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Glitza IC, Seo YD, Spencer CN, Wortman JR, Burton EM, Alayli FA, Loo CP, Gautam S, Damania A, Densmore J, Fairchild J, Cabanski CR, Wong MC, Peterson CB, Weiner B, Hicks N, Auniņš JG, McChalicher C, Walsh E, Tetzlaff MT, Hamid O, Ott PA, Boland GM, Sullivan RJ, Grossmann KF, Ajami NJ, LaVallee T, Henn MR, Tawbi HA, Wargo JA. Randomized Placebo-Controlled, Biomarker-Stratified Phase Ib Microbiome Modulation in Melanoma: Impact of Antibiotic Preconditioning on Microbiome and Immunity. Cancer Discov 2024:OF1-OF15. [PMID: 38588588 DOI: 10.1158/2159-8290.cd-24-0066] [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] [Received: 01/12/2024] [Revised: 03/01/2024] [Accepted: 03/12/2024] [Indexed: 04/10/2024]
Abstract
Gut-microbiota modulation shows promise in improving immune-checkpoint blockade (ICB) response; however, precision biomarker-driven, placebo-controlled trials are lacking. We performed a multicenter, randomized placebo-controlled, biomarker-stratified phase I trial in patients with ICB-naïve metastatic melanoma using SER-401, an orally delivered Firmicutes-enriched spore formulation. Fecal microbiota signatures were characterized at baseline; patients were stratified by high versus low Ruminococcaceae abundance prior to randomization to the SER-401 arm (oral vancomycin-preconditioning/SER-401 alone/nivolumab + SER-401), versus the placebo arm [placebo antibiotic/placebo microbiome modulation (PMM)/nivolumab + PMM (NCT03817125)]. Analysis of 14 accrued patients demonstrated that treatment with SER-401 + nivolumab was safe, with an objective response rate of 25% in the SER-401 arm and 67% in the placebo arm (though the study was under-powered related to poor accrual during the COVID-19 pandemic). Translational analyses demonstrated that vancomycin preconditioning was associated with the disruption of the gut microbiota and impaired immunity, with incomplete recovery at ICB administration (particularly in patients with high baseline Ruminococcaceae). These results have important implications for future microbiome modulation trials. SIGNIFICANCE This first-of-its-kind, placebo-controlled, randomized biomarker-driven microbiome modulation trial demonstrated that vancomycin + SER-401 and anti-PD-1 are safe in melanoma patients. Although limited by poor accrual during the pandemic, important insights were gained via translational analyses, suggesting that antibiotic preconditioning and interventional drug dosing regimens should be carefully considered when designing such trials.
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Affiliation(s)
- Isabella C Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yongwoo David Seo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Elizabeth M Burton
- Strategic Translational Research Initiative Development, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Farah A Alayli
- Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Christopher P Loo
- Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Shikha Gautam
- Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Ashish Damania
- Platform for Innovative Microbiome and Translational Research, Moon Shots Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Julie Densmore
- Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Justin Fairchild
- Parker Institute for Cancer Immunotherapy, San Francisco, California
- Portage Biotech, Westport, Connecticut
| | | | - Matthew C Wong
- Platform for Innovative Microbiome and Translational Research, Moon Shots Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christine B Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | | | - Emily Walsh
- Seres Therapeutics, Cambridge, Massachusetts
| | - Michael T Tetzlaff
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Omid Hamid
- Cutaneous Oncology, The Angeles Clinic and Research Institute, A Cedars-Sinai Affiliate, Los Angeles, California
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Genevieve M Boland
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ryan J Sullivan
- Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | | | - Nadim J Ajami
- Platform for Innovative Microbiome and Translational Research, Moon Shots Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Theresa LaVallee
- Parker Institute for Cancer Immunotherapy, San Francisco, California
- Coherus BioSciences, Redwood City, California
