AI-DRIVEN METAGENOMIC ANALYSIS TO UNCOVER MICROBIAL INFLUENCES ON CANCER DEVELOPMENT
Keywords:
AI-driven metagenomics, cancer microbiome, microbial biomarkers, precision oncology, personalized medicineAbstract
Artificial intelligence (AI)-driven metagenomic analysis is revolutionizing our understanding of the microbial influences on cancer development. The human microbiome, particularly the gut microbiota, plays a pivotal role in modulating immune responses, inflammation, and metabolic pathways, all of which are crucial in cancer initiation and progression. Advances in metagenomic sequencing, combined with AI techniques such as machine learning and deep learning, have facilitated the identification of microbial biomarkers and survival subtypes across diverse cancer types. These approaches provide insights into microbiome-immune interactions and their impact on treatment outcomes, including chemotherapy and immunotherapy efficacy. Despite the transformative potential, challenges persist, such as dataset complexity, biases, and the interpretability of AI models. Addressing these issues through explainable AI and diversified databases will enhance clinical integration and precision oncology. This article highlights the role of AI in unlocking the complex interplay between the microbiome and cancer, paving the way for innovative diagnostics, personalized therapies, and improved patient outcomes.
References
1. AI in Healthcare: Applications, Challenges, and Future Prospects. (2024). https://doi.org/10.48047/resmil.v10i1.18
2. Arsela Prelaj, Veronika Mišković, M. Zanitti, F. Trovò, C. Genova, Giuseppe Viscardi, S.E. Rebuzzi, Laura Mazzeo, L. Provenzano, S. Kosta, M. Favali, Andrea Spagnoletti, Louis Castelo-Branco, J. Dolezal, A.T. Pearson, G. Lo Russo, Claudia Proto, Monica Ganzinelli, C. Giani, … Alessandro Pedrocchi. (2023). Artificial Intelligence for predictive biomarker discovery in immuno-oncology: A systematic review. Annals of Oncology. https://doi.org/10.1016/j.annonc.2023.10.125
3. Artificial Intelligence in Cancer Research: Predictive Modeling of Angiogenesis and Biomarker Discovery. (2024). Journal of Angiotherapy. https://doi.org/10.25163/angiotherapy.889975
4. Artificial Intelligence in Oncology: Current Capabilities, Future Opportunities, and Ethical Considerations. (2022). American Society of Clinical Oncology Educational Book, 42, 842–851. https://doi.org/10.1200/edbk_350652
5. Carlos S. Casimiro-Soriguer, Carlos Loucera, Maria Peña-Chilet, & Joaquín Dopazo. (2022). Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer. Dental Science Reports, 12(1). https://doi.org/10.1038/s41598-021-04182-y
6. Danishuddin, Shawez Khan, & Jong Joo Kim. (2023). From cancer big data to treatment: Artificial intelligence in cancer research. Journal of Gene Medicine, e3629–e3629. https://doi.org/10.1002/jgm.3629
7. Gao, B., Jiang, Y., Han, M., Ji, X., Zhang, D., Gao, X., Huang, S., Zhao, C., Su, Y., Yang, S., Zhang, X., Liu, N., Han, L., Wang, L., Ren, L., Yang, J., Wu, J., Yuan, Y., & Dai, P. (2024). Targeted Linked-Read Sequencing for Direct Haplotype Phasing of Parental GJB2/SLC26A4 / SLC26A4 Alleles. JOURNAL OF MOLECULAR DIAGNOSTICS, 26(7), 638–651. https://doi.org/10.1016/j.jmoldx.2024.04.002
8. Georgios Papoutsoglou, Sonia Tarazona, Marta B. Lopes, Thomas Klammsteiner, Eliana Ibrahimi, Julia Eckenberger, Pierfrancesco Novielli, Alberto Tonda, Andrea Simeon, Rajesh Shigdel, Stéphane Béreux, Giacomo Vitali, Sabina Tangaro, Leo Lahti, A. Temko, Marcus J. Claesson, & Magali Berland. (2023). Machine learning approaches in microbiome research: Challenges and best practices. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2023.1261889
