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Trepka KR, Kidder WA, Kyaw TS, Olson CA, Upadhyay V, Noecker C, Stanfield D, Steiding P, Spanogiannopoulos P, Dumlao D, Turnbaugh JA, Stachler MD, Van Blarigan EL, Venook AP, Atreya CE, Turnbaugh PJ. Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597471. [PMID: 38895199 PMCID: PMC11185696 DOI: 10.1101/2024.06.04.597471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Herein, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal study of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. 16S rRNA gene and metagenomic sequencing revealed significant shifts in gut microbial community structure during treatment with oral fluoropyrimidines, which was validated in an independent cohort. Gene abundance was also markedly changed by oral fluoropyrimidines, including an enrichment for the preTA operon, which is sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). Higher levels of preTA led to increased 5-FU depletion by the gut microbiota grown ex vivo. Germ-free and antibiotic-treated mice had increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA+ E. coli, or CRC patient stool with high preTA levels. preTA abundance was negatively associated with patient toxicities. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach is generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.
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Affiliation(s)
- Kai R. Trepka
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Wesley A. Kidder
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Than S. Kyaw
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Christine A. Olson
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Vaibhav Upadhyay
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Cecilia Noecker
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Dalila Stanfield
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Paige Steiding
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Peter Spanogiannopoulos
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Darren Dumlao
- Department of Gastroenterology, University of California San Francisco; San Francisco, USA
| | - Jessie A. Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Matthew D. Stachler
- Department of Pathology, University of California San Francisco; San Francisco, USA
| | - Erin L. Van Blarigan
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco; San Francisco, USA
- Department of Urology, University of California San Francisco; San Francisco, USA
| | - Alan P. Venook
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Chloe E. Atreya
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Peter J. Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
- Chan Zuckerberg Biohub-San Francisco; San Francisco, USA
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2
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Loukas AT, Papadourakis M, Panagiotopoulos V, Zarmpala A, Chontzopoulou E, Christodoulou S, Katsila T, Zoumpoulakis P, Matsoukas MT. Natural Compounds for Bone Remodeling: A Computational and Experimental Approach Targeting Bone Metabolism-Related Proteins. Int J Mol Sci 2024; 25:5047. [PMID: 38732267 PMCID: PMC11084538 DOI: 10.3390/ijms25095047] [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: 03/15/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Osteoporosis, characterized by reduced bone density and increased fracture risk, affects over 200 million people worldwide, predominantly older adults and postmenopausal women. The disruption of the balance between bone-forming osteoblasts and bone-resorbing osteoclasts underlies osteoporosis pathophysiology. Standard treatment includes lifestyle modifications, calcium and vitamin D supplementation and specific drugs that either inhibit osteoclasts or stimulate osteoblasts. However, these treatments have limitations, including side effects and compliance issues. Natural products have emerged as potential osteoporosis therapeutics, but their mechanisms of action remain poorly understood. In this study, we investigate the efficacy of natural compounds in modulating molecular targets relevant to osteoporosis, focusing on the Mitogen-Activated Protein Kinase (MAPK) pathway and the gut microbiome's influence on bone homeostasis. Using an in silico and in vitro methodology, we have identified quercetin as a promising candidate in modulating MAPK activity, offering a potential therapeutic perspective for osteoporosis treatment.
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Affiliation(s)
- Alexandros-Timotheos Loukas
- Department of Food Science and Technology, University of West Attica, Ag. Spyridonos, 12243 Egaleo, Greece; (A.-T.L.); (P.Z.)
- Cloudpharm Private Company, Kifissias Avenue 44, 15125 Marousi, Greece; (V.P.); (A.Z.); (E.C.); (S.C.)
| | - Michail Papadourakis
- Cloudpharm Private Company, Kifissias Avenue 44, 15125 Marousi, Greece; (V.P.); (A.Z.); (E.C.); (S.C.)
| | - Vasilis Panagiotopoulos
- Cloudpharm Private Company, Kifissias Avenue 44, 15125 Marousi, Greece; (V.P.); (A.Z.); (E.C.); (S.C.)
