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Deyneko IV. BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function. Int J Mol Sci 2024; 25:1903. [PMID: 38339181 PMCID: PMC10856692 DOI: 10.3390/ijms25031903] [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: 12/01/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
The concept of cis-regulatory modules located in gene promoters represents today's vision of the organization of gene transcriptional regulation. Such modules are a combination of two or more single, short DNA motifs. The bioinformatic identification of such modules belongs to so-called NP-hard problems with extreme computational complexity, and therefore, simplifications, assumptions, and heuristics are usually deployed to tackle the problem. In practice, this requires, first, many parameters to be set before the search, and second, it leads to the identification of locally optimal results. Here, a novel method is presented, aimed at identifying the cis-regulatory elements in gene promoters based on an exhaustive search of all the feasible modules' configurations. All required parameters are automatically estimated using positive and negative datasets. To be computationally efficient, the search is accelerated using a multidimensional hash function, allowing the search to complete in a few hours on a regular laptop (for example, a CPU Intel i7, 3.2 GH, 32 Gb RAM). Tests on an established benchmark and real data show better performance of BestCRM compared to the available methods according to several metrics like specificity, sensitivity, AUC, etc. A great practical advantage of the method is its minimum number of input parameters-apart from positive and negative promoters, only a desired level of module presence in promoters is required.
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Affiliation(s)
- Igor V Deyneko
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya Str., Moscow 127276, Russia
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Deyneko IV. Guidelines on the performance evaluation of motif recognition methods in bioinformatics. Front Genet 2023; 14:1135320. [PMID: 36824436 PMCID: PMC9941176 DOI: 10.3389/fgene.2023.1135320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023] Open
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Engineering the gut microbiota to treat chronic diseases. Appl Microbiol Biotechnol 2020; 104:7657-7671. [PMID: 32696297 PMCID: PMC7484268 DOI: 10.1007/s00253-020-10771-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/18/2020] [Accepted: 07/02/2020] [Indexed: 12/21/2022]
Abstract
Gut microbes play vital roles in host health and disease. A number of commensal bacteria have been used as vectors for genetic engineering to create living therapeutics. This review highlights recent advances in engineering gut bacteria for the treatment of chronic diseases such as metabolic diseases, cancer, inflammatory bowel diseases, and autoimmune disorders. KEY POINTS: • Bacterial homing to tumors has been exploited to deliver therapeutics in mice models. • Engineered bacteria show promise in mouse models of metabolic diseases. • Few engineered bacterial treatments have advanced to clinical studies.
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Mansour M, Ismail S, Abou-Aisha K. Bacterial delivery of the anti-tumor azurin-like protein Laz to glioblastoma cells. AMB Express 2020; 10:59. [PMID: 32221741 PMCID: PMC7099546 DOI: 10.1186/s13568-020-00995-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/18/2020] [Indexed: 02/02/2023] Open
Abstract
Salmonella typhimurium VNP-20009 (VNP) is a non-pathogenic attenuated strain, which, as a facultative anaerobe, preferentially accumulates in hypoxic regions of solid tumors. Here, VNP was utilized as a delivery vehicle of the anti-tumor protein Lipidated azurin, Laz, which is produced by the meningitis-causing bacterium Neisseria meningitides. In brain cancer cells, Laz has been demonstrated to induce apoptosis through an interaction with the tumor suppressor protein p53. In this study, the laz gene, including its signal sequence, was cloned downstream of a hypoxia inducible promoter (HIP-1), before being electroporated into VNP. Successful ectopic expression and export of the Laz protein by VNP under hypoxic conditions were confirmed by Western blot analysis of the cell-free culture medium. Effective expression of Laz by VNP was investigated in two glioblastoma cell lines: LN-229 and U-373, with the latter line carrying a mutated version of p53; as well as in the breast cancer line MCF-7. Cytotoxicity of the VNP-Laz was assessed by determining the fluorescence of the apoptotic marker caspases 3/7. Compared to the purified Laz, VNP-Laz, significantly induced apoptosis in MCF-7, LN-229 and, to a much lower extent in U-373 cells, suggesting a p53-linked mechanism. Our results might represent a new approach of targeted gene delivery and suggest a potential application in brain tumor therapy.
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Affiliation(s)
- Manar Mansour
- Department of Microbiology and Immunology, The German University in Cairo (GUC), Main Entrance Fifth Settlement, Cairo, Egypt.
| | - Shehab Ismail
- The Cancer Research Institute CRUK Beatson Institute, Glasgow, UK
| | - Khaled Abou-Aisha
- Department of Microbiology and Immunology, The German University in Cairo (GUC), Main Entrance Fifth Settlement, Cairo, Egypt
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Abstract
The engineering of living cells and microbes is ushering in a new era of cancer therapy. Due to recent microbiome studies indicating the prevalence of bacteria within the human body and specifically in tumor tissue, bacteria have generated significant interest as potential targets for cancer therapy. Notably, a multitude of empirical studies over the past decades have demonstrated that administered bacteria home and grow in tumors due to reduced immune surveillance of tumor necrotic cores. Given their specificity for tumors, bacteria present a unique opportunity to be engineered as intelligent delivery vehicles for cancer therapy with synthetic biology techniques. In this review, we discuss the history, current state, and future challenges associated with using bacteria as a cancer therapy.
