1
|
Naffaa MM, Al-Ewaidat OA, Gogia S, Begiashvili V. Neoantigen-based immunotherapy: advancing precision medicine in cancer and glioblastoma treatment through discovery and innovation. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2025; 6:1002313. [PMID: 40309350 PMCID: PMC12040680 DOI: 10.37349/etat.2025.1002313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Accepted: 04/07/2025] [Indexed: 05/02/2025] Open
Abstract
Neoantigen-based immunotherapy has emerged as a transformative approach in cancer treatment, offering precision medicine strategies that target tumor-specific antigens derived from genetic, transcriptomic, and proteomic alterations unique to cancer cells. These neoantigens serve as highly specific targets for personalized therapies, promising more effective and tailored treatments. The aim of this article is to explore the advances in neoantigen-based therapies, highlighting successful treatments such as vaccines, tumor-infiltrating lymphocyte (TIL) therapy, T-cell receptor-engineered T cells therapy (TCR-T), and chimeric antigen receptor T cells therapy (CAR-T), particularly in cancer types like glioblastoma (GBM). Advances in technologies such as next-generation sequencing, RNA-based platforms, and CRISPR gene editing have accelerated the identification and validation of neoantigens, moving them closer to clinical application. Despite promising results, challenges such as tumor heterogeneity, immune evasion, and resistance mechanisms persist. The integration of AI-driven tools and multi-omic data has refined neoantigen discovery, while combination therapies are being developed to address issues like immune suppression and scalability. Additionally, the article discusses the ongoing development of personalized immunotherapies targeting tumor mutations, emphasizing the need for continued collaboration between computational and experimental approaches. Ultimately, the integration of cutting-edge technologies in neoantigen research holds the potential to revolutionize cancer care, offering hope for more effective and targeted treatments.
Collapse
Affiliation(s)
- Moawiah M Naffaa
- Department of Psychology and Neuroscience, Duke University, Durham, NC 27708, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ola A Al-Ewaidat
- Department of Internal Medicine, Ascension Saint Francis Hospital, Evanston, IL 60202, USA
| | - Sopiko Gogia
- Department of Internal Medicine, Ascension Saint Francis Hospital, Evanston, IL 60202, USA
| | - Valiko Begiashvili
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66103, USA
| |
Collapse
|
2
|
Chu YL, Georgeson P, Clendenning M, Mahmood K, Walker R, Como J, Joseland S, Preston SG, Rice T, Lynch BM, Milne RL, Southey MC, Giles GG, Phipps AI, Hopper JL, Win AK, Rosty C, Macrae FA, Winship I, Jenkins MA, Buchanan DD, Joo JE. Intratumoural pks +Escherichia coli is associated with risk of metachronous colorectal cancer and adenoma development in people with Lynch syndrome. EBioMedicine 2025; 114:105661. [PMID: 40158390 PMCID: PMC11995779 DOI: 10.1016/j.ebiom.2025.105661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 03/07/2025] [Accepted: 03/07/2025] [Indexed: 04/02/2025] Open
Abstract
BACKGROUND The adverse gut microbiome may underlie the variability in risks of colorectal cancer (CRC) and metachronous CRC in people with Lynch syndrome (LS). The role of pks+/-Escherichia coli (pks+/-E. coli), Enterotoxigenic Bacteroides fragilis (ETBF), and Fusobacterium nucleatum (Fn) in CRCs and adenomas in people with LS is unknown. METHODS A total of 358 LS cases, including 386 CRCs, 90 adenomas, 195 normal colonic mucosa DNA from the Australasian Colon Cancer Family Registry were tested using multiplex TaqMan qPCR. Logistic regression was used to compare the intratumoural prevalence of each bacteria in Lynch CRCs with 1336 sporadic CRCs. Cox proportional-hazards regression estimated the associations of each bacteria with the risk of metachronous CRC and neoplasia. FINDINGS Pks+ E. coli (odds ratio [95% confidence interval] = 1.60 [1.08-2.35], P = 0.017), pks-E. coli (3.87 [2.58-5.80], P < 0.001) and Fn (19.47 [13.32-28.87], P < 0.001) were significantly enriched in LS CRCs when compared with sporadic CRCs. Pks+ E. coli in the initial CRC was associated with an increased risk of metachronous CRC (hazard ratio [95% confidence interval] = 2.32 [1.29-4.17], P = 0.005) and metachronous colorectal neoplasia (1.51 [1.02-2.23], P = 0.040) when compared with CRCs without pks+ E. coli. INTERPRETATION Pks+ E. coli, pks-E. coli, and Fn are enriched within LS CRCs, suggesting possible roles in CRC development in LS. Having intratumoural pks+ E. coli is associated with increased risk of metachronous CRC, suggesting that, if validated, people with LS might benefit from pks+ E. coli screening and eradication. FUNDING This work was funded by an NHMRC Investigator grant (GNT1194896) and a Cancer Australia/Cancer Council NSW co-funded grant (GNT2012914).