- Department of Biomedical Engineering, University of West Attica, Ag. Spyridonos, 12243 Egaleo, Greece
| | - Apostolia Zarmpala
- Cloudpharm Private Company, Kifissias Avenue 44, 15125 Marousi, Greece; (V.P.); (A.Z.); (E.C.); (S.C.)
| | - Eleni Chontzopoulou
- Cloudpharm Private Company, Kifissias Avenue 44, 15125 Marousi, Greece; (V.P.); (A.Z.); (E.C.); (S.C.)
| | - Stephanos Christodoulou
- Cloudpharm Private Company, Kifissias Avenue 44, 15125 Marousi, Greece; (V.P.); (A.Z.); (E.C.); (S.C.)
| | - Theodora Katsila
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece;
| | - Panagiotis Zoumpoulakis
- Department of Food Science and Technology, University of West Attica, Ag. Spyridonos, 12243 Egaleo, Greece; (A.-T.L.); (P.Z.)
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece;
| | - Minos-Timotheos Matsoukas
- Cloudpharm Private Company, Kifissias Avenue 44, 15125 Marousi, Greece; (V.P.); (A.Z.); (E.C.); (S.C.)
- Department of Biomedical Engineering, University of West Attica, Ag. Spyridonos, 12243 Egaleo, Greece
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3
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Noto Guillen M, Li C, Rosener B, Mitchell A. Antibacterial activity of nonantibiotics is orthogonal to standard antibiotics. Science 2024; 384:93-100. [PMID: 38484036 DOI: 10.1126/science.adk7368] [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: 09/13/2023] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
Numerous nonantibiotic drugs have potent antibacterial activity and can adversely affect the human microbiome. The mechanistic underpinning of this toxicity remains largely unknown. We investigated the antibacterial activity of 200 drugs using genetic screens with thousands of barcoded Escherichia coli knockouts. We analyzed 2 million gene-drug interactions underlying drug-specific toxicity. Network-based analysis of drug-drug similarities revealed that antibiotics clustered into modules that are consistent with the mode of action of their established classes, whereas nonantibiotics remained unconnected. Half of the nonantibiotics clustered into separate modules, potentially revealing shared and unexploited targets for new antimicrobials. Analysis of efflux systems revealed that they widely affect antibiotics and nonantibiotics alike, suggesting that the impact of nonantibiotics on antibiotic cross-resistance should be investigated closely in vivo.
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Affiliation(s)
- Mariana Noto Guillen
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Carmen Li
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Brittany Rosener
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Amir Mitchell
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
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4
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Komura T, Aoki M, Nishikawa Y. Feeding on lactic acid bacteria isolated from food extends the lifespan of Caenorhabditis elegans. Lett Appl Microbiol 2024; 77:ovae020. [PMID: 38389250 DOI: 10.1093/lambio/ovae020] [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: 12/07/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 02/24/2024]
Abstract
Lactic acid bacteria (LAB) contribute to human health, and LAB functionality has been studied using Caenorhabditis elegans as an alternative host. However, many studies have focused on the efficacy of a single strain of LAB, and few reports have compared various LAB strains. In this study, we examined the effects of 15 strains of LAB isolated from vegetables, meat, and fermented foods on nematode longevity and healthy lifespan. To reduce the frequency of laborious survival observations, we performed a lifespan assay on agar plates containing 2'-deoxy-5-fluorouridine (FUdR), which inhibits egg hatching and prevents generation mixing. Four beneficial strains showed significant lifespan extension and increased spontaneous nematode mobility, regardless of treatment with or without FUdR and the frequency of survival observation. These results suggested increased longevity and an extended healthy lifespan, confirming the reliability of our method. The four strains are expected to show anti-ageing effects besides longevity and have effects on age-related degenerative diseases. Our labor-saving method can be used as an alternative to conventional methods and enable simultaneous screening of multiple strains. Future research could explore factors contributing to lifespan regulation by comparing and verifying differential strain effects on lifespan.