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Hekmatshoar Y, Rahbar Saadat Y, Hosseiniyan Khatibi SM, Ozkan T, Zununi Vahed F, Nariman-Saleh-Fam Z, Pourghassem Gargari B, Sunguroglu A, Zununi Vahed S. The impact of tumor and gut microbiotas on cancer therapy: Beneficial or detrimental? Life Sci 2019; 233:116680. [PMID: 31344431 DOI: 10.1016/j.lfs.2019.116680] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/15/2019] [Accepted: 07/21/2019] [Indexed: 12/18/2022]
Abstract
Cancer is a globally challenging health problem threatening mankind. Despite therapeutic advances in dealing with this malignancy, heterogeneous response and resistance to chemotherapeutic agents remain the hallmarks of cancer therapy. On the other hand, the involvement of the microbiota in affecting human health is well defined. An ever-growing body of evidence implicates the potential link between the microbiome and the efficacy of cancer therapies. Gut microbiota can modulate the metabolism of drugs in a number of ways. The presence of bacteria within the tumor environment can also impact the responses to cancer therapies; changing the chemical structure of chemotherapeutic drugs, affecting their activity, and local concentration. However, the underlying mechanisms by which gut and tumor microbial communities affect the response to cancer therapy are poorly understood and deciphering these mechanisms is of paramount importance. This review provides an overview of how gut and tumor microbiota might affect the efficacy of chemotherapy, radiotherapy, and immunotherapy and alleviate the adverse side effects of these therapies for the development of personalized and effective anticancer therapy.
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Affiliation(s)
- Yalda Hekmatshoar
- Department of Medical Biology, School of Medicine, Ankara University, Ankara, Turkey
| | - Yalda Rahbar Saadat
- Nutrition Research Center, Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Mahdi Hosseiniyan Khatibi
- International Rice Research Institute (IRRI), Los Banos, Philippines; Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tulin Ozkan
- Department of Medical Biology, School of Medicine, Ankara University, Ankara, Turkey
| | | | - Ziba Nariman-Saleh-Fam
- Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahram Pourghassem Gargari
- Nutrition Research Center, Department of Biochemistry and Diet Therapy, Faculty of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Asuman Sunguroglu
- Department of Medical Biology, School of Medicine, Ankara University, Ankara, Turkey
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Chien T, Doshi A, Danino T. Advances in bacterial cancer therapies using synthetic biology. CURRENT OPINION IN SYSTEMS BIOLOGY 2017; 5:1-8. [PMID: 29881788 PMCID: PMC5986102 DOI: 10.1016/j.coisb.2017.05.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Synthetic biology aims to apply engineering principles to biology by modulating the behavior of living organisms. An emerging application of this field is the engineering of bacteria as a cancer therapy by the programming of therapeutic, safety, and specificity features through genetic modification. Here, we review progress in this engineering including the targeting of bacteria to tumors, specific sensing and response to tumor microenvironments, remote induction methods, and controllable release of therapeutics. We discuss the most prominent bacteria strains used and their specific properties and the types of therapeutics tested thus far. Finally, we note current challenges, such as genetic stability, that researchers must address for successful clinical implementation of this novel therapy in humans.
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Affiliation(s)
- Tiffany Chien
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Anjali Doshi
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
- Data Science Institute, Columbia University, New York, NY 10027, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10027, USA
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Bashiardes S, Tuganbaev T, Federici S, Elinav E. The microbiome in anti-cancer therapy. Semin Immunol 2017; 32:74-81. [PMID: 28431920 DOI: 10.1016/j.smim.2017.04.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/21/2017] [Accepted: 04/05/2017] [Indexed: 02/07/2023]
Abstract
The commensal microbiome constitutes an important modulator of host physiology and risk of disease, including cancer development and progression. Lately, the microbiome has been suggested to modulate the efficacy of anti-cancer treatment. Examples include chemotherapy and total body irradiation-induced barrier function disruption, leading to microbial efflux that drives activation of anti-tumorigenic T cells; Microbiome-driven release of reactive oxygen species contributing to the efficacy of platinum salts; and microbiome-induced immune priming promoting the anti-tumor effects of alkylating chemotherapy and immune checkpoint inhibitors. Furthermore, selected commensals are able to colonize solid tumors. This 'tumor microbiome' may further impact local tumor responses to treatment and potentially be harnessed for tumor-specific targeting and therapeutic delivery. In this review, we present recent advances in understanding of the intricate role of microbiome in modulating efficacy of a number of anti-cancer treatments, and discuss how anti-cancer treatment approaches utilizing the tumor microbiome may enhance oncological treatment efficacy.
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Affiliation(s)
- Stavros Bashiardes
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Timur Tuganbaev
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Sara Federici
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel.
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