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Feng Y, Yuan Q, Newsome RC, Robinson T, Bowman RL, Zuniga AN, Hall KN, Bernsten CM, Shabashvili DE, Krajcik KI, Gunaratne C, Zaroogian ZJ, Venugopal K, Casellas Roman HL, Levine RL, Chatila WK, Yaeger R, Riva A, Jobin C, Kopinke D, Avram D, Guryanova OA. Hematopoietic-specific heterozygous loss of Dnmt3a exacerbates colitis-associated colon cancer. J Exp Med 2023; 220:e20230011. [PMID: 37615936 PMCID: PMC10450614 DOI: 10.1084/jem.20230011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/12/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023] Open
Abstract
Clonal hematopoiesis (CH) is defined as clonal expansion of mutant hematopoietic stem cells absent diagnosis of a hematologic malignancy. Presence of CH in solid tumor patients, including colon cancer, correlates with shorter survival. We hypothesized that bone marrow-derived cells with heterozygous loss-of-function mutations of DNMT3A, the most common genetic alteration in CH, contribute to the pathogenesis of colon cancer. In a mouse model that combines colitis-associated colon cancer (CAC) with experimental CH driven by Dnmt3a+/Δ, we found higher tumor penetrance and increased tumor burden compared with controls. Histopathological analysis revealed accentuated colonic epithelium injury, dysplasia, and adenocarcinoma formation. Transcriptome profiling of colon tumors identified enrichment of gene signatures associated with carcinogenesis, including angiogenesis. Treatment with the angiogenesis inhibitor axitinib eliminated the colon tumor-promoting effect of experimental CH driven by Dnmt3a haploinsufficiency and rebalanced hematopoiesis. This study provides conceptually novel insights into non-tumor-cell-autonomous effects of hematopoietic alterations on colon carcinogenesis and identifies potential therapeutic strategies.
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Affiliation(s)
- Yang Feng
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Qingchen Yuan
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Rachel C. Newsome
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Troy Robinson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert L. Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ashley N. Zuniga
- Department of Anatomy and Cell Biology, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kendra N. Hall
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Cassandra M. Bernsten
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Daniil E. Shabashvili
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kathryn I. Krajcik
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Chamara Gunaratne
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Zachary J. Zaroogian
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kartika Venugopal
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Heidi L. Casellas Roman
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K. Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| | - Christian Jobin
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| | - Daniel Kopinke
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Dorina Avram
- Department of Anatomy and Cell Biology, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
- Immunology Department, Moffitt Cancer Center, Tampa, FL, USA
| | - Olga A. Guryanova
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
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Newsome RC, Oh J, Jian W, Gharaibeh RZ, Crawford J, Jobin C. Abstract 1825: A bacterial consortium engineered from feces of patients responding to anti-PD1 treatment mediates tumor response through IFNγ in non-small cell lung cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-1825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Introduction: We previously showed that non-small cell lung cancer (NSCLC) patients that respond (R) to immune checkpoint blockade (ICB) have a different microbial community structure than non-responders (NR) pre-treatment (Genome Med 2022). Importantly, we showed that pooled R microbiota transplantation into gnotobiotic xenograft mice decreased tumor growth compared to NR colonized mice following anti-PD1 therapy, a phenomenon associated with enrichment of the Bacteroides genus. However, the bacterial strains driving this synergistic effect with anti-PD1 therapy and mechanism of action are unknown.
Method: Feces collected from R mice were used as source material for high-throughput microbial isolation performed with the GALT Prospector technology. Bacterial identification was performed with MALDI-TOF Biotyper and Sanger sequencing. The cell free supernatants and under 3 kDa small molecules of 183 Bacteroides isolates were screened for their ability to stimulate IFNγ production by primary CD8+ T cells by flow cytometry. A consortium composed of 6 IFNγ-stimulating isolates or NR feces was transplanted into a gnotobiotic mouse model of lung cancer treated with anti-PD1, with or without anti-IFNγ monoclonal antibody depletion. Tumors were harvested at endpoint for flow cytometric analysis, and blood serum for IFNγ ELISA. Bioactivity-guided fractionation coupled with LC-MS analysis was used to identify small molecules from the cell free supernatant of a single stimulating Bacteroides isolate. Potential bioactive small molecule characterization was performed using LC-MS/MS supported by computational pipelines for structural prediction followed by NMR for structural confirmation.