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Affiliation(s)
- Tomomi Komura
- School of Human Science and Environment, University of Hyogo, Himeji, Hyogo 6700092, Japan
- Research Institute for Food and Nutritional Sciences, University of Hyogo, Himeji, Hyogo 6700092, Japan
| | - Motoshi Aoki
- Central Research Institute, Marudai Food, Co., Ltd, Takatsuki, Osaka 5698577, Japan
| | - Yoshikazu Nishikawa
- Faculty of Food and Nutrition Sciences, Tezukayama Gakuin University, Sakai, Osaka 5900113, Japan
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5
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Boudignon E, Foulquier C, Soucaille P. Improvement of the Genome Editing Tools Based on 5FC/5FU Counter Selection in Clostridium acetobutylicum. Microorganisms 2023; 11:2696. [PMID: 38004708 PMCID: PMC10672894 DOI: 10.3390/microorganisms11112696] [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: 10/04/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Several genetic tools have been developed for genome engineering in Clostridium acetobutylicum utilizing 5-fluorouracil (5FU) or 5-fluorocytosine (5FC) resistance as a selection method. In our group, a method based on the integration, by single crossing over, of a suicide plasmid (pCat-upp) followed by selection for the second crossing over using a counter-selectable marker (the upp gene and 5FU resistance) was recently developed for genome editing in C. acetobutylicum. This method allows genome modification without leaving any marker or scar in a strain of C. acetobutylicum that is ∆upp. Unfortunately, 5FU has strong mutagenic properties, inducing mutations in the strain's genome. After numerous applications of the pCat-upp/5FU system for genome modification in C. acetobutylicum, the CAB1060 mutant strain became entirely resistant to 5FU in the presence of the upp gene, resulting in failure when selecting on 5FU for the second crossing over. It was found that the potential repressor of the pyrimidine operon, PyrR, was mutated at position A115, leading to the 5FU resistance of the strain. To fix this problem, we created a corrective replicative plasmid expressing the pyrR gene, which was shown to restore the 5FU sensitivity of the strain. Furthermore, in order to avoid the occurrence of the problem observed with the CAB1060 strain, a preventive suicide plasmid, pCat-upp-pyrR*, was also developed, featuring the introduction of a synthetic codon-optimized pyrR gene, which was referred to as pyrR* with low nucleotide sequence homology to pyrR. Finally, to minimize the mutagenic effect of 5FU, we also improved the pCat-upp/5FU system by reducing the concentration of 5FU from 1 mM to 5 µM using a defined synthetic medium. The optimized system/conditions were used to successfully replace the ldh gene by the sadh-hydG operon to convert acetone into isopropanol.
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Affiliation(s)
- Eglantine Boudignon
- Toulouse Biotechnology Institute (TBI), National Institute of Applied Sciences (INSA), Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse cedex 4, France; (E.B.); (C.F.)
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAe), UMR 792, 24 chemin de Borde Rouge-Auzeville, 31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique (CNRS), UMR 5504, 16 Avenue Edouard Belin, 31055 Toulouse cedex 4, France
| | - Céline Foulquier
- Toulouse Biotechnology Institute (TBI), National Institute of Applied Sciences (INSA), Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse cedex 4, France; (E.B.); (C.F.)
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAe), UMR 792, 24 chemin de Borde Rouge-Auzeville, 31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique (CNRS), UMR 5504, 16 Avenue Edouard Belin, 31055 Toulouse cedex 4, France
| | - Philippe Soucaille
- Toulouse Biotechnology Institute (TBI), National Institute of Applied Sciences (INSA), Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse cedex 4, France; (E.B.); (C.F.)