| | | | - Hussein A Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Roland CL, Nassif Haddad EF, Keung EZ, Wang WL, Lazar AJ, Lin H, Chelvanambi M, Parra ER, Wani K, Guadagnolo BA, Bishop AJ, Burton EM, Hunt KK, Torres KE, Feig BW, Scally CP, Lewis VO, Bird JE, Ratan R, Araujo D, Zarzour MA, Patel S, Benjamin R, Conley AP, Livingston JA, Ravi V, Tawbi HA, Lin PP, Moon BS, Satcher RL, Mujtaba B, Witt RG, Traweek RS, Cope B, Lazcano R, Wu CC, Zhou X, Mohammad MM, Chu RA, Zhang J, Damania A, Sahasrabhojane P, Tate T, Callahan K, Nguyen S, Ingram D, Morey R, Crosby S, Mathew G, Duncan S, Lima CF, Blay JY, Fridman WH, Shaw K, Wistuba I, Futreal A, Ajami N, Wargo JA, Somaiah N. A randomized, non-comparative phase 2 study of neoadjuvant immune-checkpoint blockade in retroperitoneal dedifferentiated liposarcoma and extremity/truncal undifferentiated pleomorphic sarcoma. Nat Cancer 2024; 5:625-641. [PMID: 38351182 DOI: 10.1038/s43018-024-00726-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/10/2024] [Indexed: 04/30/2024]
Abstract
Based on the demonstrated clinical activity of immune-checkpoint blockade (ICB) in advanced dedifferentiated liposarcoma (DDLPS) and undifferentiated pleomorphic sarcoma (UPS), we conducted a randomized, non-comparative phase 2 trial ( NCT03307616 ) of neoadjuvant nivolumab or nivolumab/ipilimumab in patients with resectable retroperitoneal DDLPS (n = 17) and extremity/truncal UPS (+ concurrent nivolumab/radiation therapy; n = 10). The primary end point of pathologic response (percent hyalinization) was a median of 8.8% in DDLPS and 89% in UPS. Secondary end points were the changes in immune infiltrate, radiographic response, 12- and 24-month relapse-free survival and overall survival. Lower densities of regulatory T cells before treatment were associated with a major pathologic response (hyalinization > 30%). Tumor infiltration by B cells was increased following neoadjuvant treatment and was associated with overall survival in DDLPS. B cell infiltration was associated with higher densities of regulatory T cells before treatment, which was lost upon ICB treatment. Our data demonstrate that neoadjuvant ICB is associated with complex immune changes within the tumor microenvironment in DDLPS and UPS and that neoadjuvant ICB with concurrent radiotherapy has significant efficacy in UPS.
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Affiliation(s)
- Christina L Roland
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Elise F Nassif Haddad
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Centre Léon-Bérard, University Claude Bernard Lyon I, Lyon, France
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emily Z Keung
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei-Lien Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander J Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heather Lin
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manoj Chelvanambi
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Khalida Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - B Ashleigh Guadagnolo
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew J Bishop
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elizabeth M Burton
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kelly K Hunt
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keila E Torres
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barry W Feig
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher P Scally
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Valerae O Lewis
- Department of Orthopedic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Justin E Bird
- Department of Orthopedic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ravin Ratan
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dejka Araujo
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M Alexandra Zarzour
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shreyaskumar Patel
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert Benjamin
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anthony P Conley
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Andrew Livingston
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vinod Ravi
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hussein A Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick P Lin
- Department of Orthopedic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bryan S Moon
- Department of Orthopedic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert L Satcher
- Department of Orthopedic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bilal Mujtaba
- Department of Musculoskeletal Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Russell G Witt
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Raymond S Traweek
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brandon Cope
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiao Zhou
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mohammad M Mohammad
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Randy A Chu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashish Damania
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pranoti Sahasrabhojane
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Taylor Tate