Results: We cultured and identified 679 isolates from 30 unique species. The cell free supernatant from 6 out of 183 Bacteroides isolates stimulated IFNγ production from primary CD8+ T cells. Small molecules from the six stimulatory isolates’ supernatants significantly induced IFNγ production compared to 6 taxonomy-matched non-stimulatory isolates (P=0.039). A defined consortium composed of the six stimulatory isolates (R-consortium) was able to colonize germ free mice, and decreased tumor growth compared to NR feces-colonized mice (P=0.041). IFNγ depletion of R-consortium mice significantly increased tumor growth (P=0.012) compared to non-depleted mice. Intratumor IFNγ+ CD8+ T cell frequency and circulating serum IFNγ was elevated only in R-consortium mice. Bioassay guided fractionation revealed 5 small molecule metabolites produced by Bacteroides and their structure and bioactivity are currently being investigated.
Conclusion: A microbial consortium engineered from R patients’ feces synergizes with anti-PD1 therapy to reduce lung cancer growth through an IFNγ-dependent mechanism which may be mediated by small molecule metabolites.
Citation Format: Rachel C. Newsome, Joonseok Oh, Wenya Jian, Raad Z. Gharaibeh, Jason Crawford, Christian Jobin. A bacterial consortium engineered from feces of patients responding to anti-PD1 treatment mediates tumor response through IFNγ in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1825.
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Yu Q, Newsome RC, Beveridge M, Hernandez MC, Gharaibeh RZ, Jobin C, Thomas RM. Intestinal microbiota modulates pancreatic carcinogenesis through intratumoral natural killer cells. Gut Microbes 2022; 14:2112881. [PMID: 35980869 PMCID: PMC9397420 DOI: 10.1080/19490976.2022.2112881] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Preclinical data demonstrate that the gut microbiota can promote pancreatic ductal adenocarcinoma (PDAC), but mechanisms remain unclear. We hypothesized that intestinal microbiota alters anti-tumor innate immunity response to facilitate PDAC progression. Human PDAC L3.6pl cells were heterotopically implanted into Rag1-/- mice after microbiota depletion with antibiotics, while syngeneic murine PDAC Pan02 cells were implanted intrapancreatic into germ-free (GF) C57BL/6 J mice. Natural killer (NK) cells and their IFNγ expression were quantitated by flow cytometry. NK cells were depleted in vivo using anti-Asialo GM1 antibody to confirm the role of NK cells. Bacteria-free supernatant from SPF and GF mice feces was used to test its effect on NK-92MI cell anti-tumor response in vitro. SPF and ex-GF mice (reconstituted with SPF microbiota) developed larger PDAC tumors with decreased NK cell tumor infiltration and IFNγ expression versus GF-Rag1-/-. Microbiota-induced PDAC tumorigenesis was attenuated by antibiotic exposure, a process reversed following NK cell depletion in both Rag1-/- and C57BL/6 J mice. Compared to GF, SPF-Rag1-/- abiotic stool culture supernatant inhibited NK-92MI cytotoxicity, migration, and anti-cancer related gene expression. Gut microbiota promotes PDAC tumor progression through modulation of the intratumoral infiltration and activity of NK cells.