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAe), UMR 792, 24 chemin de Borde Rouge-Auzeville, 31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique (CNRS), UMR 5504, 16 Avenue Edouard Belin, 31055 Toulouse cedex 4, France
- (BBSRC)/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
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6
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Yang KB, Cameranesi M, Gowder M, Martinez C, Shamovsky Y, Epshtein V, Hao Z, Nguyen T, Nirenstein E, Shamovsky I, Rasouly A, Nudler E. High-resolution landscape of an antibiotic binding site. Nature 2023; 622:180-187. [PMID: 37648864 PMCID: PMC10550828 DOI: 10.1038/s41586-023-06495-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Antibiotic binding sites are located in important domains of essential enzymes and have been extensively studied in the context of resistance mutations; however, their study is limited by positive selection. Using multiplex genome engineering1 to overcome this constraint, we generate and characterize a collection of 760 single-residue mutants encompassing the entire rifampicin binding site of Escherichia coli RNA polymerase (RNAP). By genetically mapping drug-enzyme interactions, we identify an alpha helix where mutations considerably enhance or disrupt rifampicin binding. We find mutations in this region that prolong antibiotic binding, converting rifampicin from a bacteriostatic to bactericidal drug by inducing lethal DNA breaks. The latter are replication dependent, indicating that rifampicin kills by causing detrimental transcription-replication conflicts at promoters. We also identify additional binding site mutations that greatly increase the speed of RNAP.Fast RNAP depletes the cell of nucleotides, alters cell sensitivity to different antibiotics and provides a cold growth advantage. Finally, by mapping natural rpoB sequence diversity, we discover that functional rifampicin binding site mutations that alter RNAP properties or confer drug resistance occur frequently in nature.
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Affiliation(s)
- Kevin B Yang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Maria Cameranesi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Manjunath Gowder
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Criseyda Martinez
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Yosef Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Vitaliy Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Thao Nguyen
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Eric Nirenstein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Aviram Rasouly
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
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7
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Sayin S, Mitchell A. Functional Assay for Measuring Bacterial Degradation of Gemcitabine Chemotherapy. Bio Protoc 2023; 13:e4797. [PMID: 37719072 PMCID: PMC10501921 DOI: 10.21769/bioprotoc.4797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 09/19/2023] Open
Abstract
Drug biotransformation by the host microbiome can impact the therapeutic success of treatment. In the context of cancer, drug degradation can take place within the microenvironment of the targeted tumor by intratumor bacteria. In pancreatic cancer, increased chemo-resistance against the frontline chemotherapy gemcitabine is thought to arise from drug degradation by the tumor microbiome. This bacterial-drug interaction highlights the need for developing rapid assays for monitoring bacterial gemcitabine breakdown. While chemical approaches such as high-performance liquid chromatography are suitable for this task, they require specialized equipment and expertise and are limited in throughput. Functional cell-based assays represent an alternate approach for performing this task. We developed a functional assay to monitor the rate of bacterial gemcitabine breakdown using a highly sensitive bacterial reporter strain. Our method relies on standard laboratory equipment and can be implemented at high throughput to monitor drug breakdown by hundreds of strains simultaneously. This functional assay can be readily adapted to monitor degradation of other drugs. Key features Quantification of gemcitabine breakdown by incubating bacteria that degrades the drug and subsequently testing the growth of a reporter strain on filtered supernatant. Use of an optimized reporter strain that was genetically engineered to be a non-degrader strain and highly sensitive to gemcitabine. A high-throughput assay performed in microplates that can be adjusted for identifying bacteria with a fast or slow gemcitabine degradation rate. The assay results can be compared to results from a standard curve with known drug concentrations to quantify degradation rate.
