2024
National Category
Medical Genetics and Genomics
Identifiers
urn:nbn:se:umu:diva-229381 (URN)10.1038/s41467-024-51821-9 (DOI)001299163800001 ()39191776 (PubMedID)2-s2.0-85202346452 (Scopus ID)
Available from: 2024-09-12 Created: 2024-09-12 Last updated: 2025-02-10Bibliographically approved
Dmowski, M., Makiela-Dzbenska, K., Sharma, S., Chabes, A. & Fijalkowska, I. J. (2023). Impairment of the non-catalytic subunit Dpb2 of DNA Pol ɛ results in increased involvement of Pol δ on the leading strand. DNA Repair, 129, Article ID 103541.
Open this publication in new window or tab >>Impairment of the non-catalytic subunit Dpb2 of DNA Pol ɛ results in increased involvement of Pol δ on the leading strand
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2023 (English)In: DNA Repair, ISSN 1568-7864, E-ISSN 1568-7856, Vol. 129, article id 103541Article in journal (Refereed) Published
Abstract [en]

The generally accepted model assumes that leading strand synthesis is performed by Pol ε, while lagging-strand synthesis is catalyzed by Pol δ. Pol ε has been shown to target the leading strand by interacting with the CMG helicase [Cdc45 Mcm2–7 GINS(Psf1–3, Sld5)]. Proper functioning of the CMG-Pol ɛ, the helicase-polymerase complex is essential for its progression and the fidelity of DNA replication. Dpb2p, the essential non-catalytic subunit of Pol ε plays a key role in maintaining the correct architecture of the replisome by acting as a link between Pol ε and the CMG complex. Using a temperature-sensitive dpb2–100 mutant previously isolated in our laboratory, and a genetic system which takes advantage of a distinct mutational signature of the Pol δ-L612M variant which allows detection of the involvement of Pol δ in the replication of particular DNA strands we show that in yeast cells with an impaired Dpb2 subunit, the contribution of Pol δ to the replication of the leading strand is significantly increased.

Place, publisher, year, edition, pages
Elsevier, 2023
Keywords
CMG (Cdc45 Mcm2–7 GINS), DNA polymerase delta, DNA polymerase epsilon, DNA replication fidelity, Dpb2, Genome stability, Pol δ, Pol ε, Replication fork
National Category
Medical Genetics and Genomics
Identifiers
urn:nbn:se:umu:diva-212493 (URN)10.1016/j.dnarep.2023.103541 (DOI)001048000100001 ()37481989 (PubMedID)2-s2.0-85165586443 (Scopus ID)
Funder
Swedish Cancer SocietySwedish Research Council, SNM79Swedish Research Council, YTAK002
Available from: 2023-08-01 Created: 2023-08-01 Last updated: 2025-04-24Bibliographically approved
Wanrooij, P. H. & Chabes, A. (2023). NME6: ribonucleotide salvage sustains mitochondrial transcription. EMBO Journal, 42(18), Article ID e114990.
Open this publication in new window or tab >>NME6: ribonucleotide salvage sustains mitochondrial transcription
2023 (English)In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 42, no 18, article id e114990Article in journal (Refereed) Published
Abstract [en]

The building blocks for RNA and DNA are made in the cytosol, meaning mitochondria depend on the import and salvage of ribonucleoside triphosphates (rNTPs) and deoxyribonucleoside triphosphates (dNTPs) for the synthesis of their own genetic material. While extensive research has focused on mitochondrial dNTP homeostasis due to its defects being associated with various mitochondrial DNA (mtDNA) depletion and deletion syndromes, the investigation of mitochondrial rNTP homeostasis has received relatively little attention. In this issue of the EMBO Journal, Grotehans et al provide compelling evidence of a major role for NME6, a mitochondrial nucleoside diphosphate kinase, in the conversion of pyrimidine ribonucleoside diphosphates into the corresponding triphosphates. These data also suggest a significant physiological role for NME6, as its absence results in the depletion of mitochondrial transcripts and destabilization of the electron transport chain (Grotehans et al, 2023).