9. Ghufran Ahmed & Shahid Hussain. (2023). A Survey on Cancer Molecular Subtype Classification using Deep learning. 1–5. https://doi.org/10.1109/iCoMET57998.2023.10099055
10. Haohong Zhang, Xinghao Xiong, Mingyue Cheng, Lei Ji, & Kang Ning. (2024). Deep learning enabled integration of tumor microenvironment microbial profiles and host gene expressions for interpretable survival subtyping in diverse types of cancers. MSystems, e0139524–e0139524. https://doi.org/10.1128/msystems.01395-24
11. Huriye Armağan Doğan. (2023). Human interpretable artificial intelligence applications for microbial-related diseases. https://doi.org/10.51415/10321/4701
12. İlhami KİZİROĞLU. (2023). Artificial Intelligence Application to Microbiomics Data for Improved Clinical Decision Making in Precision Oncology (pp. 157–177). https://doi.org/10.1007/978-3-031-21506-3_8
13. Istuti Saraswat & Anjana Goel. (2024). Therapeutic Modulation of the Microbiome in Oncology: Current Trends and Future Directions. Current Pharmaceutical Biotechnology, 26. https://doi.org/10.2174/0113892010353600241109132441
14. Ivania Valdés, Alberto Martin, Eduardo Martínez, Daniel Carvajal Hausdorf, & Erick Riquelme. (2024). Abstract 1280: Role of the tumor microbiome in the lung adenocarcinoma immune microenvironment through multi meta-omics analysis. Cancer Research. https://doi.org/10.1158/1538-7445.am2024-1280
15. J. Keyl, Philipp Keyl, Grégoire Montavon, René Hosch, Alexandra Brehmer, Liliana Mochmann, Philipp Jurmeister, Gabriel Dernbach, Moon Kim, Sven Koitka, Sebastian Bauer, Nikolaos Bechrakis, Michael Forsting, -. DagmarFührer, Sakel, Martin Glas, Viktor Grünwald, Boris Hadaschik, Johannes, … Jens Kleesiek. (2023). Decoding pan-cancer treatment outcomes using multimodal real-world data and explainable artificial intelligence. medRxiv. https://doi.org/10.1101/2023.10.12.23296873
16. Jiuxin Qu & Shimin Shuai. (2023). Pan-cancer analysis reveals tumor microbiome associations with host molecular aberrations. bioRxiv. https://doi.org/10.1101/2023.04.13.536730
17. Liu, Y., Yoshizawa, A. C., Ling, Y., & Okuda, S. (2024). Insights into predicting small molecule retention times in liquid chromatography using deep learning. Journal of Cheminformatics, 16(1), 113. https://doi.org/10.1186/s13321-024-00905-1
18. Machine Learning on Microbiome Research in Gastrointestinal Cancer (pp. 193–200). (2023). https://doi.org/10.1007/978-981-19-4492-5_13
19. Md. Fakruddin, Md. Asaduzzaman Shishir, Israk Iram Oyshe, S.M. Tasbir Amin, Amana Hossain, Israt Jahan Sarna, Nusrat Jerin, & Dipak Kumar Mitra. (2023). Microbial Architects of Malignancy: Exploring the Gut Microbiome’s Influence in Cancer Initiation and Progression. Cancer Plus. https://doi.org/10.18063/cp.397
20. Microbiomes, Their Function, and Cancer: How Metatranscriptomics Can Close the Knowledge Gap. (2023). International Journal of Molecular Sciences. https://doi.org/10.3390/ijms241813786
21. Miodrag Cekikj, Milena Jakimovska Özdemir, Slobodan Kalajdzhiski, Orhan Özcan, & Ugur Sezerman. (2022). Understanding the Role of the Microbiome in Cancer Diagnostics and Therapeutics by Creating and Utilizing ML Models. Applied Sciences, 12(9), 4094–4094. https://doi.org/10.3390/app12094094
22. Natascha Brandhorst. (2022). The microbiome and precision oncology: An emerging paradigm in anticancer therapy. Critical Reviews In Microbiology, 48(6), 770–783. https://doi.org/10.1080/1040841x.2022.2035313
23. Nick Ting, Harry Cheuk Hay Lau, & Jun Yu. (2022). Cancer pharmacomicrobiomics: Targeting microbiota to optimise cancer therapy outcomes. Gut, 71(7), 1412–1425. https://doi.org/10.1136/gutjnl-2021-326264