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Affiliation(s)
- Qin Yu
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Rachel C. Newsome
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Mark Beveridge
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Maria C. Hernandez
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Raad Z. Gharaibeh
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Christian Jobin
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA,Department of Infectious Diseases and Immunology, University of Florida College of Medicine, Gainesville, Florida, USA,Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA,Christian Jobin Department of Medicine, University of Florida, 2033 Mowry Rd, 461, Gainesville, Florida32610, USA
| | - Ryan M. Thomas
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida, USA,Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA,CONTACT Ryan M. Thomas Department of Surgery, University of Florida, PO Box 100109, Gainesville, Florida32610, USA
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Newsome RC, Yang Y, Jobin C. The microbiome, gastrointestinal cancer, and immunotherapy. J Gastroenterol Hepatol 2022; 37:263-272. [PMID: 34820895 PMCID: PMC9922516 DOI: 10.1111/jgh.15742] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022]
Abstract
The gastrointestinal tract greatly contributes to global cancer burden and cancer-related deaths. The microbiota represents the population of microorganisms that live in and around the body, located primarily in the gastrointestinal tract. The microbiota has been implicated in colorectal cancer development and progression, but its role in cancer therapy for the gastrointestinal tract is less defined, especially for extra-intestinal cancers. In this review, we discuss the past 5 years of research into microbial involvement in immune-related therapies for colorectal, pancreatic, hepatic, and gastric cancers, with the goal of highlighting recent advances and new areas for investigation in this field.
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Affiliation(s)
- Rachel C Newsome
- Departments of Medicine, University of Florida, Gainesville, Florida, USA
| | - Ye Yang
- Departments of Medicine, University of Florida, Gainesville, Florida, USA
| | - Christian Jobin
- Departments of Medicine, University of Florida, Gainesville, Florida, USA
- Infectious Diseases and Immunology, University of Florida, Gainesville, Florida, USA
- Anatomy and Cell Biology, University of Florida, Gainesville, Florida, USA
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5
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Newsome RC, Gauthier J, Hernandez MC, Abraham GE, Robinson TO, Williams HB, Sloan M, Owings A, Laird H, Christian T, Pride Y, Wilson KJ, Hasan M, Parker A, Senitko M, Glover SC, Gharaibeh RZ, Jobin C. The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort. Gut Microbes 2021; 13:1-15. [PMID: 34100340 PMCID: PMC8205023 DOI: 10.1080/19490976.2021.1926840] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/06/2021] [Accepted: 04/22/2021] [Indexed: 02/04/2023] Open
Abstract
To investigate the relationship between intestinal microbiota and SARS-CoV-2-mediated pathogenicity in a United States, majority African American cohort. We prospectively collected fecal samples from 50 SARS-CoV-2 infected patients, 9 SARS-CoV-2 recovered patients, and 34 uninfected subjects seen by the hospital with unrelated respiratory medical conditions (controls). 16S rRNA sequencing and qPCR analysis was performed on fecal DNA/RNA. The fecal microbial composition was found to be significantly different between SARS-CoV-2 patients and controls (PERMANOVA FDR-P = .004), independent of antibiotic exposure. Peptoniphilus, Corynebacterium and Campylobacter were identified as the three most significantly enriched genera in COVID-19 patients compared to controls. Actively infected patients were also found to have a different gut microbiota than recovered patients (PERMANOVA FDR-P = .003), and the most enriched genus in infected patients was Campylobacter, with Agathobacter and Faecalibacterium being enriched in the recovered patients. No difference in microbial community structure between recovered patients and uninfected controls was observed, nor a difference in alpha diversity between the three groups. 24 of the 50 COVID-19 patients (48%) tested positive via RT-qPCR for fecal SARS-CoV-2 RNA. A significant difference in gut microbial composition between SARS-CoV-2 positive and negative samples was observed, with Klebsiella and Agathobacter being enriched in the positive cohort. No significant associations between microbiome composition and disease severity was found. The intestinal microbiota is sensitive to the presence of SARS-CoV-2, with increased relative abundance of genera (Campylobacter, Klebsiella) associated with gastrointestinal (GI) disease. Further studies are needed to investigate the functional impact of SARS-CoV-2 on GI health.