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kate Callahan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sa Nguyen
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davis Ingram
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rohini Morey
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shadarra Crosby
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Grace Mathew
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sheila Duncan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cibelle F Lima
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jean-Yves Blay
- Centre Léon-Bérard, University Claude Bernard Lyon I, Lyon, France
| | - Wolf Herman Fridman
- Centre de Recherche des Cordeliers, Inserm, Université Paris-Cité, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Kenna Shaw
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio Wistuba
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nadim Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neeta Somaiah
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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3
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Witt RG, Cass SH, Tran T, Damania A, Nelson EE, Sirmans E, Burton EM, Chelvanambi M, Johnson S, Tawbi HA, Gershenwald JE, Davies MA, Spencer C, Mishra A, Wong MC, Ajami NJ, Peterson CB, Daniel CR, Wargo JA, McQuade JL, Nelson KC. Gut Microbiome in Patients With Early-Stage and Late-Stage Melanoma. JAMA Dermatol 2023; 159:1076-1084. [PMID: 37647056 PMCID: PMC10469295 DOI: 10.1001/jamadermatol.2023.2955] [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: 11/01/2022] [Accepted: 06/20/2023] [Indexed: 09/01/2023]
Abstract
Importance The gut microbiome modulates the immune system and responses to immunotherapy in patients with late-stage melanoma. It is unknown whether fecal microbiota profiles differ between healthy individuals and patients with melanoma or if microbiota profiles differ among patients with different stages of melanoma. Defining gut microbiota profiles in individuals without melanoma and those with early-stage and late-stage melanoma may reveal features associated with disease progression. Objective To characterize and compare gut microbiota profiles between healthy volunteers and patients with melanoma and between patients with early-stage and late-stage melanoma. Design, Setting, and Participants This single-site case-control study took place at an academic comprehensive cancer center. Fecal samples were collected from systemic treatment-naive patients with stage I to IV melanoma from June 1, 2015, to January 31, 2019, and from healthy volunteers from June 1, 2021, to January 31, 2022. Patients were followed up for disease recurrence until November 30, 2021. Main Outcomes and Measures Fecal microbiota was profiled by 16S ribosomal RNA sequencing. Clinical and pathologic characteristics, treatment, and disease recurrence were extracted from electronic medical records. Fecal microbiome diversity, taxonomic profiles and inferred functional profiles were compared between groups. Results A total of 228 participants were enrolled (126 men [55.3%]; median age, 59 [range, 21-90] years), including 49 volunteers without melanoma, 38 patients with early-stage melanoma (29 with stage I or melanoma in situ and 9 with stage II), and 141 with late-stage melanoma (66 with stage III and 75 with stage IV). Community differences were observed between patients with melanoma and volunteers. Patients with melanoma had a higher relative abundance of Fusobacterium compared with controls on univariate analysis (0.19% vs 0.003%; P < .001), but this association was attenuated when adjusted for covariates (log2 fold change of 5.18 vs controls; P = .09). Microbiomes were distinct between patients with early-stage and late-stage melanoma. Early-stage melanoma had a higher alpha diversity (Inverse Simpson Index 14.6 [IQR, 9.8-23.0] vs 10.8 [IQR, 7.2-16.8]; P = .003), and a higher abundance of the genus Roseburia on univariate analysis (2.4% vs 1.2%; P < .001) though statistical significance was lost with covariate adjustment (log2 fold change of 0.86 vs controls; P = .13). Multiple functional pathways were differentially enriched between groups. No associations were observed between the microbial taxa and disease recurrence in patients with stage III melanoma treated with adjuvant immunotherapy. Conclusions and Relevance The findings of this case-control study suggest that fecal microbiota profiles were significantly different among patients with melanoma and controls and between patients with early-stage and late-stage melanoma. Prospective investigations of the gut microbiome and changes that occur with disease progression may identify future microbial targets for intervention.