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Affiliation(s)
- Serkan Sayin
- Department of Systems Biology, University of Massachusetts Chan
Medical School, Worcester, MA, USA
| | - Amir Mitchell
- Department of Systems Biology, University of Massachusetts Chan
Medical School, Worcester, MA, USA
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8
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Algavi YM, Borenstein E. A data-driven approach for predicting the impact of drugs on the human microbiome. Nat Commun 2023; 14:3614. [PMID: 37330560 PMCID: PMC10276880 DOI: 10.1038/s41467-023-39264-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/02/2023] [Indexed: 06/19/2023] Open
Abstract
Many medications can negatively impact the bacteria residing in our gut, depleting beneficial species, and causing adverse effects. To guide personalized pharmaceutical treatment, a comprehensive understanding of the impact of various drugs on the gut microbiome is needed, yet, to date, experimentally challenging to obtain. Towards this end, we develop a data-driven approach, integrating information about the chemical properties of each drug and the genomic content of each microbe, to systematically predict drug-microbiome interactions. We show that this framework successfully predicts outcomes of in-vitro pairwise drug-microbe experiments, as well as drug-induced microbiome dysbiosis in both animal models and clinical trials. Applying this methodology, we systematically map a large array of interactions between pharmaceuticals and human gut bacteria and demonstrate that medications' anti-microbial properties are tightly linked to their adverse effects. This computational framework has the potential to unlock the development of personalized medicine and microbiome-based therapeutic approaches, improving outcomes and minimizing side effects.
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Affiliation(s)
- Yadid M Algavi
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
- Santa Fe Institute, Santa Fe, NM, USA.
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9
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Sayin S, Rosener B, Li CG, Ho B, Ponomarova O, Ward DV, Walhout AJM, Mitchell A. Evolved bacterial resistance to the chemotherapy gemcitabine modulates its efficacy in co-cultured cancer cells. eLife 2023; 12:83140. [PMID: 36734518 PMCID: PMC9931390 DOI: 10.7554/elife.83140] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
Drug metabolism by the microbiome can influence anticancer treatment success. We previously suggested that chemotherapies with antimicrobial activity can select for adaptations in bacterial drug metabolism that can inadvertently influence the host's chemoresistance. We demonstrated that evolved resistance against fluoropyrimidine chemotherapy lowered its efficacy in worms feeding on drug-evolved bacteria (Rosener et al., 2020). Here, we examine a model system that captures local interactions that can occur in the tumor microenvironment. Gammaproteobacteria-colonizing pancreatic tumors can degrade the nucleoside-analog chemotherapy gemcitabine and, in doing so, can increase the tumor's chemoresistance. Using a genetic screen in Escherichia coli, we mapped all loss-of-function mutations conferring gemcitabine resistance. Surprisingly, we infer that one third of top resistance mutations increase or decrease bacterial drug breakdown and therefore can either lower or raise the gemcitabine load in the local environment. Experiments in three E. coli strains revealed that evolved adaptation converged to inactivation of the nucleoside permease NupC, an adaptation that increased the drug burden on co-cultured cancer cells. The two studies provide complementary insights on the potential impact of microbiome adaptation to chemotherapy by showing that bacteria-drug interactions can have local and systemic influence on drug activity.
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Affiliation(s)
- Serkan Sayin
- Department of Systems Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Brittany Rosener
- Department of Systems Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Carmen G Li
- Department of Systems Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Bao Ho
- Department of Systems Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Olga Ponomarova
- Department of Systems Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Doyle V Ward
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Program in Microbiome Dynamics, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Albertha JM Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Amir Mitchell
- Department of Systems Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Program in Microbiome Dynamics, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
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10
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LaCourse KD, Zepeda-Rivera M, Kempchinsky AG, Baryiames A, Minot SS, Johnston CD, Bullman S. The cancer chemotherapeutic 5-fluorouracil is a potent Fusobacterium nucleatum inhibitor and its activity is modified by intratumoral microbiota. Cell Rep 2022; 41:111625. [PMID: 36384132 PMCID: PMC10790632 DOI: 10.1016/j.celrep.2022.111625] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/26/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022] Open
Abstract
Fusobacterium nucleatum (Fn) is a dominant bacterial species in colorectal cancer (CRC) tissue that is associated with cancer progression and poorer patient prognosis. Following a small-molecule inhibitor screen of 1,846 bioactive compounds against a Fn CRC isolate, we find that 15% of inhibitors are antineoplastic agents including fluoropyrimidines. Validation of these findings reveals that 5-fluorouracil (5-FU), a first-line CRC chemotherapeutic, is a potent inhibitor of Fn CRC isolates. We also identify members of the intratumoral microbiota, including Escherichia coli, that are resistant to 5-FU. Further, CRC E. coli isolates can modify 5-FU and relieve 5-FU toxicity toward otherwise-sensitive Fn and human CRC epithelial cells. Lastly, we demonstrate that ex vivo patient CRC tumor microbiota undergo community disruption after 5-FU exposure and have the potential to deplete 5-FU levels, reducing local drug efficacy. Together, these observations argue for further investigation into the role of the CRC intratumoral microbiota in patient response to chemotherapy.