Collapse
Affiliation(s)
- Yen Lin Chu
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Susan G Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Toni Rice
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Brigid M Lynch
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Amanda I Phipps
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Aung K Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; University of Queensland, Brisbane, Queensland, Australia; Envoi Specialist Pathologists, Brisbane, Queensland, Australia
| | - Finlay A Macrae
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Melbourne, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Ingrid Winship
- Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Melbourne, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Melbourne, Victoria, Australia
| | - Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Collaborative Centre for Genomic Cancer Medicine, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia.
| |
Collapse
|
3
|
Quevedo-Olmos A, Wang S, Meyer TF. Decoding microbe-diet-host synergy in colorectal cancer. Nat Microbiol 2025; 10:819-820. [PMID: 40119149 DOI: 10.1038/s41564-025-01971-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2025]
Affiliation(s)
- Alvaro Quevedo-Olmos
- Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Shihan Wang
- Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Thomas F Meyer
- Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel and University Hospital Schleswig-Holstein, Kiel, Germany.
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.
| |
Collapse
|
4
|
Thakur BK, Malaise Y, Choudhury SR, Neustaeter A, Turpin W, Streutker C, Copeland J, Wong EOY, Navarre WW, Guttman DS, Jobin C, Croitoru K, Martin A. Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer. Nat Microbiol 2025; 10:855-870. [PMID: 40033140 DOI: 10.1038/s41564-025-01938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 01/14/2025] [Indexed: 03/05/2025]
Abstract
Diet, microbiome, inflammation and host genetics have been linked to colorectal cancer development; however, it is not clear whether and how these factors interact to promote carcinogenesis. Here we used Il10-/- mice colonized with bacteria previously associated with colorectal cancer: enterotoxigenic Bacteroides fragilis, Helicobacter hepaticus or colibactin-producing (polyketide synthase-positive (pks+)) Escherichia coli and fed either a low-carbohydrate (LC) diet deficient in soluble fibre, a high-fat and high-sugar diet, or a normal chow diet. Colonic polyposis was increased in mice colonized with pks+ E. coli and fed the LC diet. Mechanistically, mucosal inflammation was increased in the LC-diet-fed mice, leading to diminished colonic PPAR-γ signalling and increased luminal nitrate levels. This promoted both pks+ E. coli growth and colibactin-induced DNA damage. PPAR-γ agonists or supplementation with dietary soluble fibre in the form of inulin reverted inflammatory and polyposis phenotypes. The pks+ E. coli also induced more polyps in mismatch-repair-deficient mice by inducing a senescence-associated secretory phenotype. Moreover, oncogenic effects were further potentiated by inflammatory triggers in the mismatch-repair-deficient model. These data reveal that diet and host genetics influence the oncogenic potential of a common bacterium.
Collapse
Affiliation(s)
| | - Yann Malaise
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | | | - Anna Neustaeter
- Division of Gastroenterology, Department of Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Williams Turpin
- Division of Gastroenterology, Department of Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Catherine Streutker
- Department of Laboratory Medicine, Unity Health Toronto, Toronto, Ontario, Canada
| | - Julia Copeland
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Erin O Y Wong
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - William W Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Christian Jobin
- Department of Infectious Diseases and Pathology, University of Florida College of Veterinary Medicine, Gainesville, FL, USA
| | - Kenneth Croitoru
- Division of Gastroenterology, Department of Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
5
|
Dougherty MW, Hoffmann RM, Hernandez MC, Airan Y, Gharaibeh RZ, Herzon SB, Yang Y, Jobin C. Genome-scale CRISPR/Cas9 screening reveals the role of PSMD4 in colibactin-mediated cell cycle arrest. mSphere 2025; 10:e0069224. [PMID: 39918307 PMCID: PMC11934320 DOI: 10.1128/msphere.00692-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 01/14/2025] [Indexed: 03/26/2025] Open
Abstract
Colibactin is a genotoxic secondary metabolite produced by certain Enterobacteriaceae strains that populate the intestine and produces a specific mutational signature in human colonocytes. However, the host pathways involved in colibactin response remain unclear. To address this gap, we performed genome-wide CRISPR/Cas9 knockout screens and RNA sequencing utilizing live pks+ bacteria and a synthetic colibactin analog. We identified 20 enriched genes with a MAGeCK score of >2.0 in both screens, including proteasomal subunits (e.g., PSMG4 and PSMD4), RNA processing factors (e.g., SF1 and PRPF8), and RNA polymerase III (e.g., CRCP), and validated the role of PSMD4 in colibactin sensitization. PSMD4 knockout in HEK293T and HT-29 cells promoted cell viability and ameliorated G2-M cell cycle arrest but did not affect the amount of phosphorylated H2AX foci after exposure to synthetic colibactin 742. Consistent with these observations, PSMD4-/- cells had a significantly higher colony formation rate and bigger colony size than control cells after 742 exposure. These findings suggest that PSMD4 regulates cell cycle arrest following colibactin-induced DNA damage and that cells with PSMD4 deficiency may continue to replicate despite DNA damage, potentially