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Affiliation(s)
- Russell G. Witt
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Samuel H. Cass
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Tiffaney Tran
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston
| | - Ashish Damania
- Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Emelie E. Nelson
- John P. and Kathrine G. McGovern Medical School at UTHealth Houston, Houston, Texas
| | - Elizabeth Sirmans
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Elizabeth M. Burton
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Manoj Chelvanambi
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Sarah Johnson
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Hussein A. Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Jeffrey E. Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Christine Spencer
- Department of Informatics, Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Aditya Mishra
- John P. and Kathrine G. McGovern Medical School at UTHealth Houston, Houston, Texas
| | - Matthew C. Wong
- John P. and Kathrine G. McGovern Medical School at UTHealth Houston, Houston, Texas
| | - Nadim J. Ajami
- John P. and Kathrine G. McGovern Medical School at UTHealth Houston, Houston, Texas
| | - Christine B. Peterson
- Department of Biostatistics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston
| | - Carrie R. Daniel
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston
| | - Jennifer A. Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Jennifer L. McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Kelly C. Nelson
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston
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White MG, Damania A, Alshenaifi J, Sahasrabhojane P, Peacock O, Losh J, Wong MC, Lutter-Berkova Z, Chang GJ, Futreal A, Wargo JA, Ajami NJ, Kopetz S, You YN. Young-onset Rectal Cancer: Unique Tumoral Microbiome and Correlation With Response to Neoadjuvant Therapy. Ann Surg 2023; 278:538-548. [PMID: 37465976 PMCID: PMC10528779 DOI: 10.1097/sla.0000000000006015] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 07/20/2023]
Abstract
OBJECTIVE External exposures, the host, and the microbiome interact in oncology. We aimed to investigate tumoral microbiomes in young-onset rectal cancers (YORCs) for profiles potentially correlative with disease etiology and biology. BACKGROUND YORC is rapidly increasing, with 1 in 4 new rectal cancer cases occurring under the age of 50 years. Its etiology is unknown. METHODS YORC (<50 y old) or later-onset rectal cancer (LORC, ≥50 y old) patients underwent pretreatment biopsied of tumor and tumor-adjacent normal (TAN) tissue. After whole genome sequencing, metagenomic analysis quantified microbial communities comparing tumors versus TANs and YORCs versus LORCs, controlling for multiple testing. Response to neoadjuvant therapy (NT) was categorized as major pathological response (MPR, ≤10% residual viable tumor) versus non-MPR. RESULTS Our 107 tumors, 75 TANs from 37 (35%) YORCs, and 70 (65%) LORCs recapitulated bacterial species were previously associated with colorectal cancers (all P <0.0001). YORC and LORC tumoral microbiome signatures were distinct. After NT, 13 patients (12.4%) achieved complete pathologic response, whereas MPR occurred in 47 patients (44%). Among YORCs, MPR was associated with Fusobacterium nucleaum , Bacteroides dorei, and Ruminococcus bromii (all P <0.001), but MPR in LORC was associated with R. bromii ( P <0.001). Network analysis of non-MPR tumors demonstrated a preponderance of oral bacteria not observed in MPR tumors. CONCLUSIONS Microbial signatures were distinct between YORC and LORC. Failure to achieve an MPR was associated with oral bacteria in tumors. These findings urge further studies to decipher correlative versus mechanistic associations but suggest a potential for microbial modulation to augment current treatments.
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Affiliation(s)
- Michael G. White
- Department of Colon & Rectal Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ashish Damania
- Platform for Innovative Microbiome and Translational research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jumanah Alshenaifi
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pranoti Sahasrabhojane
- Platform for Innovative Microbiome and Translational research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Oliver Peacock
- Department of Colon & Rectal Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jillian Losh
- Platform for Innovative Microbiome and Translational research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew C Wong
- Platform for Innovative Microbiome and Translational research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zuzana Lutter-Berkova
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - George J. Chang
- Department of Colon & Rectal Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer A. Wargo
- Platform for Innovative Microbiome and Translational research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nadim J. Ajami
