Vakil Takhaveev

Last Name

Takhaveev

First Name

Vakil

ORCID

0000-0002-3474-5241

Organisational unit

03853 - Sturla, Shana / Sturla, Shana

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Publications 1 - 7 of 7

Trabectedin derails transcription-coupled nucleotide excision repair to induce DNA breaks in highly transcribed genes
Son, Kook; Takhaveev, Vakil; Mor, Visesato; et al. (2024)
Nature Communications
Most genotoxic anticancer agents fail in tumors with intact DNA repair. Therefore, trabectedin, anagent more toxic to cells with active DNA repair, specifically transcription-coupled nucleotide excision repair (TC-NER), provides therapeutic opportunities. To unlock the potential of trabectedin and inform its application in precision oncology, an understanding of the mechanism of the drug’s TC-NER-dependent toxicity is needed. Here, we determine that abortive TC-NER of trabectedin-DNA adducts forms persistent single-strand breaks (SSBs) as the adducts block the second of the two sequential NER incisions. We map the 3’-hydroxyl groups of SSBs originating from the first NER incision at trabectedin lesions, recording TC-NER on a genome-wide scale. Trabectedin-induced SSBs primarily occur in transcribed strands of active genes and peak near transcription start sites. Frequent SSBs are also found outside gene bodies, connecting TC-NER to divergent transcription from promoters. This work advances the use of trabectedin for precision oncology and for studying TC-NER and transcription.
Quantification and Mapping of Alkylation in the Human Genome Reveal Single Nucleotide Resolution Precursors of Mutational Signatures
Jiang, Yang; Mingard, Cécile; Huber, Sabrina M.; et al. (2023)
ACS Central Science
Chemical modifications to DNA bases, including DNA adducts arising from reactions with electrophilic chemicals, are well-known to impact cell growth, miscode during replication, and influence disease etiology. However, knowledge of how genomic sequences and structures influence the accumulation of alkylated DNA bases is not broadly characterized with high resolution, nor have these patterns been linked with overall quantities of modified bases in the genome. For benzo(a) pyrene (BaP), a ubiquitous environmental carcinogen, we developed a single-nucleotide resolution damage sequencing method to map in a human lung cell line the main mutagenic adduct arising from BaP. Furthermore, we combined this analysis with quantitative mass spectrometry to evaluate the dose-response profile of adduct formation. By comparing damage abundance with DNase hypersensitive sites, transcription levels, and other genome annotation data, we found that although overall adduct levels rose with increasing chemical exposure concentration, genomic distribution patterns consistently correlated with chromatin state and transcriptional status. Moreover, due to the single nucleotide resolution characteristics of this DNA damage map, we could determine preferred DNA triad sequence contexts for alkylation accumulation, revealing a characteristic DNA damage signature. This new BaP damage signature had a profile highly similar to mutational signatures identified previously in lung cancer genomes from smokers. Thus, these data provide insight on how genomic features shape the accumulation of alkylation products in the genome and predictive strategies for linking single-nucleotide resolution in vitro damage maps with human cancer mutations.
Click-code-seq reveals strand biases of DNA oxidation and depurination in human genome
Takhaveev, Vakil; Püllen, Nikolai; Singh, Navnit Kaur; et al. (2025)
Nature Chemical Biology
DNA modifications drive aging, neurodegeneration, carcinogenesis and chemotherapy drug action. Accurate mapping of diverse DNA modifications with single-nucleotide precision in complex genomes remains challenging. We upgraded click-code-seq, a click-chemistry-aided DNA-modification mapping strategy, to enable its first application for sequencing oxidation and depurination in the human genome. We developed a companion fluorescence assay, click-fluoro-quant, to rapidly quantify common DNA modifications and novel adaptors to minimize false positives and assess modification frequency. We uncovered that endogenous DNA oxidation in a human cell line mirrors cancer mutational signatures linked to oxidative stress. The chemotherapy drug irofulven preferentially induces depurination in ApA dimers and promoters. Notably, oxidized guanines and apurinic sites, both irofulven induced and endogenous, are depleted in gene transcribed strands, with the strand bias increasing with gene expression. This work substantially advances click-code-seq for deciphering the impacts of key modifications in human DNA on cellular physiology and toxicological responses.
Single-nucleotide-resolution genomic maps of O6-methylguanine from the glioblastoma drug temozolomide
Kubitschek, Jasmina; Takhaveev, Vakil; Mingard, Cécile; et al. (2025)
Nucleic Acids Research
