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Mendes I, Vale N. How Can the Microbiome Induce Carcinogenesis and Modulate Drug Resistance in Cancer Therapy? Int J Mol Sci 2023; 24:11855. [PMID: 37511612 PMCID: PMC10380870 DOI: 10.3390/ijms241411855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Over the years, cancer has been affecting the lives of many people globally and it has become one of the most studied diseases. Despite the efforts to understand the cell mechanisms behind this complex disease, not every patient seems to respond to targeted therapies or immunotherapies. Drug resistance in cancer is one of the limiting factors contributing to unsuccessful therapies; therefore, understanding how cancer cells acquire this resistance is essential to help cure individuals affected by cancer. Recently, the altered microbiome was observed to be an important hallmark of cancer and therefore it represents a promising topic of cancer research. Our review aims to provide a global perspective of some cancer hallmarks, for instance how genetic and epigenetic modifications may be caused by an altered human microbiome. We also provide information on how an altered human microbiome can lead to cancer development as well as how the microbiome can influence drug resistance and ultimately targeted therapies. This may be useful to develop alternatives for cancer treatment, i.e., future personalized medicine that can help in cases where traditional cancer treatment is unsuccessful.
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Affiliation(s)
- Inês Mendes
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- School of Life and Environmental Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Edifício de Geociências, 5000-801 Vila Real, Portugal
| | - Nuno Vale
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, 4200-450 Porto, Portugal
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Pienkowska M, Choufani S, Turinsky AL, Guha T, Merino DM, Novokmet A, Brudno M, Weksberg R, Shlien A, Hawkins C, Bouffet E, Tabori U, Gilbertson R, Finlay JL, Jabado N, Thomas C, Sill M, Capper D, Hasselblatt M, Malkin D. DNA methylation signature is prognostic of choroid plexus tumor aggressiveness. Clin Epigenetics 2019; 11:117. [PMID: 31409384 PMCID: PMC6692938 DOI: 10.1186/s13148-019-0708-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/22/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Histological grading of choroid plexus tumors (CPTs) remains the best prognostic tool to distinguish between aggressive choroid plexus carcinoma (CPC) and the more benign choroid plexus papilloma (CPP) or atypical choroid plexus papilloma (aCPP); however, these distinctions can be challenging. Standard treatment of CPC is very aggressive and often leads to severe damage to the young child's brain. Therefore, it is crucial to distinguish between CPC and less aggressive entities (CPP or aCPP) to avoid unnecessary exposure of the young patient to neurotoxic therapy. To better stratify CPTs, we utilized DNA methylation (DNAm) to identify prognostic epigenetic biomarkers for CPCs. METHODS We obtained DNA methylation profiles of 34 CPTs using the HumanMethylation450 BeadChip from Illumina, and the data was analyzed using the Illumina Genome Studio analysis software. Validation of differentially methylated CpG sites chosen as biomarkers was performed using pyrosequencing analysis on additional 22 CPTs. Sensitivity testing of the CPC DNAm signature was performed on a replication cohort of 61 CPT tumors obtained from Neuropathology, University Hospital Münster, Germany. RESULTS Generated genome-wide DNAm profiles of CPTs showed significant differences in DNAm between CPCs and the CPPs or aCPPs. The prediction of clinical outcome could be improved by combining the DNAm profile with the mutational status of TP53. CPCs with homozygous TP53 mutations clustered as a group separate from those carrying a heterozygous TP53 mutation or CPCs with wild type TP53 (TP53-wt) and showed the worst survival outcome. Specific DNAm signatures for CPCs revealed AK1, PER2, and PLSCR4 as potential biomarkers for CPC that can be used to improve molecular stratification for diagnosis and treatment. CONCLUSIONS We demonstrate that combining specific DNAm signature for CPCs with histological approaches better differentiate aggressive tumors from those that are not life threatening. These findings have important implications for future prognostic risk prediction in clinical disease management.
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Affiliation(s)
- Malgorzata Pienkowska
- Genetics and Genome Biology Program, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
| | - Andrei L. Turinsky
- Genetics and Genome Biology Program, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
- Center for Computational Medicine, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
| | - Tanya Guha
- Genetics and Genome Biology Program, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
| | - Diana M. Merino
- Friends of Cancer Research, 1800 M Street, NW, Suite 1050 South, Washington, DC 20036 USA
| | - Ana Novokmet
- Genetics and Genome Biology Program, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
| | - Michael Brudno
- Genetics and Genome Biology Program, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
- Center for Computational Medicine, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
- Department of Computer Science, University of Toronto, 40 St. George Street, Toronto, Ontario M5S 2E4 Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8 Canada
- Department of Pediatrics, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8 Canada
| | - Adam Shlien
- Genetics and Genome Biology Program, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
- Paediatric Laboratory Medicine, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8 Canada
| | - Cynthia Hawkins
- Genetics and Genome Biology Program, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
- Paediatric Laboratory Medicine, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8 Canada
| | - Eric Bouffet
- Division of Hematology/Oncology, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8 Canada
- Department of Pediatrics, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8 Canada
| | - Uri Tabori
- Genetics and Genome Biology Program, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
- Division of Hematology/Oncology, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8 Canada
- Department of Pediatrics, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8 Canada