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Affiliation(s)
- Kaitlyn D LaCourse
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Martha Zepeda-Rivera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Andrew G Kempchinsky
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Alexander Baryiames
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Samuel S Minot
- Data Core, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Christopher D Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA.
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA.
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11
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Spanogiannopoulos P, Kyaw TS, Guthrie BGH, Bradley PH, Lee JV, Melamed J, Malig YNA, Lam KN, Gempis D, Sandy M, Kidder W, Van Blarigan EL, Atreya CE, Venook A, Gerona RR, Goga A, Pollard KS, Turnbaugh PJ. Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism. Nat Microbiol 2022; 7:1605-1620. [PMID: 36138165 PMCID: PMC9530025 DOI: 10.1038/s41564-022-01226-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
Pharmaceuticals have extensive reciprocal interactions with the microbiome, but whether bacterial drug sensitivity and metabolism is driven by pathways conserved in host cells remains unclear. Here we show that anti-cancer fluoropyrimidine drugs inhibit the growth of gut bacterial strains from 6 phyla. In both Escherichia coli and mammalian cells, fluoropyrimidines disrupt pyrimidine metabolism. Proteobacteria and Firmicutes metabolized 5-fluorouracil to its inactive metabolite dihydrofluorouracil, mimicking the major host mechanism for drug clearance. The preTA operon was necessary and sufficient for 5-fluorouracil inactivation by E. coli, exhibited high catalytic efficiency for the reductive reaction, decreased the bioavailability and efficacy of oral fluoropyrimidine treatment in mice and was prevalent in the gut microbiomes of colorectal cancer patients. The conservation of both the targets and enzymes for metabolism of therapeutics across domains highlights the need to distinguish the relative contributions of human and microbial cells to drug efficacy and side-effect profiles.
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Affiliation(s)
- Peter Spanogiannopoulos
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Than S Kyaw
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Ben G H Guthrie
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Patrick H Bradley
- Gladstone Institutes, San Francisco, CA, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Joyce V Lee
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Melamed
- Clinical Toxicology and Environmental Biomonitoring Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Ysabella Noelle Amora Malig
- Clinical Toxicology and Environmental Biomonitoring Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Kathy N Lam
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Daryll Gempis
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Moriah Sandy
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wesley Kidder
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Erin L Van Blarigan
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Chloe E Atreya
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Alan Venook
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Roy R Gerona
- Clinical Toxicology and Environmental Biomonitoring Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Andrei Goga
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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12
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Bacterial diet modulates tamoxifen-induced death via host fatty acid metabolism. Nat Commun 2022; 13:5595. [PMID: 36151093 PMCID: PMC9508336 DOI: 10.1038/s41467-022-33299-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 09/06/2022] [Indexed: 11/18/2022] Open
Abstract
Tamoxifen is a selective estrogen receptor (ER) modulator that is used to treat ER-positive breast cancer, but that at high doses kills both ER-positive and ER-negative breast cancer cells. We recapitulate this off-target effect in Caenorhabditis elegans, which does not have an ER ortholog. We find that different bacteria dramatically modulate tamoxifen toxicity in C. elegans, with a three-order of magnitude difference between animals fed Escherichia coli, Comamonas aquatica, and Bacillus subtilis. Remarkably, host fatty acid (FA) biosynthesis mitigates tamoxifen toxicity, and different bacteria provide the animal with different FAs, resulting in distinct FA profiles. Surprisingly these bacteria modulate tamoxifen toxicity by different death mechanisms, some of which are modulated by FA supplementation and others by antioxidants. Together, this work reveals a complex interplay between microbiota, FA metabolism and tamoxifen toxicity that may provide a blueprint for similar studies in more complex mammals. Here, Diot et al. use the nematode Caenorhabditis elegans as a model to identify off-target toxicity mechanisms for tamoxifen, and find that these include fatty acid metabolism and cell death, which can be modulated by different bacterial species.