- Platform for Innovative Microbiome and Translational research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Y. Nancy You
- Department of Colon & Rectal Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Weathers SPS, Zhu H, Knafl M, Damania A, Kamiya-Matsuoka C, Harrison RA, Lyons L, Yun C, Darbonne WC, Loghin M, Penas-Prado M, Majd N, Yung WKA, O'Brien BJ, Wistuba II, Futreal A, Wargo JA, Ajami NJ, Woodman SE, de Groot JF. Baseline tumor genomic and gut microbiota association with clinical outcomes in newly diagnosed glioblastoma (GBM) treated with atezolizumab in combination with temozolomide (TMZ) and radiation. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.2006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2006 Background: Checkpoint inhibitor (CPI) therapy has demonstrated overall limited efficacy in the treatment of GBM. Sixty newly diagnosed GBM patients unselected for MGMT status underwent treatment with concurrent atezolizumab with radiation therapy and TMZ followed by adjuvant atezolizumab and TMZ (NCT03174197). Clinical data has been reported previously. Methods: Genomic (WES with somatic mutation and SCNA determination N = total 42 samples, 33 baseline, 9 TP-2), transcriptomic (RNA seq N = total 72 samples, 54 baseline, 18 TP-2), and metagenomic sequencing of fecal samples (N = total 45 samples, 26 pre samples, 13 post RT samples, six 6m samples) analyses were conducted on pre-treatment samples. Findings were correlated with clinical outcome including OS and PFS. Twenty of the 60 patients underwent re-resection for suspected recurrent disease of which nine patients had WES and RNA seq performed successfully on paired pre and post treatment samples. Results: Somatic mutation, copy number and ploidy profiles were consistent with known aberrations in GBM. An unsupervised molecular network-based stratification of pre-treatment tumor mutations resulted in patients being grouped in 3 clusters with survival difference. Patients with GBM harboring an EGFR aberrancy were associated with a relatively worse mOS following treatment compared to patients with tumors enriched with PTEN alterations, while patients with IDH1 mutations had the longest mOS. Gene set enrichment analysis of gene expression in tumors from patients ( < mOS vs ≥mOS) identified genes associated with lymphocyte activation and immune response in patients with longer survival (p < 0.01) Unsupervised hierarchical clustering of bacterial taxa demonstrated two distinct clusters with significant difference by OS. Survival analysis and Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) revealed distinct taxa associated with OS ( Ruminococcus spp.) and response to treatment ( Eubacterium spp.), respectively. Conclusions: In this small CPI-treated GBM cohort, WES, SCNA and RNA seq identified pre-treatment tumor features that separated patients by survival. The fecal microbiome observations in our GBM cohort warrants further investigation. Clinical trial information: NCT03174197.
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Affiliation(s)
- Shiao-Pei S. Weathers
- The University of Texas MD Anderson Cancer Center, Department of Neuro-Oncology, Houston, TX
| | - Haifeng Zhu
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Ashish Damania
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carlos Kamiya-Matsuoka
- The University of Texas MD Anderson Cancer Center, Department of Neuro-Oncology, Houston, TX
| | | | | | | | | | - Monica Loghin
- University of Texas, MD Anderson Cancer Center, Houston, TX
| | | | - Nazanin Majd
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - W. K. Alfred Yung
- The University of Texas MD Anderson Cancer Center, Department of Neuro-Oncology, Houston, TX
| | - Barbara Jane O'Brien
- The University of Texas MD Anderson Cancer Center, Department of Neuro-Oncology, Houston, TX
| | - Ignacio Ivan Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Nadim J. Ajami
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - John Frederick de Groot
- The University of Texas, MD Anderson Cancer Center, Department of Neuro-Oncology, Houston, TX
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6
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Nassif EF, Chelvanambi M, Chen L, Wu CC, Damania A, Keung EZY, Witt RG, White M, Ajami NJ, Wong MC, Somaiah N, Sepesi B, Basu S, Allison JP, Sharma P, McBride K, Fridman WH, Wargo JA, Cascone T, Roland CL. Identifying gut microbial signatures associated with B cells and tertiary lymphoid structures (TLS) in the tumor microenvironment (TME) in response to immune checkpoint blockade (ICB). J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.2511] [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: 11/20/2022] Open
Abstract
