Computational analysis of cancer genome sequencing data DOI
Isidro Cortés‐Ciriano, D. Gulhan, Jake June-Koo Lee

et al.

Nature Reviews Genetics, Journal Year: 2021, Volume and Issue: 23(5), P. 298 - 314

Published: Dec. 8, 2021

Language: Английский

A compendium of mutational cancer driver genes DOI
Francisco Martínez-Jiménez, Ferran Muiños, Inés Sentís

et al.

Nature reviews. Cancer, Journal Year: 2020, Volume and Issue: 20(10), P. 555 - 572

Published: Aug. 10, 2020

Language: Английский

Citations

1021
Mechanisms of APOBEC3 mutagenesis in human cancer cells DOI Creative Commons
Mia Petljak, Alexandra Dananberg, Kevan Chu

et al.

Nature, Journal Year: 2022, Volume and Issue: 607(7920), P. 799 - 807

Published: July 20, 2022

The APOBEC3 family of cytosine deaminases has been implicated in some the most prevalent mutational signatures cancer1-3. However, a causal link between endogenous enzymes and human cancer genomes not established, leaving mechanisms mutagenesis poorly understood. Here, to investigate mutagenesis, we deleted genes from cell lines that naturally generate APOBEC3-associated over time4. Analysis non-clustered clustered across whole-genome sequences 251 breast, bladder lymphoma line clones revealed APOBEC3A deletion diminished signatures. Deletion both APOBEC3B further decreased mutation burdens, without eliminating them. increased protein levels, activity APOBEC3A-mediated lines. uracil glycosylase UNG was required for APOBEC3-mediated transversions, whereas loss translesion polymerase REV1 overall burdens. Together, these data represent direct evidence cells. Our results identify as main driver mutations, indicate can restrain APOBEC3A-dependent while contributing its own smaller burdens dissect translate activities into distinct

Language: Английский

Citations

185
Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination DOI Creative Commons
Riccardo Pecori, Salvatore Di Giorgio, Jose Paulo Lorenzo

et al.

Nature Reviews Genetics, Journal Year: 2022, Volume and Issue: 23(8), P. 505 - 518

Published: March 7, 2022

The AID/APOBEC polynucleotide cytidine deaminases have historically been classified as either DNA mutators or RNA editors based on their first identified nucleic acid substrate preference. can generate functional diversity at antibody genes but also cause genomic instability in cancer. informational the transcriptome of innate immune cells, and cancer cells. Members both classes act antiviral restriction factors. Recent structural work has illuminated differences similarities between enzymes that catalyse mutation, editing both, suggesting strict classification members this family should be reconsidered. As many these employed for targeted genome (or transcriptome) editing, a more holistic understanding will help improve design therapeutically relevant programmable base editors. In Perspective, Pecori et al. provide an overview deaminase family, discussing key features, how they contribute to viral tumour evolution harnessed (potentially therapeutic) base-editing purposes.

Language: Английский

Citations

182
CRISPR-based genome editing through the lens of DNA repair DOI Creative Commons

Tarun S. Nambiar,

Lou Baudrier,

Pierre Billon

et al.

Molecular Cell, Journal Year: 2022, Volume and Issue: 82(2), P. 348 - 388

Published: Jan. 1, 2022

Language: Английский

Citations

158
APOBEC: A molecular driver in cervical cancer pathogenesis DOI Open Access

Sundaramoorthy Revathidevi,

Avaniyapuram Kannan Murugan, Hirofumi Nakaoka

et al.

Cancer Letters, Journal Year: 2020, Volume and Issue: 496, P. 104 - 116

Published: Oct. 7, 2020

Language: Английский

Citations

154
Clinical cancer genomic profiling DOI
Debyani Chakravarty, David B. Solit

Nature Reviews Genetics, Journal Year: 2021, Volume and Issue: 22(8), P. 483 - 501

Published: March 24, 2021

Language: Английский

Citations

143
MutationalPatterns: the one stop shop for the analysis of mutational processes DOI Creative Commons
Freek Manders, Arianne M. Brandsma, Jurrian K. de Kanter

et al.

BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)

Published: Feb. 15, 2022

The collective of somatic mutations in a genome represents record mutational processes that have been operative cell. These can be investigated by extracting relevant patterns from sequencing data.

Language: Английский

Citations

125
Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA DOI Creative Commons
Erik N. Bergstrom, Jens Luebeck, Mia Petljak

et al.

Nature, Journal Year: 2022, Volume and Issue: 602(7897), P. 510 - 517

Published: Feb. 9, 2022

Clustered somatic mutations are common in cancer genomes and previous analyses reveal several types of clustered single-base substitutions, which include doublet- multi-base substitutions

Language: Английский

Citations

120
Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence DOI
Sarah Moody, S. Senkin, S. M. Ashiqul Islam

et al.

Nature Genetics, Journal Year: 2021, Volume and Issue: 53(11), P. 1553 - 1563

Published: Oct. 18, 2021

Language: Английский

Citations

118
Therapy-induced APOBEC3A drives evolution of persistent cancer cells DOI
Hideko Isozaki, Ramin Sakhtemani, Ammal Abbasi

et al.

Nature, Journal Year: 2023, Volume and Issue: 620(7973), P. 393 - 401

Published: July 5, 2023

Language: Английский

Citations

82