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13
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Parisutham V, Chhabra S, Ali MZ, Brewster RC. Tunable transcription factor library for robust quantification of regulatory properties in Escherichia coli. Mol Syst Biol 2022; 18:e10843. [PMID: 35694815 PMCID: PMC9189660 DOI: 10.15252/msb.202110843] [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: 11/30/2021] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/12/2022] Open
Abstract
Predicting the quantitative regulatory function of transcription factors (TFs) based on factors such as binding sequence, binding location, and promoter type is not possible. The interconnected nature of gene networks and the difficulty in tuning individual TF concentrations make the isolated study of TF function challenging. Here, we present a library of Escherichia coli strains designed to allow for precise control of the concentration of individual TFs enabling the study of the role of TF concentration on physiology and regulation. We demonstrate the usefulness of this resource by measuring the regulatory function of the zinc‐responsive TF, ZntR, and the paralogous TF pair, GalR/GalS. For ZntR, we find that zinc alters ZntR regulatory function in a way that enables activation of the regulated gene to be robust with respect to ZntR concentration. For GalR and GalS, we are able to demonstrate that these paralogous TFs have fundamentally distinct regulatory roles beyond differences in binding affinity.
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Affiliation(s)
- Vinuselvi Parisutham
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Shivani Chhabra
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Md Zulfikar Ali
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Robert C Brewster
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
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14
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Leigh SJ, Lynch CMK, Bird BRH, Griffin BT, Cryan JF, Clarke G. Gut microbiota-drug interactions in cancer pharmacotherapies: implications for efficacy and adverse effects. Expert Opin Drug Metab Toxicol 2022; 18:5-26. [PMID: 35176217 DOI: 10.1080/17425255.2022.2043849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The gut microbiota is involved in host physiology and health. Reciprocal microbiota-drug interactions are increasingly recognized as underlying some individual differences in therapy response and adverse events. Cancer pharmacotherapies are characterized by a high degree of interpatient variability in efficacy and side effect profile and recently, the microbiota has emerged as a factor that may underlie these differences. AREAS COVERED The effects of cancer pharmacotherapy on microbiota composition and function are reviewed with consideration of the relationship between baseline microbiota composition, microbiota modification, antibiotics exposure and cancer therapy efficacy. We assess the evidence implicating the microbiota in cancer therapy-related adverse events including impaired gut function, cognition and pain perception. Finally, potential mechanisms underlying microbiota-cancer drug interactions are described, including direct microbial metabolism, and microbial modulation of liver metabolism and immune function. This review focused on preclinical and clinical studies conducted in the last 5 years. EXPERT OPINION Preclinical and clinical research supports a role for baseline microbiota in cancer therapy efficacy, with emerging evidence that the microbiota modification may assist in side effect management. Future efforts should focus on exploiting this knowledge towards the development of microbiota-targeted therapies. Finally, a focus on specific drug-microbiota-cancer interactions is warranted.