2511 Background: While ICB has significantly improved clinical outcomes across several cancer types, only 15-20% of patients develop a durable response. Thus, novel and targetable biomarkers are needed. There is increased appreciation of the role of the gut microbiome, and TLS and B-cells in the TME in response to ICB. Here, we investigate the association between these two determinants of response in patient specimens from three randomized phase 2 neoadjuvant ICB trials of nivolumab +/- ipilimumab (melanoma (MEL; NCT02519322; n=23), non-small-cell lung cancer (NSCLC; NCT03158129; n=31), sarcoma (SARC; NCT02301039; n=17). Methods: Patients were categorized as responders (R) or non-responders (NR) based on major pathologic response, as defined in each histotype (MEL and NSCLC viable tumor ≤10%; SARC hyalinization>30%). Baseline fecal samples were profiled via 16S rRNA gene sequencing from all three cohorts to assess the composition of patient gut microbiomes. Transcriptional profiles of biopsies collected pre-ICB for MEL and SARC, and post-ICB for MEL, SARC, and NSCLC were used to assess TLS (CXCL13, CCL18, CCL19, CCL21) and B-cell (PAX5, CD79B, CR2, MS4A1) signatures in the TME, by calculated mean values of normalized gene expressions. Comparison between samples were carried out using the Wilcoxon signed-rank test. Results: There were 21 R overall (NSCLC n=9; MEL n=9; SARC n=3). Despite significant differences in alpha and beta diversity across cohorts, relative abundance of Ruminococcus was significantly higher in R (p=0.003; NSCLC p<0.001; MEL p=0.049; SARC p=0.7). B-cell signature was significantly higher post-ICB in R (R vs NR, post, TLS p=0.13; B-cell p=0.003), with consistent trends in each cohort. Longitudinal evaluation of transcriptional profiles showed that expression of TLS and B-cell signatures increased with treatment in R (pre vs post, MEL and SARC; TLS p=0.0098; B-cell p<0.001) but not NR (pre vs post; TLS p= 0.87; B-cell p= 0.15), with consistent trends in sarcoma and melanoma subgroups. Combined correlative analysis with matched specimen showed that patients with higher pre-ICB relative abundance of Ruminococcus (above median) had significant increase in B-cell signatures (pre vs post, MEL and SARC; TLS p=0.052; B-cell p=0.002) which was not seen in patients with low abundance (below median) of Ruminococcus (pre vs post, MEL and SARC; TLS p=0.56; B-cell p=0.69). Conclusions: Unifying signatures in the gut microbiome are associated with response to ICB and increased B-cell infiltration and TLS formation in the TME. We expect these findings to energize mechanistic studies and new microbiome-based interventional approaches to improve clinical outcomes with ICB. Clinical trial information: NCT02519322, NCT03158129, NCT02301039.
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Affiliation(s)
- Elise F Nassif
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lili Chen
- MD Anderson Cancer Center, Houston, TX
| | - Chia-Chin Wu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ashish Damania
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Michael White
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nadim J. Ajami
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Neeta Somaiah
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Boris Sepesi
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sreyashi Basu
- University of Texas MD Anderson Cancer Center, Department of Immunology, Houston, TX
| | | | - Padmanee Sharma
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kevin McBride
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Tina Cascone
- The University of Texas MD Anderson Cancer Center, Houston, TX
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7
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Sun H, Damania A, Mair ML, Otukoya E, Li YD, Polsky K, Zeng Y, Alt JA, Citardi MJ, Corry DB, Luong AU, Knight JM. STAT6 Blockade Abrogates Aspergillus-Induced Eosinophilic Chronic Rhinosinusitis and Asthma, A Model of Unified Airway Disease. Front Immunol 2022; 13:818017. [PMID: 35281012 PMCID: PMC8904741 DOI: 10.3389/fimmu.2022.818017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/28/2022] [Indexed: 12/25/2022] Open
Abstract
Unified airway disease, including concurrent asthma and chronic rhinosinusitis (CRS), is a common, but poorly understood disorder with no curative treatment options. To establish a murine model of chronic unified eosinophilic airway inflammation, mice were challenged with Aspergillus niger, and sinonasal mucosa and lung tissue were evaluated by immunohistochemistry, flow cytometry, and gene expression. Inhalation of A niger conidia resulted in a Th2-biased lung and sinus inflammation that typifies allergic asthma and CRS. Gene network and pathway analysis correlated with human disease with upregulation of not only the JAK-STAT and helper T-cell pathways, but also less expected pathways governing the spliceosome, osteoclast differentiation, and coagulation pathways. Utilizing a specific inhibitor and gene-deficient mice, we demonstrate that STAT6 is required for mycosis-induced sinus inflammation. These findings confirm the relevance of this new model and portend future studies that further extend our understanding of the immunopathologic basis of airway mycosis and unified airway disease.