increasing the risk of malignant transformation. IMPORTANCE Colibactin has been implicated as a causative agent of colorectal cancer. However, colibactin-producing bacteria are also present in many healthy individuals, leading to the hypothesis that some aspects of colibactin regulation or host response dictate the molecule's carcinogenic potential. Elucidating the host-response pathways involved in dictating cell fate after colibactin intoxication has been difficult, partially due to an inability to isolate the molecule. This study provides the first high-throughput CRISPR/Cas9 screening to identify genes conferring colibactin sensitivity. Here, we utilize both bacterial infection and a synthetic colibactin analog to identify genes directly involved in colibactin response. These findings provide insight into how differences in gene expression may render certain individuals more vulnerable to colibactin-initiated tumor formation after DNA damage.
Collapse
Affiliation(s)
- Michael W. Dougherty
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Ryan M. Hoffmann
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Maria C. Hernandez
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Yougant Airan
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Raad Z. Gharaibeh
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Seth B. Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Departments of Pharmacology, Yale University, New Haven, Connecticut, USA
| | - Ye Yang
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Christian Jobin
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
- Department of Infectious Diseases and Immunology, University of Florida College of Medicine, Gainesville, Florida, USA
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| |
Collapse
|
6
|
Thomas RM. Microbial molecules, metabolites, and malignancy. Neoplasia 2025; 60:101128. [PMID: 39827500 PMCID: PMC11787689 DOI: 10.1016/j.neo.2025.101128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Revised: 01/09/2025] [Accepted: 01/14/2025] [Indexed: 01/22/2025]
Abstract
Research elucidating the role of the microbiome in carcinogenesis has grown exponentially over the past decade. Initially isolated to associative studies on colon cancer development, the field has expanded to encompass nearly every solid and liquid malignancy that may afflict the human body. Investigations are rapidly progressing from association to causation and one particular area of causal effect relates to microbial metabolites and how they influence cancer development, progression, and treatment response. These metabolites can be produced de novo from individual members of the microbiome, whether that be bacteria, fungi, archaea, or other microbial organisms, or they can be through metabolic processing of dietary compounds or even host-derived molecules. In this review, contemporary research elucidating mechanisms whereby microbial-derived molecules and metabolites impact carcinogenesis and cancer treatment efficacy will be presented. While many of the examples focus on bacterial metabolites in colon carcinogenesis, this simply illustrates the accelerated nature of these investigations that occurred early in microbiome research but provides an opportunity for growth in other cancer areas. Indeed, research into the interaction of microbiome-derived metabolites in other malignancies is growing as well as investigations that involve non-bacterial metabolites. This review will provide the reader a framework to expand their knowledge regarding this complex and exciting field of cancer research.
Collapse
Affiliation(s)
- Ryan M Thomas
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, USA; Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA.
| |
Collapse
|
7
|
Lowry E, Mitchell A. Colibactin-induced damage in bacteria is cell contact independent. mBio 2025; 16:e0187524. [PMID: 39576109 PMCID: PMC11708049 DOI: 10.1128/mbio.01875-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 10/28/2024] [Indexed: 11/27/2024] Open
Abstract
The bacterial toxin colibactin, produced primarily by the B2 phylogroup of Escherichia coli, underlies some cases of colorectal cancers. Colibactin crosslinks DNA and induces genotoxic damage in both mammalian and bacterial cells. While the mechanisms facilitating colibactin delivery remain unclear, results from multiple studies supported a delivery model that necessitates cell-cell contact. We directly tested this requirement in bacterial cultures by monitoring the spatiotemporal dynamics of the DNA damage response using a fluorescent transcriptional reporter. We found that in mixed-cell populations, DNA damage saturated within 12 hours and was detectable even in reporter cells separated from colibactin producers by hundreds of microns. Experiments with distinctly separated producer and reporter colonies revealed that the intensity of DNA damage decays similarly with distance regardless of colony contact. Our work reveals that cell contact is inconsequential for colibactin delivery in bacteria and suggests that contact dependence needs to be reexamined in mammalian cells as well. IMPORTANCE Colibactin is a bacteria-produced toxin that binds and damages DNA. It has been widely studied in mammalian cells due to its potential role in tumorigenesis. However, fundamental questions about its impact in bacteria remain underexplored. We used Escherichia coli as a model system to study colibactin toxicity in neighboring bacteria and directly tested if cell-cell contact is required for toxicity, as has previously been proposed. We found that colibactin can induce DNA damage in bacteria hundreds of microns away, and the intensity of DNA damage presents similarly regardless of cell-cell contact. Our work further suggests that the requirement for cell-cell contact for colibactin-induced toxicity also needs to be reevaluated in mammalian cells.