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
National Category
Biochemistry Molecular Biology Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-212988 (URN)10.15252/embj.2023114990 (DOI)001043742100001 ()37548337 (PubMedID)2-s2.0-85167349571 (Scopus ID)
Funder
Knut and Alice Wallenberg FoundationSwedish Cancer SocietySwedish Research Council
Available from: 2023-08-21 Created: 2023-08-21 Last updated: 2025-02-20Bibliographically approved
Sharma, S., Kong, Z., Jia, S., Tran, P., Nilsson, A. K. & Chabes, A. (2023). Quantitative analysis of nucleoside triphosphate pools in mouse muscle using hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry detection. In: Thomas J. Nicholls; Jay P. Uhler; Maria Falkenberg (Ed.), Mitochondrial DNA: methods and protocols (pp. 267-280). New York: Humana Press, 2615
Open this publication in new window or tab >>Quantitative analysis of nucleoside triphosphate pools in mouse muscle using hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry detection
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2023 (English)In: Mitochondrial DNA: methods and protocols / [ed] Thomas J. Nicholls; Jay P. Uhler; Maria Falkenberg, New York: Humana Press, 2023, Vol. 2615, p. 267-280Chapter in book (Refereed)
Abstract [en]

Defects in deoxyribonucleoside triphosphate (dNTP) metabolism are associated with a number of mitochondrial DNA (mtDNA) depletion syndromes (MDS). These disorders affect the muscles, liver, and brain, and the concentrations of dNTPs in these tissues are already normally low and are, therefore, difficult to measure. Thus, information about the concentrations of dNTPs in tissues of healthy animals and animals with MDS are important for mechanistic studies of mtDNA replication, analysis of disease progression, and the development of therapeutic interventions. Here, we present a sensitive method for the simultaneous analysis of all four dNTPs as well as all four ribonucleoside triphosphates (NTPs) in mouse muscles using hydrophilic interaction liquid chromatography coupled with triple quadrupole mass spectrometry. The simultaneous detection of NTPs allows them to be used as internal standards for the normalization of dNTP concentrations. The method can be applied for measuring dNTP and NTP pools in other tissues and organisms.

Place, publisher, year, edition, pages
New York: Humana Press, 2023
Series
Methods in Molecular Biology, ISSN 1064-3745, E-ISSN 1940-6029 ; 2615
Keywords
Deoxyribonucleoside triphosphates, Differentiated tissues, Liquid chromatography, Triple quadrupole mass spectrometry, ZIC–HILIC
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-205508 (URN)10.1007/978-1-0716-2922-2_19 (DOI)001116120000020 ()36807798 (PubMedID)2-s2.0-85148679156 (Scopus ID)9781071629215 (ISBN)9781071629222 (ISBN)
Available from: 2023-03-15 Created: 2023-03-15 Last updated: 2025-04-24Bibliographically approved
Batté, A., van der Horst, S. C., Tittel-Elmer, M., Sun, S. M., Sharma, S., van Leeuwen, J., . . . van Attikum, H. (2022). Chl1 helicase controls replication fork progression by regulating dNTP pools. Life Science Alliance, 5(4)
Open this publication in new window or tab >>Chl1 helicase controls replication fork progression by regulating dNTP pools
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2022 (English)In: Life Science Alliance, E-ISSN 2575-1077, Vol. 5, no 4Article in journal (Refereed) Published
Abstract [en]

Eukaryotic cells have evolved a replication stress response that helps to overcome stalled/collapsed replication forks and ensure proper DNA replication. The replication checkpoint protein Mrc1 plays important roles in these processes, although its functional interactions are not fully understood. Here, we show that MRC1 negatively interacts with CHL1, which encodes the helicase protein Chl1, suggesting distinct roles for these factors during the replication stress response. Indeed, whereas Mrc1 is known to facilitate the restart of stalled replication forks, we uncovered that Chl1 controls replication fork rate under replication stress conditions. Chl1 loss leads to increased RNR1 gene expression and dNTP levels at the onset of S phase likely without activating the DNA damage response. This in turn impairs the formation of RPA-coated ssDNA and subsequent checkpoint activation. Thus, the Chl1 helicase affects RPA-dependent checkpoint activation in response to replication fork arrest by ensuring proper intracellular dNTP levels, thereby controlling replication fork progression under replication stress conditions.