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Affiliation(s)
- Rachel C. Newsome
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Josee Gauthier
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Maria C. Hernandez
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - George E. Abraham
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Tanya O. Robinson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Haley B. Williams
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Meredith Sloan
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Anna Owings
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Hannah Laird
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Taylor Christian
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yilianys Pride
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Kenneth J. Wilson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Mohammad Hasan
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Adam Parker
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Michal Senitko
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sarah C. Glover
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Raad Z. Gharaibeh
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Christian Jobin
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Infectious Diseases and Immunology, University of Florida College of Veterinary Medicine, Gainesville, FL, USA
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
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Affiliation(s)
| | - Christian Jobin
- Department of Medicine.,Department of Infectious Diseases and Pathology.,Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL, 32611, USA
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Murthy HS, Gharaibeh RZ, Al-Mansour Z, Kozlov A, Trikha G, Newsome RC, Gauthier J, Farhadfar N, Wang Y, Kelly DL, Lybarger J, Jobin C, Wang GP, Wingard JR. Baseline Gut Microbiota Composition Is Associated with Major Infections Early after Hematopoietic Cell Transplantation. Biol Blood Marrow Transplant 2020; 26:2001-2010. [PMID: 32717434 DOI: 10.1016/j.bbmt.2020.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/17/2020] [Accepted: 07/19/2020] [Indexed: 01/03/2023]
Abstract
Infection is a major cause of morbidity and mortality after hematopoietic cell transplantation (HCT). Gut microbiota (GM) composition and metabolites provide colonization resistance against dominance of potential pathogens, and GM dysbiosis following HCT can be deleterious to immune reconstitution. Little is known about the composition, diversity, and evolution of GM communities in HCT patients and their association with subsequent febrile neutropenia (FN) and infection. Identification of markers before HCT that predict subsequent infection could be useful in developing individualized antimicrobial strategies. Fecal samples were collected prospectively from 33 HCT recipients at serial time points: baseline, post-conditioning regimen, neutropenia onset, FN onset (if present), and hematologic recovery. GM was assessed by 16S rRNA sequencing. FN and major infections (ie, bloodstream infection, typhlitis, invasive fungal infection, pneumonia, and Clostridium difficile enterocolitis) were identified. Significant shifts in GM composition and diversity were observed during HCT, with the largest alterations occurring after initiation of antibiotics. Loss of diversity persisted without a return to baseline at hematologic recovery. GM in patients with FN was enriched in Mogibacterium, Bacteroides fragilis, and Parabacteroides distasonis, whereas increased abundance of Prevotella, Ruminococcus, Dorea, Blautia, and Collinsella was observed in patients without fever. A baseline protective GM profile (BPGMP) was predictive of protection from major infection. The BPGMP was associated with subsequent major infections with 77% accuracy and an area under the curve of 79%, with sensitivity, specificity, and positive and negative predictive values of 0.71, 0.91, 0.77, and 0.87, respectively. Our data show that large shifts in GM composition occur early after HCT, and differences in baseline GM composition are associated with the development of subsequent major infections.
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Affiliation(s)
- Hemant S Murthy
- Division of Hematology/Oncology, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida; UF Health Cancer Center, Gainesville, Florida
| | - Raad Z Gharaibeh
- UF Health Cancer Center, Gainesville, Florida; Division of Gastroenterology, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Zeina Al-Mansour
- Division of Hematology/Oncology, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida; UF Health Cancer Center, Gainesville, Florida
| | - Andrew Kozlov
- Division of Infectious Disease and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Gaurav Trikha
- Division of Hematology/Oncology, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Rachel C Newsome
- Division of Gastroenterology, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Josee Gauthier
- Division of Gastroenterology, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Nosha Farhadfar
- Division of Hematology/Oncology, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida; UF Health Cancer Center, Gainesville, Florida
| | - Yu Wang
- Division of Quantitative Sciences And Biostatistics, University of Florida Health Cancer Center, Gainesville, Florida
| | - Debra Lynch Kelly
- UF Health Cancer Center, Gainesville, Florida; College of Nursing, University of Florida, Gainesville, Florida
| | - John Lybarger
- Division of Hematology/Oncology, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Christian Jobin
- UF Health Cancer Center, Gainesville, Florida; Division of Gastroenterology, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Gary P Wang
- Division of Infectious Disease and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - John R Wingard
- Division of Hematology/Oncology, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida; UF Health Cancer Center, Gainesville, Florida.