Collapse
Affiliation(s)
- Emily Lowry
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Amir Mitchell
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| |
Collapse
|
8
|
Agrawal R, Al-Hiyari S, Hugh-White R, Hromas R, Patel Y, Williamson EA, Mootor MFE, Gonzalez A, Fu J, Haas R, Jordan M, Wickes BL, Mohammed G, Tian M, Doris MJ, Jobin C, Wernke KM, Pan Y, Yamaguchi TN, Herzon SB, Boutros PC, Liss MA. Colibactin Exerts Androgen-dependent and -independent Effects on Prostate Cancer. Eur Urol Oncol 2024:S2588-9311(24)00245-1. [PMID: 39547899 PMCID: PMC12075626 DOI: 10.1016/j.euo.2024.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/23/2024] [Accepted: 10/26/2024] [Indexed: 11/17/2024]
Abstract
BACKGROUND AND OBJECTIVE The etiology of prostate cancer (PC) is multifactorial and poorly understood. It has been suggested that colibactin-producing Escherichia coli positive for the pathogenicity island pks (pks+) initiate cancers via induction of genomic instability. In PC, androgens promote oncogenic translocations. Our aim was to investigate the association of pks+E. coli with PC diagnosis and molecular architecture, and its relationship with androgens. METHODS We quantified the association of pks+E. coli with PC diagnosis in a volunteer-sampled 235-person cohort from two institutional practices (UT San Antonio). We then used colibactin 742 and DNA/RNA sequencing to evaluate the effects of colibactin 742, dihydrotestosterone (DHT), and their combination in vitro. KEY FINDINGS AND LIMITATIONS Colibactin exposure was positively associated with PC diagnosis (p = 0.04) in our clinical cohort, and significantly increased replication fork stalling and fusions in vitro (p < 0.01). Combined in vitro exposure to colibactin 742 and DHT induced more somatic mutations of all types than exposure to either alone. The combination also elicited kataegis, with a higher density of somatic point mutations. Laboratory analyses were conducted using a single cell line, which limited our ability to fully recapitulate the complexity of PC etiology. CONCLUSIONS AND CLINICAL IMPLICATIONS Our findings are consistent with synergistic induction of genome instability and kataegis by colibactin 742 and DHT in cell culture. Colibactin-producing pks+ E. coli may plausibly contribute to PC etiology. PATIENT SUMMARY We investigated whether a bacterial toxin that is linked to colon cancer can also cause prostate cancer. Our results support this idea by showing a link between the toxin and prostate cancer diagnosis in a large patient population. We also found that this toxin causes genetic dysfunction in prostate cancer cells when combined with testosterone.
Collapse
Affiliation(s)
- Raag Agrawal
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA
| | - Sarah Al-Hiyari
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA
| | - Rupert Hugh-White
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health-San Antonio, San Antonio, TX, USA
| | - Yash Patel
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA
| | - Elizabeth A Williamson
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health-San Antonio, San Antonio, TX, USA
| | - Mohammed F E Mootor
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA
| | - Alfredo Gonzalez
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA
| | - Jianmin Fu
- Department of Microbiology and Immunology, University of Texas Health-San Antonio, San Antonio, TX, USA
| | - Roni Haas
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA
| | - Madison Jordan
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA
| | - Brian L Wickes
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas, San Antonia, TC, USA
| | - Ghouse Mohammed
- Office of Health Informatics and Analytics, University of California-Los Angeles, Los Angeles, CA, USA
| | - Mao Tian
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA
| | - Molly J Doris
- Department of Urology, University of Texas Health-San Antonio, San Antonio, TX, USA
| | - Christian Jobin
- Departments of Medicine, Infectious Diseases and Immunology, and Anatomy and Cell Physiology, University of Florida, Gainesville, FL, USA
| | - Kevin M Wernke
- Department of Chemistry, Yale University, New Haven, CT, USA; Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Yu Pan
- Office of Health Informatics and Analytics, University of California-Los Angeles, Los Angeles, CA, USA
| | - Takafumi N Yamaguchi
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, CT, USA; Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Paul C Boutros
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA; Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Michael A Liss
- Department of Urology, University of Texas Health-San Antonio, San Antonio, TX, USA.
