The DOI matches its Crossref record; 52 of the 52 references it cites were found in a registry or an index.
Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer
Open accessAbstract
Co-culture of intestinal organoids with a colibactin-producing pks + E. coli strain (EcC) revealed mutational signatures also found in colorectal cancer (CRC). E. coli Nissle 1917 (EcN) remains a commonly used probiotic, despite harboring the pks operon and inducing double strand DNA breaks. We determine the mutagenicity of EcN and three CRC-derived pks + E. coli strains with an analytical framework based on sequence characteristic of colibactin-induced mutations. All strains, including EcN, display varying levels of mutagenic activity. Furthermore, a machine learning approach attributing individual mutations to colibactin reveals that patients with colibactin-induced mutations are diagnosed at a younger age and that colibactin can induce a specific APC mutation. These approaches allow the sensitive detection of colibactin-induced mutations in ∼12% of CRC genomes and even in whole exome sequencing data, representing a crucial step toward pinpointing the mutagenic activity of distinct pks + E. coli strains.
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“having the capability of synthetizing and releasing colibactin, a mutagenic substance described to promote colorectal polyposis and cancer, and reducing cancer response to irinotecan [26, 34–39].”
From Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces (2026) · cites this paper as [39]
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“Indeed, pks-positive CRC occurs mainly in young people [39].”
From Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces (2026) · cites this paper as [39]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“the pks genetic island is absent in the E. coli 5C but present and productive in the E. coli Nissle 1917 [39].”
From Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces (2026) · cites this paper as [39]
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“the most widely used E. coli-based probiotic, known as E. coli Nissle 1917 (DSM 6601), is pks-positive.”
From Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces (2026) · cites this paper as [39]
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Cites
ggplot2: Elegant Graphics for Data Analysis
Ginestet, C. E. (2011) · Journal of the Royal Statistical Society Series A (Statistics in Society) · doi:10.1111/j.1467-985x.2010.00676_9.x · Cited by 14,511
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The Cancer Genome Atlas Network (2015) · Nature · doi:10.1038/nature14129 · Cited by 4,147
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Self-citationThe repertoire of mutational signatures in human cancer
Alexandrov, L. B., Kim, J., Haradhvala, N. J., Huang, M. N., Tian Ng, A. W., Wu, Y., Boot, A., Covington, K. R., Gordenin, D. A., Bergstrom, E. N., et al. (2020) · Nature · doi:10.1038/s41586-020-1943-3 · Cited by 3,496
Intestinal inflammation targets cancer-inducing activity of the microbiota
Arthur, J. C., Perez-Chanona, E., Mühlbauer, M., Tomkovich, S., Uronis, J. M., Fan, T.-J., Campbell, B. J., Abujamel, T., Dogan, B., Rogers, A. B., et al. (2012) · Science · doi:10.1126/science.1224820 · Cited by 2,263
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Research works printed but not linked: 1
- Buc, 2013, High prevalence of mucosa-associated E. coli producing cyclomodulin and genotoxin in colon cancer, PLoS One, 8, e56964, 10.1371/journal.pone.0056964 · DOI · Paper page
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Items 101–106 of 106
Deeb, N., Otinov, G. D., & Koshel, E. I. (2026) · Russian Journal of Bioorganic Chemistry · doi:10.1134/s1068162026602120
Lin, J., Lin, H., Zhang, Z., & Wang, H. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1892843
Gut microbiome in gastrointestinal cancer
Xie, M., & Jun, Y. U. (2026) · Shengming kexue · doi:10.3724/cbls.2026044
Early-onset cancer: State of the science and future opportunities
Demb, J., Daunov, K., & Warner, E. L. (2026) · Preventive Oncology & Epidemiology · doi:10.1080/28322134.2026.2739637
Giang, V. S., Hồ, V. S., Manh, Đ. T., Tùng, N. T., Thảo, N. T. P., Thân, N. T., Tung, N. L., Hao, T. V., & Cuong, L. D. (2026) · Microorganisms · doi:10.3390/microorganisms14102325
The pan-cancer whole-genome landscape of Adolescent and Young Adult solid cancersPreprint
van Putten, J., Huber, A. R., Koster, R., Roerink, S., de Ligt, J., Roepman, P., Kas, S. M., van Boxtel, R., van der Graaf, W., Cuppen, E. P. J. G., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.10.15.759320
Self-citation
Metadata
- Authors
- Rosendahl Huber, A., Pleguezuelos-Manzano, C., Puschhof, J., Ubels, J., Boot, C., Saftien, A., Verheul, M., Trabut, L. T., Groenen, N., van Roosmalen, M., Ouyang, K. S., Wood, H., Quirke, P., Meijer, G., Cuppen, E., Clevers, H., & van Boxtel, R.
- Affiliations
- Royal Netherlands Academy of Arts and Sciences (NL)
- Oncode Institute (NL)
- German Cancer Research Center (DE)
- University of Leeds (GB)
- The Netherlands Cancer Institute (NL)
- University Medical Center Utrecht (NL)
- F. Hoffmann-La Roche AG (CH)
- Corresponding author
- Puschhof, Jens
- Clevers, Hans
- ORCID
- Venue
- Cancer Cell
- Publisher
- Elsevier BV
- Published
- 2024-03
- Volume
- 42
- Issue
- 3
- Pages
- 487-496.e6
- ISSN
- 1535-6108 (ISSN-L)
- OpenAlex
- W4392638507
- Cited by
- 106
- References
- 52
- Citations by year
- 2026: 53 · 2025: 39 · 2024: 14
- FWCI
- 32.02
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cancer Cell (publishedVersion, cc-by)
- PubMed (publishedVersion)
- KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) (publishedVersion, other-oa)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion, cc-by)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- American Association for Cancer Research (SU2C-3.1416)
- European Research Council (864499)
- Hubrecht Institute
- Cancer Research UK (C10674/A27140)
- Ministerie van Onderwijs, Cultuur en Wetenschap
- National Human Genome Research Institute
- Entertainment Industry Foundation
- Oncode Institute
- National Cancer Institute
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- New York Stem Cell Foundation
- Princess Máxima Center for Pediatric Oncology
- KWF Kankerbestrijding
- Koninklijke Nederlandse Akademie van Wetenschappen
- Energy Council of Canada (2F8, CFF16-2F8, CFF159-19H2, 19H2)
- Topics
- Health Sciences › Medicine › Pathology and Forensic Medicine › Genetic factors in colorectal cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Carcinogens and Genotoxicity Assessment
- Keywords
- colibactin, Escherichia coli, colorectal cancer, intestinal organoids, mutagenicity, genotoxicity, Escherichia coli Nissle 1917, probiotics, DNA double-strand breaks, APC mutation, mutational signatures, age at diagnosis
- MeSH terms
- DNA Damage, Escherichia coli, Humans, Mutagens, Mutation, Organoids, Peptides, Colorectal Neoplasms, Polyketides
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