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Yang Y, Gharaibeh RZ, Newsome RC, Jobin C. Amending microbiota by targeting intestinal inflammation with TNF blockade attenuates development of colorectal cancer. Nat Cancer 2020; 1:723-734. [PMID: 33768208 PMCID: PMC7990316 DOI: 10.1038/s43018-020-0078-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 05/14/2020] [Indexed: 12/15/2022]
Abstract
Intestinal inflammation and microbiota are two important components of colorectal cancer (CRC) etiology. However, it is not clear how tuning inflammation using clinically relevant anti-inflammatory treatment impacts microbiota or whether this consequently influences CRC outcome. Here, using chemically induced (DSS/Apc min/+) and spontaneous (Apc min/+ ;Il10 -/-) mouse CRC models colonized by colibactin-producing Escherichia coli, we established the role of microbiota in mediating the antitumorigenic effect of anti-tumor necrosis factor (TNF) therapy. We found that TNF blockade attenuated colitis and CRC development. Microbiota community structure and gene activities significantly changed with disease development, which was prevented by TNF blockade. Several microbiota functional pathways underwent similar changes in patients following anti-TNF therapy. Under cohousing condition, TNF blockade failed to prevent colitis, cancer development and disease-associated microbiota structural changes. Finally, microbiota transplantation showed reduced carcinogenic activity of microbiota from anti-TNF-treated mice. Together, our data demonstrate the plasticity of microbiota, which could be reverted to noncarcinogenic status by targeting inflammation.
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Affiliation(s)
- Ye Yang
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Rachel C Newsome
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL, USA.
- Deptartment of Infectious Diseases and Immunology, University of Florida, Gainesville, FL, USA.
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Tomkovich S, Gharaibeh RZ, Dejea CM, Pope JL, Jiang J, Winglee K, Gauthier J, Newsome RC, Yang Y, Fodor AA, Schmittgen TD, Sears CL, Jobin C. Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer. mSystems 2020; 5:e00451-19. [PMID: 31937674 PMCID: PMC6967385 DOI: 10.1128/msystems.00451-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/21/2019] [Indexed: 01/09/2023] Open
Abstract
Disrupted interactions between host and intestinal bacteria are implicated in colorectal cancer (CRC) development. However, activities derived from these bacteria and their interplay with the host are unclear. Here, we examine this interplay by performing mouse and microbiota RNA sequencing on colon tissues and 16S and small RNA sequencing on stools from germfree (GF) and gnotobiotic ApcMin Δ 850/+ ;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BF+T) and biofilm-negative healthy (BF-bx) tissues. The bacteria in BF+T mice differentially expressed (DE) >2,900 genes, including genes related to bacterial secretion, virulence, and biofilms but affected only 62 host genes. Small RNA sequencing of stools from these cohorts revealed eight significant DE host microRNAs (miRNAs) based on biofilm status and several miRNAs that correlated with bacterial taxon abundances. Additionally, computational predictions suggest that some miRNAs preferentially target bacterial genes while others primarily target mouse genes. 16S rRNA sequencing of mice that were reassociated with mucosa-associated communities from the initial association revealed a set of 13 bacterial genera associated with cancer that were maintained regardless of whether the reassociation inoculums were initially obtained from murine proximal or distal colon tissues. Our findings suggest that complex interactions within bacterial communities affect host-derived miRNA, bacterial composition, and CRC development.IMPORTANCE Bacteria and bacterial biofilms have been implicated in colorectal cancer (CRC), but it is still unclear what genes these microbial communities express and how they influence the host. MicroRNAs regulate host gene expression and have been explored as potential biomarkers for CRC. An emerging area of research is the ability of microRNAs to impact growth and gene expression of members of the intestinal microbiota. This study examined the bacteria and bacterial transcriptome associated with microbes derived from biofilm-positive human cancers that promoted tumorigenesis in a murine model of CRC. The murine response to different microbial communities (derived from CRC patients or healthy people) was evaluated through RNA and microRNA sequencing. We identified a complex interplay between biofilm-associated bacteria and the host during CRC in mice. These findings may lead to the development of new biomarkers and therapeutics for identifying and treating biofilm-associated CRCs.