24. Pan-Cancer Analysis of Microbiome Quantitative Trait Loci. (2022). Cancer Research, 82(19), 3449–3456. https://doi.org/10.1158/0008-5472.can-22-1854
25. Ryza Rynazal. (2023). Leveraging explainable AI for gut microbiome-based colorectal cancer classification. https://doi.org/10.52843/cassyni.pm26b6
26. Saksham Garg, Nikita Sharma, Bharmjeet, & Asmita Das. (2023). Unraveling the intricate relationship: Influence of microbiome on the host immune system in carcinogenesis. Cancer Reports, e1892–e1892. https://doi.org/10.1002/cnr2.1892
27. Sona Ciernikova, Aneta Sevcikova, Beata Mladosievicova, & Michal Mego. (2023). Microbiome in Cancer Development and Treatment. Microorganisms. https://doi.org/10.3390/microorganisms12010024
28. Tamizhini Loganathan & George Priya Doss C. (2022). The influence of machine learning technologies in gut microbiome research and cancer studies—A review. Life Sciences, 311 Pt A, 121118–121118. https://doi.org/10.1016/j.lfs.2022.121118
29. Teng Wang, Nan Wang, Haohong Zhang, Yuguo Zha, Yuwen Chu, & Kang Ning. (2023). Artificial intelligence-enabled microbiome-based diagnosis models for a broad spectrum of cancer types. Briefings in Bioinformatics, 24(3). https://doi.org/10.1093/bib/bbad178
30. Tewabe Edmew Worku. (2023). DeepGeni: Deep generalized interpretable autoencoder elucidates gut microbiota for better cancer immunotherapy. Dental Science Reports, 13(1). https://doi.org/10.1038/s41598-023-31210-w
31. Veeksha V Shetty & Shilpa S. Shetty. (2024). Exploring the gut microbiome and head and neck cancer interplay. Pathology Research and Practice, 263, 155603–155603. https://doi.org/10.1016/j.prp.2024.155603
32. Xifeng Wu, Wenyuan Li, & Huakang Tu. (2023). Big data and artificial intelligence in cancer research. Trends in Cancer. https://doi.org/10.1016/j.trecan.2023.10.006
33. Yuan-Gu Wei, Meiyan Gao, Jun Xiao, Chi-Hung Liu, Yupeng Tian, & Yaru He. (2023). Research and Implementation of Cancer Gene Data Classification Based on Deep Learning. Journal of Software Engineering and Applications, 16(06), 155–169. https://doi.org/10.4236/jsea.2023.166009
34. Zahraa Rahal, Yuejiang Liu, Fuduan Peng, Matthew Ross, Ansam Sinjab, Ke Liang, Jiping Feng, Chidera O. Chukwuocha, Manvi Sharma, Elizabeth L. Tang, Camille Abaya, Joseph Petrosino, Junya Fujimoto, Seyed Javad Moghaddam, Linghua Wang, Kristi L Hoffman, & Humam Kadara. (2023). 1330 Gut microbiome dysbiosis promotes immune suppression and lung cancer development. https://doi.org/10.1136/jitc-2023-sitc2023.1330
35. Zhou Chen, Defeng Guan, Zheng Wang, Xin Liu, Shi-Zhen Dong, Junjun Huang, & Wence Zhou. (2023). Microbiota in cancer: Molecular mechanisms and therapeutic interventions. MedComm, 4. https://doi.org/10.1002/mco2.417
36. Zsuzsánna Réthi‐Nagy & Szilvia Juhász. (2024). Microbiome’s Universe: Impact on health, disease and cancer treatment. Journal of Biotechnology. https://doi.org/10.1016/j.jbiotec.2024.07.002
37. Zuzanna Chilimoniuk, Dominik Dudziński, Aleksandra Borkowska, Aleksandra Chałupnik, Piotr Więsyk, Beata Chilimoniuk, Łukasz Gawłowicz, Filip Grzegorzak, & Katarzyna Stasiak. (2024). Correlation between gut microbiota dysbiosis and colorectal cancer: Review. Quality in Sport, 22, 54326–54326. https://doi.org/10.12775/qs.2024.22.54326
38. Л. Г. Соленова, Н. И. Рыжова, I. A. Antonova, Gennady A. Belitsky, Kirill Kirsanov, & Marianna G. Yakubovskaya. (2024). Features of the microbiota for various malignant neoplasms. Issledovaniâ i Praktika v Medicine, 11(3), 85–102. https://doi.org/10.17709/2410-1893-2024-11-3-7