| |
Collapse
|
9
|
Halawa M, Newman PM, Aderibigbe T, Carabetta VJ. Conjugated therapeutic proteins as a treatment for bacteria which trigger cancer development. iScience 2024; 27:111029. [PMID: 39635133 PMCID: PMC11615139 DOI: 10.1016/j.isci.2024.111029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2024] Open
Abstract
In recent years, an increasing amount of research has focused on the intricate and complex correlation between bacterial infections and the development of cancer. Some studies even identified specific bacterial species as potential culprits in the initiation of carcinogenesis, which generated a great deal of interest in the creation of innovative therapeutic strategies aimed at addressing both the infection and the subsequent risk of cancer. Among these strategies, there has been a recent emergence of the use of conjugated therapeutic proteins, which represent a highly promising avenue in the field of cancer therapeutics. These proteins offer a dual-targeting approach that seeks to effectively combat both the bacterial infection and the resulting malignancies that may arise because of such infections. This review delves into the landscape of conjugated therapeutic proteins that have been intricately designed with the purpose of specifically targeting bacteria that have been implicated in the induction of cancer.
Collapse
Affiliation(s)
- Mohamed Halawa
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Precious M. Newman
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Tope Aderibigbe
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Valerie J. Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| |
Collapse
|
10
|
Willenbockel HF, Dowerg B, Cordes T. Multifaceted metabolic role of infections in the tumor microenvironment. Curr Opin Biotechnol 2024; 89:103183. [PMID: 39197341 DOI: 10.1016/j.copbio.2024.103183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/16/2024] [Accepted: 08/05/2024] [Indexed: 09/01/2024]
Abstract
The impact of bacteria and viruses on tumor growth has long been recognized. In recent decades, interest in the role of microorganisms in the tumor microenvironment (TME) has expanded. Infections induce metabolic reprogramming and influence immune responses within the TME that may either support proliferation and metastasis or limit tumor growth. The natural ability to infect cells and alter the TME is also utilized for cancer detection and treatment. In this review, we discuss recent discoveries about the mechanisms of bacteria and viruses affecting TME, as well as strategies in cancer therapy focusing on metabolic alterations. Infections with engineered bacteria and viruses represent promising therapeutic approaches to develop novel and more effective therapies to constrain tumor growth.
Collapse
Affiliation(s)
- Hanna F Willenbockel
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany; Research Group Cellular Metabolism in Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Birte Dowerg
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany; Research Group Cellular Metabolism in Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Thekla Cordes
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany; Research Group Cellular Metabolism in Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany.
| |
Collapse
|
11
|
Lowry E, Wang Y, Dagan T, Mitchell A. Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage. Genome Res 2024; 34:1154-1164. [PMID: 39152036 PMCID: PMC11444178 DOI: 10.1101/gr.279517.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
Colibactin produced primarily by Escherichia coli strains of the B2 phylogroup cross-links DNA and can promote colon cancer in human hosts. Here, we investigate the toxin's impact on colibactin producers and on bacteria cocultured with producing cells. Using genome-wide genetic screens and mutation accumulation experiments, we uncover the cellular pathways that mitigate colibactin damage and reveal the specific mutations it induces. We discover that although colibactin targets A/T-rich motifs, as observed in human colon cells, it induces a bacteria-unique mutation pattern. Based on this pattern, we predict that long-term colibactin exposure will culminate in a genomic bias in trinucleotide composition. We test this prediction by analyzing thousands of E. coli genomes and find that colibactin-producing strains indeed show the predicted skewness in trinucleotide composition. Our work reveals a bacteria-specific mutation pattern and suggests that the resistance protein encoded on the colibactin pathogenicity island is insufficient in preventing self-inflicted DNA damage.