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Affiliation(s)
- Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Christine M Dejea
- Bloomberg-Kimmel Institute of Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- Department of Oncology and Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jillian L Pope
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jinmai Jiang
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Kathryn Winglee
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Josee Gauthier
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Rachel C Newsome
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Ye Yang
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Thomas D Schmittgen
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Cynthia L Sears
- Bloomberg-Kimmel Institute of Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- Department of Oncology and Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida, USA
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, Florida, USA
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Pope JL, Yang Y, Newsome RC, Sun W, Sun X, Ukhanova M, Neu J, Issa JP, Mai V, Jobin C. Microbial Colonization Coordinates the Pathogenesis of a Klebsiella pneumoniae Infant Isolate. Sci Rep 2019; 9:3380. [PMID: 30833613 PMCID: PMC6399262 DOI: 10.1038/s41598-019-39887-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/28/2019] [Indexed: 12/22/2022] Open
Abstract
Enterobacteriaceae are among the first colonizers of neonate intestine. Members of this family, such as Escherichia and Klebsiella, are considered pathobionts and as such are capable of inducing local and systemic disease under specific colonization circumstances. Interplay between developing microbiota and pathogenic function of pathobionts are poorly understood. In this study, we investigate the functional interaction between various colonization patterns on an early colonizer, K. pneumoniae. K. pneumoniae 51-5 was isolated from stool of a healthy, premature infant, and found to contain the genotoxin island pks associated with development of colorectal cancer. Using intestinal epithelial cells, macrophages, and primary splenocytes, we demonstrate K. pneumoniae 51-5 upregulates expression of proinflammatory genes in vitro. Gnotobiotic experiments in Il10-/- mice demonstrate the neonate isolate induces intestinal inflammation in vivo, with increased expression of proinflammatory genes. Regulation of microbiota assembly revealed K. pneumoniae 51-5 accelerates onset of inflammation in Il10-/- mice, most significantly when microbiota is naturally acquired. Furthermore, K. pneumoniae 51-5 induces DNA damage and cell cycle arrest. Interestingly, K. pneumoniae 51-5 induced tumors in ApcMin/+; Il10-/- mice was not significantly affected by absence of colibactin activating enzyme, ClbP. These findings demonstrate pathogenicity of infant K. pneumoniae isolate is sensitive to microbial colonization status.
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Affiliation(s)
- Jillian L Pope
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Ye Yang
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Rachel C Newsome
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Wei Sun
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Department of Immunology & Microbial Disease, Albany Medical College, Albany, New York, USA
| | - Xiaolun Sun
- Department of Medicine, University of Florida, Gainesville, Florida, USA
- Department of Poultry Science, University of Arkanasas, Fayetteville, Arkansas, USA
| | - Maria Ukhanova
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
| | - Josef Neu
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jean-Pierre Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA, 19140, USA
| | - Volker Mai
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida, USA.
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida, USA.