| | - Richard Gilbertson
- Department of Oncology, Cambridge Cancer Center, Robinson Way, Cambridge, CB2 0RE England
| | - Jonathan L. Finlay
- Neuro-Oncology Program, Nationwide Children’s Hospital and The Ohio State University, 700 Children’s Dr, Columbus, OH 43205 USA
| | - Nada Jabado
- Division of Hematology/Oncology, Montreal Children’s Hospital of the McGill University Health Centre (RI-MUHC), 1001 Decarie Blvd, Montreal, Québec, H4A 3 J1 Canada
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, 48149 Münster, Germany
| | - Martin Sill
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - David Capper
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Charitéplatz 1, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, Invalidenstrasse 80, 10117, Berlin, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, 48149 Münster, Germany
| | - David Malkin
- Genetics and Genome Biology Program, Hospital for Sick Children, PGCRL, 686 Bay Street, Toronto, Ontario M5G 0A4 Canada
- Division of Hematology/Oncology, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8 Canada
- Department of Pediatrics, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8 Canada
- Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower, MaRS Centre, 101 College Street, Toronto, Ontario M5G 1 L7 Canada
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Farhana L, Banerjee HN, Verma M, Majumdar APN. Role of Microbiome in Carcinogenesis Process and Epigenetic Regulation of Colorectal Cancer. Methods Mol Biol 2018; 1856:35-55. [PMID: 30178245 DOI: 10.1007/978-1-4939-8751-1_3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Epigenetic changes during the development of colorectal cancer (CRC) play a significant role. Along with factors such as diet, lifestyle, and genetics, oncogenic infection, bacteria alone or whole microbiome, has been associated with this tumor type. How gut microbiome contributes to CRC pathogenesis in the host is not fully understood. Most of the epigenetic studies in CRC have been conducted in populations infected with Helicobacter pylori. In the current review, we summarize how the gut microbiota contributes in colon carcinogenesis and the potential role of epigenetic mechanism in gene regulation. We discuss microbiota-mediated initiation and progression of colon tumorigenesis and have also touched upon the role of microbial metabolites as an initiator or an inhibitor for procarcinogenic or antioncogenic activities. The hypothesis of gut microbiota associated CRC revealed the dynamic and complexity of microbial interaction in initiating the development of CRC. In the multifaceted processes of colonic carcinogenesis, gradual alteration of microbiota along with their microenvironment and the potential oncopathogenic microbes mediated modulation of cancer therapy and other factors involved in microbiome dysbiosis leading to the CRC have also been discussed. This review provides a comprehensive summary of the mechanisms of CRC development, the role of microbiome or single bacterial infection in regulating the processes of carcinogenesis, and the intervention by novel therapeutics. Epigenetic mechanism involved in CRC is also discussed.
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Affiliation(s)
- Lulu Farhana
- Veterans Affairs Medical Center, Research Service, Detroit, MI, USA
- Department of Internal Medicine, Wayne State University, Detroit, MI, USA
| | | | - Mukesh Verma
- Epidemiology and Genomics Research Program, National Cancer Institute, Rockville, MD, USA
| | - Adhip P N Majumdar
- Veterans Affairs Medical Center, Research Service, Detroit, MI, USA.
- Department of Internal Medicine, Wayne State University, Detroit, MI, USA.
- Karmanos Cancer Institute, Wayne State University-School of Medicine, Detroit, MI, USA.
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The role of primary tumour sidedness, EGFR gene copy number and EGFR promoter methylation in RAS/BRAF wild-type colorectal cancer patients receiving irinotecan/cetuximab. Br J Cancer 2017. [PMID: 28632725 PMCID: PMC5537494 DOI: 10.1038/bjc.2017.178] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The data from randomised trials suggested that primary tumour sidedness could represent a prognostic and predictive factor in colorectal cancer (CRC) patients, particularly during treatment with anti-epidermal growth factor receptor (EGFR) therapy. However, an in-deep molecular selection might overcome the predictive role of primary tumour location in this setting. METHODS We conducted a retrospective analysis in which tumour samples from RAS/BRAF wild-type (WT) metastatic CRC patients treated with second-third-line irinotecan/cetuximab were analysed for EGFR gene copy number (GCN) and promoter methylation. Study objective was to evaluate the correlation of tumour sidedness, EGFR promoter methylation and EGFR GCN with clinical outcome. Median follow-up duration was 14.3 months. RESULTS Eighty-eight patients were included in the study, 27.3% had right-sided CRC, 72.7% had left-sided CRC; 36.4% had EGFR GCN<2.12 tumour, 63.6% had EGFR GCN⩾2.12 tumour; 50% had EGFR promoter-methylated tumour. Right-sided colorectal cancer (RSCRC) were associated with reduced overall response rate (ORR) (4.2% for RSCRC vs 35.9% for left sided colorectal cancer (LSCRC), P=0.0030), shorter progression-free survival (PFS) (3.0 vs 6.75 months, P<0.0001) and shorter overall survival (OS) (8 vs 13.6 months, P<0.0001). EGFR GCN<2.12 tumours were associated with reduced ORR (6.2% for EGFR GCN<2.12 vs 39.3% for EGFR GCN⩾2.12 tumours, P=0.0009), shorter PFS (3.5 vs 6.5 months, P=0.0006) and shorter OS (8.5 vs 14.0 months, P<0.0001). Epidermal growth factor receptor-methylated tumours were associated with reduced ORR (9.1% for methylated vs 45.5% for unmethylated, P=0.0001), shorter PFS (3 vs 7.67 months, P<0.0001) and shorter OS (8 vs 17 months, P<0.0001). At multivariate analysis, EGFR GCN and EGFR promoter methylation maintained their independent role for ORR (respectively P=0.0082 and 0.0025), PFS (respectively P=0.0048 and<0.0001) and OS (respectively P=0.0001 and<0.0001). CONCLUSIONS In our study, an accurate molecular selection based on an all RAS and BRAF analysis along with EGFR GCN and EGFR promoter methylation status seems to be more relevant than primary tumour sidedness in the prediction of clinical outcome during cetuximab/irinotecan therapy. However, these data need to be validated with future prospective and translational studies.
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