Collapse
Affiliation(s)
- Emily Lowry
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Yiqing Wang
- Institute of General Microbiology, Kiel University, 24118 Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, 24118 Kiel, Germany
| | - Amir Mitchell
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA;
| |
Collapse
|
12
|
Crisafulli G. Mutational Signatures in Colorectal Cancer: Translational Insights, Clinical Applications, and Limitations. Cancers (Basel) 2024; 16:2956. [PMID: 39272814 PMCID: PMC11393898 DOI: 10.3390/cancers16172956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
A multitude of exogenous and endogenous processes have the potential to result in DNA damage. While the repair mechanisms are typically capable of correcting this damage, errors in the repair process can result in mutations. The findings of research conducted in 2012 indicate that mutations do not occur randomly but rather follow specific patterns that can be attributed to known or inferred mutational processes. The process of mutational signature analysis allows for the inference of the predominant mutational process for a given cancer sample, with significant potential for clinical applications. A deeper comprehension of these mutational signatures in CRC could facilitate enhanced prevention strategies, facilitate the comprehension of genotoxic drug activity, predict responses to personalized treatments, and, in the future, inform the development of targeted therapies in the context of precision oncology. The efforts of numerous researchers have led to the identification of several mutational signatures, which can be categorized into different mutational signature references. In CRC, distinct mutational signatures are identified as correlating with mismatch repair deficiency, polymerase mutations, and chemotherapy treatment. In this context, a mutational signature analysis offers considerable potential for enhancing minimal residual disease (MRD) tests in stage II (high-risk) and stage III CRC post-surgery, stratifying CRC based on the impacts of genetic and epigenetic alterations for precision oncology, identifying potential therapeutic vulnerabilities, and evaluating drug efficacy and guiding therapy, as illustrated in a proof-of-concept clinical trial.
Collapse
|
13
|
Martinek R, Lózsa R, Póti Á, Németh E, Várady G, Szabó P, Szüts D. Comprehensive investigation of the mutagenic potential of six pesticides classified by IARC as probably carcinogenic to humans. CHEMOSPHERE 2024; 362:142700. [PMID: 38936485 DOI: 10.1016/j.chemosphere.2024.142700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/13/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Pesticides are significant environmental pollutants, and many of them possess mutagenic potential, which is closely linked to carcinogenesis. Here we tested the mutagenicity of all six pesticides classified probably carcinogenic (Group 2A) by the International Agency of Research on Cancer: 4,4'-DDT, captafol, dieldrin, diazinon, glyphosate and malathion. Whole genome sequencing of TK6 human lymphoblastoid cell clones following 30-day exposure at subtoxic concentrations revealed a clear mutagenic effect of treatment with captafol or malathion when added at 200 nM or 100 μM initial concentrations, respectively. Each pesticide induced a specific base substitution mutational signature: captafol increased C to A mutations primarily, while malathion induced mostly C to T mutations. 4,4'-DDT, dieldrin, diazinon and glyphosate were not mutagenic. Whereas captafol induced chromosomal instability, H2A.X phosphorylation and cell cycle arrest in G2/M phase, all indicating DNA damage, malathion did not induce DNA damage markers or cell cycle alterations despite its mutagenic effect. Hypersensitivity of REV1 and XPA mutant DT40 chicken cell lines suggests that captafol induces DNA adducts that are bypassed by translesion DNA synthesis and are targets for nucleotide excision repair. The experimentally identified mutational signatures of captafol and malathion could shed light on the mechanism of action of these compounds. The signatures are potentially suitable for detecting past exposure in tumour samples, but the reanalysis of large cancer genome databases did not reveal any evidence of captafol or malathion exposure.
Collapse
Affiliation(s)
- Regina Martinek
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary; Doctoral School of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary.
| | - Rita Lózsa
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
| | - Ádám Póti
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
| | - Eszter Németh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
| | - György Várady
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
| | - Pál Szabó
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
| | - Dávid Szüts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
| |
Collapse
|
14
|
González A, Fullaondo A, Odriozola A. Microbiota-associated mechanisms in colorectal cancer. ADVANCES IN GENETICS 2024; 112:123-205. [PMID: 39396836 DOI: 10.1016/bs.adgen.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide, ranking third in terms of incidence and second as a cause of cancer-related death. There is growing scientific evidence that the gut microbiota plays a key role in the initiation and development of CRC. Specific bacterial species and complex microbial communities contribute directly to CRC pathogenesis by promoting the neoplastic transformation of intestinal epithelial cells or indirectly through their interaction with the host immune system. As a result, a protumoural and immunosuppressive environment is created conducive to CRC development. On the other hand, certain bacteria in the gut microbiota contribute to protection against CRC. In this chapter, we analysed the relationship of the gut microbiota to CRC and the associations identified with specific bacteria. Microbiota plays a key role in CRC through various mechanisms, such as increased intestinal permeability, inflammation and immune system dysregulation, biofilm formation, genotoxin production, virulence factors and oxidative stress. Exploring the interaction between gut microbiota and tumourigenesis is essential for developing innovative therapeutic approaches in the fight against CRC.