Temozolomide kills cancer cells by forming O⁶-methylguanine (O⁶-MeG), which leads to cell cycle arrest and apoptosis. However, O⁶-MeG repair by O⁶-methylguanine-DNA methyltransferase (MGMT) contributes to drug resistance. Characterizing genomic profiles of O⁶-MeG could elucidate how O⁶-MeG accumulation is influenced by repair, but there are no methods to map genomic locations of O⁶-MeG. Here, we developed an immunoprecipitation- and polymerase-stalling-based method, termed O⁶-MeG-seq, to locate O⁶-MeG across the whole genome at single-nucleotide resolution. We analyzed O⁶-MeG formation and repair across sequence contexts and functional genomic regions in relation to MGMT expression in a glioblastoma-derived cell line. O⁶-MeG signatures were highly similar to mutational signatures from patients previously treated with temozolomide. Furthermore, MGMT did not preferentially repair O⁶-MeG with respect to sequence context, chromatin state or gene expression level, however, may protect oncogenes from mutations. Finally, we found an MGMT-independent strand bias in O⁶-MeG accumulation in highly expressed genes. These data provide high resolution insight on how O⁶-MeG formation and repair are impacted by genome structure and nucleotide sequence. Further, O⁶-MeG-seq is expected to enable future studies of DNA modification signatures as diagnostic markers for addressing drug resistance and preventing secondary cancers.
Temporal segregation of biosynthetic processes is responsible for metabolic oscillations during the budding yeast cell cycle
Takhaveev, Vakil; Özsezen, Serdar; Smith, Edward N.; et al. (2023)
Nature Metabolism
Many cell biological and biochemical mechanisms controlling the fundamental process of eukaryotic cell division have been identified; however, the temporal dynamics of biosynthetic processes during the cell division cycle are still elusive. Here, we show that key biosynthetic processes are temporally segregated along the cell cycle. Using budding yeast as a model and single-cell methods to dynamically measure metabolic activity, we observe two peaks in protein synthesis, in the G1 and S/G2/M phase, whereas lipid and polysaccharide synthesis peaks only once, during the S/G2/M phase. Integrating the inferred biosynthetic rates into a thermodynamic-stoichiometric metabolic model, we find that this temporal segregation in biosynthetic processes causes flux changes in primary metabolism, with an acceleration of glucose-uptake flux in G1 and phase-shifted oscillations of oxygen and carbon dioxide exchanges. Through experimental validation of the model predictions, we demonstrate that primary metabolism oscillates with cell-cycle periodicity to satisfy the changing demands of biosynthetic processes exhibiting unexpected dynamics during the cell cycle.
Dissection of Cancer Mutational Signatures with Individual Components of Cigarette Smoking
Mingard, Cécile; Battey, James N.D.; Takhaveev, Vakil; et al. (2023)
Chemical Research in Toxicology
Tobacco smoke delivers a complex mixture of hazardous and potentially hazardous chemicals. Some of these may induce the formation of DNA mutations, which increases the risk of various cancers that display characteristic patterns of accumulated mutations arising from the causative exposures. Tracking the contributions of individual mutagens to mutational signatures present in human cancers can help understand cancer etiology and advance disease prevention strategies. To characterize the potential contributions of individual constituents of tobacco smoke to tobacco exposure-associated mutational signatures, we first assessed the toxic potential of 13 tobacco-relevant compounds by determining their impact on the viability of a human bronchial lung epithelial cell line (BEAS-2B). Experimentally derived high-resolution mutational profiles were characterized for the seven most potent compounds by sequencing the genomes of clonally expanded mutants that arose after exposure to the individual chemicals. Analogous to the classification of mutagenic processes on the basis of signatures from human cancers, we extracted mutational signatures from the mutant clones. We confirmed the formation of previously characterized benzo[a]pyrene mutational signatures. Furthermore, we discovered three novel mutational signatures. The mutational signatures arising from benzo[a]pyrene and norharmane were similar to human lung cancer signatures attributed to tobacco smoking. However, the signatures arising from N-methyl-N '-nitro-N-nitrosoguanidine and 4-(acetoxymethyl)nitrosamino]-1-(3-pyridyl)-1-butanone were not directly related to known tobacco-linked mutational signatures from human cancers. This new data set expands the scope of the in vitro mutational signature catalog and advances understanding of how environmental agents mutate DNA.
When DNA Repair Backfires - Trabectedin Induces DNA Breaks in Active Genes
Takhaveev, Vakil; Son, Kook; Mor, Visesato; et al. (2025)
Chimia
Many anticancer drugs are ineffective in tumors that have functional DNA repair mechanisms. In contrast, trabectedin, a tetrahydroisoquinoline alkaloid marine natural product, stands out as it is more lethal to cancer cells with active DNA repair, particularly transcription-coupled nucleotide excision repair (TC-NER), making it an intriguing alternative to standard chemotherapeutic agents. To optimize trabectedin's use in precision oncology, it is essential to understand how its toxicity depends on TC-NER. In this study, we reveal that incomplete TC-NER of trabectedin-DNA adducts generates persistent single-strand breaks (SSBs). These adducts are found to obstruct the second of two sequential NER-mediated DNA incisions. By mapping the 3'-hydroxyl groups of SSBs resulting from the first NER incision at trabectedin-DNA adducts, we achieve genome-wide visualization of TC-NER. Our findings show that trabectedin-induced SSBs predominantly occur in the transcribed strands of active genes, accumulating near transcription start sites. This work provides new insights into how trabectedin can be leveraged for targeted cancer therapies and for studying TC-NER and transcription.

Publications 1 - 7 of 7

Vakil Takhaveev

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