National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-192154 (URN)10.26508/lsa.202101153 (DOI)000768225700001 ()35017203 (PubMedID)2-s2.0-85123459270 (Scopus ID)
Funder
Swedish Cancer SocietySwedish Research Council
Available from: 2022-02-04 Created: 2022-02-04 Last updated: 2023-09-05Bibliographically approved
Das, B., Mishra, P., Pandey, P., Sharma, S. & Chabes, A. (2022). dNTP concentrations do not increase in mammalian cells in response to DNA damage [Letter to the editor]. Cell Metabolism, 34(12), 1895-1896
Open this publication in new window or tab >>dNTP concentrations do not increase in mammalian cells in response to DNA damage
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2022 (English)In: Cell Metabolism, ISSN 1550-4131, E-ISSN 1932-7420, Vol. 34, no 12, p. 1895-1896Article in journal, Letter (Refereed) Published
Place, publisher, year, edition, pages
Elsevier, 2022
National Category
Cell and Molecular Biology Cell Biology
Identifiers
urn:nbn:se:umu:diva-201614 (URN)10.1016/j.cmet.2022.11.002 (DOI)000901818900001 ()36476929 (PubMedID)2-s2.0-85143132439 (Scopus ID)
Available from: 2022-12-14 Created: 2022-12-14 Last updated: 2023-09-05Bibliographically approved
Dmowski, M., Jedrychowska, M., Makiela-Dzbenska, K., Denkiewicz-Kruk, M., Sharma, S., Chabes, A., . . . Fijalkowska, I. J. (2022). Increased contribution of DNA polymerase delta to the leading strand replication in yeast with an impaired CMG helicase complex. DNA Repair, 110, Article ID 103272.
Open this publication in new window or tab >>Increased contribution of DNA polymerase delta to the leading strand replication in yeast with an impaired CMG helicase complex
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2022 (English)In: DNA Repair, ISSN 1568-7864, E-ISSN 1568-7856, Vol. 110, article id 103272Article in journal (Refereed) Published
Abstract [en]

DNA replication is performed by replisome proteins, which are highly conserved from yeast to humans. The CMG [Cdc45-Mcm2–7-GINS(Psf1–3, Sld5)] helicase unwinds the double helix to separate the leading and lagging DNA strands, which are replicated by the specialized DNA polymerases epsilon (Pol ε) and delta (Pol δ), respectively. This division of labor was confirmed by both genetic analyses and in vitro studies. Exceptions from this rule were described mainly in cells with impaired catalytic polymerase ε subunit. The central role in the recruitment and establishment of Pol ε on the leading strand is played by the CMG complex assembled on DNA during replication initiation. In this work we analyzed the consequences of impaired functioning of the CMG complex for the division labor between DNA polymerases on the two replicating strands. We showed in vitro that the GINSPsf1–1 complex poorly bound the Psf3 subunit. In vivo, we observed increased rates of L612M Pol δ-specific mutations during replication of the leading DNA strand in psf1–1 cells. These findings indicated that defective functioning of GINS impaired leading strand replication by Pol ε and necessitated involvement of Pol δ in the synthesis on this strand with a possible impact on the distribution of mutations and genomic stability. These are the first results to imply that the division of labor between the two main replicases can be severely influenced by a defective nonpolymerase subunit of the replisome.

Place, publisher, year, edition, pages
Elsevier, 2022
Keywords
CMG (Cdc45 Mcm2–7 GINS), DNA polymerase delta, DNA polymerase epsilon, DNA replication fidelity, Genome stability, Pol δ, Pol ε, Replication fork
National Category
Cell and Molecular Biology Genetics and Genomics
Identifiers
urn:nbn:se:umu:diva-191623 (URN)10.1016/j.dnarep.2022.103272 (DOI)000820523300005 ()2-s2.0-85122685836 (Scopus ID)
Available from: 2022-01-20 Created: 2022-01-20 Last updated: 2025-02-01Bibliographically approved
Projects
dNTPs and maintenance of genome stability [2010-03552_VR]; Umeå UniversitydNTPs and maintenance of genome stability [2014-02262_VR]; Umeå UniversityAltered dNTP pools and genome instability [2018-02579_VR]; Umeå University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-1708-8259

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