Collapse
Affiliation(s)
- Adriana González
- Hologenomics Research Group, Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country, Spain.
| | - Asier Fullaondo
- Hologenomics Research Group, Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country, Spain
| | - Adrian Odriozola
- Hologenomics Research Group, Department of Genetics, Physical Anthropology, and Animal Physiology, University of the Basque Country, Spain
| |
Collapse
|
15
|
Salim F, Mizutani S, Shiba S, Takamaru H, Yamada M, Nakajima T, Yachida T, Soga T, Saito Y, Fukuda S, Yachida S, Yamada T. Fusobacterium species are distinctly associated with patients with Lynch syndrome colorectal cancer. iScience 2024; 27:110181. [PMID: 38993678 PMCID: PMC11237946 DOI: 10.1016/j.isci.2024.110181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/11/2024] [Accepted: 06/01/2024] [Indexed: 07/13/2024] Open
Abstract
Accumulating evidence demonstrates clear correlation between the gut microbiota and sporadic colorectal cancer (CRC). Despite this, there is limited understanding of the association between the gut microbiota and CRC in Lynch Syndrome (LS), a hereditary type of CRC. Here, we analyzed fecal shotgun metagenomic and targeted metabolomic of 71 Japanese LS subjects. A previously published Japanese sporadic CRC cohort, which includes non-LS controls, was utilized as a non-LS cohort (n = 437). LS subjects exhibited reduced microbial diversity and low-Faecalibacterium enterotypes compared to non-LS. Patients with LS-CRC had higher levels of Fusobacterium nucleatum and fap2. Differential fecal metabolites and functional genes suggest heightened degradation of lysine and arginine in LS-CRC. A comparison between LS and non-LS subjects prior to adenoma formation revealed distinct fecal metabolites of LS subjects. These findings suggest that the gut microbiota plays a more responsive role in CRC tumorigenesis in patients with LS than those without LS.
Collapse
Affiliation(s)
- Felix Salim
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Sayaka Mizutani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
- Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
| | - Satoshi Shiba
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Hiroyuki Takamaru
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku 104-0045, Tokyo, Japan
| | - Masayoshi Yamada
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku 104-0045, Tokyo, Japan
| | - Takeshi Nakajima
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku 104-0045, Tokyo, Japan
| | - Tatsuo Yachida
- Department of Gastroenterology & Neurology, Faculty of Medicine, Kagawa University, Miki-cho, Kagawa 761-0793, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Yutaka Saito
- Endoscopy Division, National Cancer Center Hospital, Chuo-ku 104-0045, Tokyo, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa 210-0821, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
- Metagen, Inc., Tsuruoka, Yamagata 997-0052, Japan
- Metagen Theurapeutics, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
- Metagen, Inc., Tsuruoka, Yamagata 997-0052, Japan
- Metagen Theurapeutics, Inc., Tsuruoka, Yamagata 997-0052, Japan
- digzyme, Inc., Minato-ku, Tokyo 105-0004, Japan
| |
Collapse
|
16
|
Lowry E, Mitchell A. Colibactin-induced damage in bacteria is cell contact independent. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600066. [PMID: 38948699 PMCID: PMC11212979 DOI: 10.1101/2024.06.21.600066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The bacterial toxin colibactin, produced primarily by the B2 phylogroup of Escherichia coli, underlies some cases of colorectal cancers. Colibactin crosslinks DNA and induces genotoxic damage in both mammalian and bacterial cells. While the mechanisms facilitating colibactin delivery remain unclear, results from multiple studies supported a delivery model that necessitates cell-cell contact. We directly tested this requirement in bacterial cultures by monitoring the spatiotemporal dynamics of the DNA damage response using a fluorescent transcriptional reporter. We found that in mixed-cell populations, DNA damage saturated within twelve hours and was detectable even in reporter cells separated from colibactin producers by hundreds of microns. Experiments with distinctly separated producer and reporter colonies revealed that the intensity of DNA damage decays similarly with distance regardless of colony contact. Our work reveals that cell contact is inconsequential for colibactin delivery in bacteria and suggests that contact-dependence needs to be reexamined in mammalian cells as well. Importance Colibactin is a bacteria-produced toxin that binds and damages DNA. It has been widely studied in mammalian cells due to its potential role in tumorigenesis. However, fundamental questions about its impact in bacteria remain underexplored. We used E. coli as a model system to study colibactin toxicity in neighboring bacteria and directly tested if cell-cell contact is required for toxicity, as has previously been proposed. We found that colibactin can induce DNA damage in bacteria hundreds of microns away and that the intensity of DNA damage presents similarly regardless of cell-cell contact. Our work further suggests that the requirement for cell-cell contact for colibactin-induced toxicity also needs to be reevaluated in mammalian cells.