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Affiliation(s)
| | | | | | | | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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15
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Noto Guillen M, Rosener B, Sayin S, Mitchell A. Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods. Cell Syst 2021; 12:1064-1078.e7. [PMID: 34469744 PMCID: PMC8602757 DOI: 10.1016/j.cels.2021.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/18/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022]
Abstract
Metabolic cross-feeding frequently underlies mutualistic relationships in natural microbial communities and is often exploited to assemble synthetic microbial consortia. We systematically identified all single-gene knockouts suitable for imposing cross-feeding in Escherichia coli and used this information to assemble syntrophic communities. Most strains benefiting from shared goods were dysfunctional in biosynthesis of amino acids, nucleotides, and vitamins or mutants in central carbon metabolism. We tested cross-feeding potency in 1,444 strain pairs and mapped the interaction network between all functional groups of mutants. This network revealed that auxotrophs for vitamins are optimal cooperators. Lastly, we monitored how assemblies composed of dozens of auxotrophs change over time and observed that they rapidly and repeatedly coalesced to seven strain consortia composed primarily from vitamin auxotrophs. The composition of emerging consortia suggests that they were stabilized by multiple cross-feeding interactions. We conclude that vitamins are ideal shared goods since they optimize consortium growth while still imposing member co-dependence.
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Affiliation(s)
- Mariana Noto Guillen
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Brittany Rosener
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Serkan Sayin
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Amir Mitchell
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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16
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Takeda Y, Chijimatsu R, Vecchione A, Arai T, Kitagawa T, Ofusa K, Yabumoto M, Hirotsu T, Eguchi H, Doki Y, Ishii H. Impact of One-Carbon Metabolism-Driving Epitranscriptome as a Therapeutic Target for Gastrointestinal Cancer. Int J Mol Sci 2021; 22:ijms22147278. [PMID: 34298902 PMCID: PMC8306097 DOI: 10.3390/ijms22147278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/22/2022] Open
Abstract
One-carbon (1C) metabolism plays a key role in biological functions linked to the folate cycle. These include nucleotide synthesis; the methylation of DNA, RNA, and proteins in the methionine cycle; and transsulfuration to maintain the redox condition of cancer stem cells in the tumor microenvironment. Recent studies have indicated that small therapeutic compounds affect the mitochondrial folate cycle, epitranscriptome (RNA methylation), and reactive oxygen species reactions in cancer cells. The epitranscriptome controls cellular biochemical reactions, but is also a platform for cell-to-cell interaction and cell transformation. We present an update of recent advances in the study of 1C metabolism related to cancer and demonstrate the areas where further research is needed. We also discuss approaches to therapeutic drug discovery using animal models and propose further steps toward developing precision cancer medicine.
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Affiliation(s)
- Yu Takeda
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (Y.T.); (R.C.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.)
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan; (H.E.); (Y.D.)
| | - Ryota Chijimatsu
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (Y.T.); (R.C.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.)
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, University of Rome “Sapienza”, Santo Andrea Hospital, Via di Grottarossa, 1035-00189 Rome, Italy;
| | - Takahiro Arai
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (Y.T.); (R.C.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.)
- Unitech Co., Ltd., Kashiwa 277-0005, Japan
| | - Toru Kitagawa
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (Y.T.); (R.C.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.)
- Kyowa-kai Medical Corporation, Osaka 540-0008, Japan
| | - Ken Ofusa
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (Y.T.); (R.C.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.)
- Food and Life-Science Laboratory, Prophoenix Division, Idea Consultants, Inc., Osaka 559-8519, Japan
| | - Masami Yabumoto
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (Y.T.); (R.C.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.)
- Kinshu-kai Medical Corporation, Osaka 558-0041, Japan
| | - Takaaki Hirotsu
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (Y.T.); (R.C.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.)
- Hirotsu Bio Science Inc., Tokyo 107-0062, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan; (H.E.); (Y.D.)
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan; (H.E.); (Y.D.)
| | - Hideshi Ishii
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Yamadaoka 2-2, Osaka 565-0871, Japan; (Y.T.); (R.C.); (T.A.); (T.K.); (K.O.); (M.Y.); (T.H.)
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan; (H.E.); (Y.D.)
- Correspondence: ; Tel.: +81-(0)6-6210-8406 (ext. 8405); Fax: +81-(0)6-6210-8407
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