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He Z, Gharaibeh RZ, Newsome RC, Pope JL, Dougherty MW, Tomkovich S, Pons B, Mirey G, Vignard J, Hendrixson DR, Jobin C. Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin. Gut 2019; 68:289-300. [PMID: 30377189 PMCID: PMC6352414 DOI: 10.1136/gutjnl-2018-317200] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/12/2018] [Accepted: 10/04/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Campylobacter jejuni produces a genotoxin, cytolethal distending toxin (CDT), which has DNAse activity and causes DNA double-strand breaks. Although C. jejuni infection has been shown to promote intestinal inflammation, the impact of this bacterium on carcinogenesis has never been examined. DESIGN Germ-free (GF) ApcMin/+ mice, fed with 1% dextran sulfate sodium, were used to test tumorigenesis potential of CDT-producing C. jejuni. Cells and enteroids were exposed to bacterial lysates to determine DNA damage capacity via γH2AX immunofluorescence, comet assay and cell cycle assay. To examine the interplay of CDT-producing C. jejuni, gut microbiome and host in tumorigenesis, colonic RNA-sequencing and faecal 16S rDNA sequencing were performed. Rapamycin was administrated to investigate the prevention of CDT-producing C. jejuni-induced tumorigenesis. RESULTS GF ApcMin/+ mice colonised with human clinical isolate C. jejuni81-176 developed significantly more and larger tumours when compared with uninfected mice. C. jejuni with a mutated cdtB subunit, mutcdtB, attenuated C. jejuni-induced tumorigenesis in vivo and decreased DNA damage response in cells and enteroids. C. jejuni infection induced expression of hundreds of colonic genes, with 22 genes dependent on the presence of cdtB. The C. jejuni-infected group had a significantly different microbial gene expression profile compared with the mutcdtB group as shown by metatranscriptomic data, and different microbial communities as measured by 16S rDNA sequencing. Finally, rapamycin could diminish the tumorigenic capability of C. jejuni. CONCLUSION Human clinical isolate C. jejuni 81-176 promotes colorectal cancer and induces changes in microbial composition and transcriptomic responses, a process dependent on CDT production.
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Affiliation(s)
- Zhen He
- Department of Medicine, University of Florida, Gainesville, Florida, USA,Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Rachel C Newsome
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jllian L Pope
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | | | - Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Benoit Pons
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP- Purpan, UPS, Toulouse, France
| | - Gladys Mirey
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP- Purpan, UPS, Toulouse, France
| | - Julien Vignard
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP- Purpan, UPS, Toulouse, France
| | - David R Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida, USA,Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida, USA,Department of Infectious Diseases and Immunology, University of Florida, Gainesville, Florida, USA
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Mousa JJ, Newsome RC, Yang Y, Jobin C, Bruner SD. ClbM is a versatile, cation-promiscuous MATE transporter found in the colibactin biosynthetic gene cluster. Biochem Biophys Res Commun 2016; 482:1233-1239. [PMID: 27939886 DOI: 10.1016/j.bbrc.2016.12.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/02/2016] [Indexed: 11/30/2022]
Abstract
Multidrug transporters play key roles in cellular drug resistance to toxic molecules, yet these transporters are also involved in natural product transport as part of biosynthetic clusters in bacteria and fungi. The genotoxic molecule colibactin is produced by strains of virulent and pathobiont Escherichia coli and Klebsiella pneumoniae. In the biosynthetic cluster is a multidrug and toxic compound extrusion protein (MATE) proposed to transport the prodrug molecule precolibactin across the cytoplasmic membrane, for subsequent cleavage by the peptidase ClbP and cellular export. We recently determined the X-ray structure of ClbM, and showed preliminary data suggesting its specific role in precolibactin transport. Here, we define a functional role of ClbM by examining transport capabilities under various biochemical conditions. Our data indicate ClbM responds to sodium, potassium, and rubidium ion gradients, while also having substantial transport activity in the absence of alkali cations.
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Affiliation(s)
- Jarrod J Mousa
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Rachel C Newsome
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Ye Yang
- Department of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
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