Collapse
|
17
|
Addington E, Sandalli S, Roe AJ. Current understandings of colibactin regulation. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001427. [PMID: 38314762 PMCID: PMC10924459 DOI: 10.1099/mic.0.001427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024]
Abstract
The biosynthetic machinery for the production of colibactin is encoded by 19 genes (clbA - S) within the pks pathogenicity island harboured by many E. coli of the B2-phylogroup. Colibactin is a potent genotoxic metabolite which causes DNA-damage and which has potential roles in microbial competition and fitness of pks+ bacteria. Colibactin has also been strongly implicated in the development of colorectal cancer. Given the genotoxicity of colibactin and the metabolic cost of its synthesis, the regulatory system governing the clb cluster is accordingly highly complex, and many of the mechanisms remain to be elucidated. In this review we summarise the current understanding of regulation of colibactin biosynthesis by internal molecular components and how these factors are modulated by signals from the external environment.
Collapse
Affiliation(s)
- Emily Addington
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Scotland, UK
| | - Sofia Sandalli
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Scotland, UK
| | - Andrew J. Roe
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Scotland, UK
| |
Collapse
|
18
|
Han J, Zhang B, Zhang Y, Yin T, Cui Y, Liu J, Yang Y, Song H, Shang D. Gut microbiome: decision-makers in the microenvironment of colorectal cancer. Front Cell Infect Microbiol 2023; 13:1299977. [PMID: 38156313 PMCID: PMC10754537 DOI: 10.3389/fcimb.2023.1299977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
Colorectal cancer (CRC) is a common malignancy of the gastrointestinal tract, accounting for the second most common cause of gastrointestinal tumors. As one of the intestinal barriers, gut bacteria form biofilm, participate in intestinal work, and form the living environment of intestinal cells. Metagenomic next-generation sequencing (mNGS) of the gut bacteria in a large number of CRC patients has been established, enabling specific microbial signatures to be associated with colorectal adenomato-carcinoma. Gut bacteria are involved in both benign precursor lesions (polyps), in situ growth and metastasis of CRC. Therefore, the term tumorigenic bacteria was proposed in 2018, such as Escherichia coli, Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, etc. Meanwhile, bacteria toxins (such as cytolethal distending toxin (CDT), Colibactin (Clb), B. fragilis toxin) affect the tumor microenvironment and promote cancer occurrence and tumor immune escape. It is important to note that there are differences in the bacteria of different types of CRC. In this paper, the role of tumorigenic bacteria in the polyp-cancer transformation and the effects of their secreted toxins on the tumor microenvironment will be discussed, thereby further exploring new ideas for the prevention and treatment of CRC.
Collapse
Affiliation(s)
- Jingrun Han
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Biao Zhang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yongnian Zhang
- Departments of Gastrointestinal Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Tianyi Yin
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yuying Cui
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Jinming Liu
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yanfei Yang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Huiyi Song
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Dong Shang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| |
Collapse
|
19
|
Jans M, Kolata M, Blancke G, Ciers M, Dohlman AB, Kusakabe T, Sze M, Thiran A, Berx G, Tejpar S, van Loo G, Iliev ID, Remaut H, Vereecke L. Colibactin-induced genotoxicity and colorectal cancer exacerbation critically depends on adhesin-mediated epithelial binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553526. [PMID: 37645947 PMCID: PMC10462063 DOI: 10.1101/2023.08.16.553526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Various bacteria are suggested to contribute to colorectal cancer (CRC) development, including pks+ E. coli which produce the genotoxin colibactin that induces characteristic mutational signatures in host epithelial cells. It remains unclear how the highly unstable colibactin molecule is able to access host epithelial cells and its DNA to cause harm. Using the microbiota-dependent ZEB2-transgenic mouse model of invasive CRC, we found that pks+ E. coli drives CRC exacerbation and tissue invasion in a colibactin-dependent manner. Using isogenic mutant strains, we further demonstrate that CRC exacerbation critically depends on expression of the E. coli type-1 pilus adhesin FimH and the F9-pilus adhesin FmlH. Blocking bacterial adhesion using a pharmacological FimH inhibitor attenuates colibactin-mediated genotoxicity and CRC exacerbation. Together, we show that the oncogenic potential of pks+ E. coli critically depends on bacterial adhesion to host epithelial cells and is critically mediated by specific bacterial adhesins. Adhesin-mediated epithelial binding subsequently allows production of the genotoxin colibactin in close proximity to host epithelial cells, which promotes DNA damage and drives CRC development. These findings present promising therapeutic avenues for the development of anti-adhesive therapies aiming at mitigating colibactin-induced DNA damage and inhibiting the initiation and progression of CRC, particularly in individuals at risk for developing CRC.
Collapse
|