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Affiliation(s)
- Hua Sun
- Center for Immunology and Autoimmune Diseases, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Department of Otorhinolaryngology-Head and Neck Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Ashish Damania
- Department of Pediatrics-Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Megan L Mair
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Eniola Otukoya
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Yi-Dong Li
- Center for Immunology and Autoimmune Diseases, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Department of Otorhinolaryngology-Head and Neck Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Katherine Polsky
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Yuying Zeng
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jeremiah A Alt
- Division of Otolaryngology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Martin J Citardi
- Department of Otorhinolaryngology-Head and Neck Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - David B Corry
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States.,Michael E. Debakey VA Center for Translational Research in Inflammatory Diseases, Houston, TX, United States
| | - Amber U Luong
- Center for Immunology and Autoimmune Diseases, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Department of Otorhinolaryngology-Head and Neck Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - John Morgan Knight
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
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8
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Iyer R, Damania A. Shotgun metagenomics of indigenous bacteria collected from the banks of the San Jacinto River for biodegradation of aromatic waste. FEMS Microbiol Lett 2021; 367:5881932. [PMID: 32761171 DOI: 10.1093/femsle/fnaa133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/13/2020] [Accepted: 08/04/2020] [Indexed: 12/24/2022] Open
Abstract
Several Eastern Harris County communities lie near the now enclosed San Jacinto River (SJR) Waste Pit Superfund, a dumping ground for chlorinated dioxins and other paper mill waste products. Currently, no active monitoring of the SJR is conducted for these toxins with the exact concentration and health impact to the area unknown. As such, remediation and monitoring efforts outside of the Superfund itself could be necessary. To better understand the possible environmental fate of these aromatics, here we provide a shotgun metagenomic analysis of the structural and putative functional diversity of the SJR microbiome from two impacted Channelview, Texas communities bordering the Superfund. Results show that the underlying SJR microbiome possesses a core of metabolic enzymes related to the β-ketoadipate and benzoate degradation pathways. This suggests possible endpoints for many aromatics found deposited in the SJR including dioxin-like compounds. However, degradation biomarkers related to the priming and initial cleavage of chlorinated dioxin-like aromatics while present, are poorly concentrated across sampled sites. This may be due in part to decreased coverage of low abundance bacterial species, but also be a contributing factor leading to increased recalcitrance of these compounds in this environment compared to other aromatics.
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Affiliation(s)
- Rupa Iyer
- Center for Life Sciences Technology, Engineering Technology, University of Houston, 300 Technology Building, Houston 77204, TX, USA
| | - Ashish Damania
- Department of Pediatrics-Tropical Medicine, Baylor College of Medicine, One Baylor Plaza, Houston 77030, TX, USA
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9
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Clark E, Pritchard H, Hemmige V, Restrepo A, Bautista K, Damania A, Ricciardi A, Nutman TB, Mejia R. Strongyloides stercoralis Infection in Solid Organ Transplant Patients Is Associated With Eosinophil Activation and Intestinal Inflammation: A Cross-sectional Study. Clin Infect Dis 2021; 71:e580-e586. [PMID: 32155244 DOI: 10.1093/cid/ciaa233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 12/24/2019] [Accepted: 03/04/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Strongyloidiasis can cause devastating morbidity and death in immunosuppressed patients. Identification of reliable biomarkers for strongyloidiasis in immunosuppressed patients is critical for the prevention of severe disease. METHODS In this cross-sectional study of solid organ transplant (SOT) candidates and recipients, we quantified Strongyloides-specific IgG to the recombinant NIE-Strongyloides antigen and/or to a soluble extract of S. stercoralis somatic antigens ("crude antigen") using enzyme-linked immunosorbent assays (ELISAs). We also measured peripheral eosinophilia, 4 different eosinophil granule proteins, and intestinal fatty acid-binding protein (IFABP). RESULTS We evaluated serum biomarkers in 149 individuals; 77 (52%) pre-SOT and 72 (48%) post-SOT. Four percent (6/149) tested positive by NIE ELISA and 9.6% (11/114) by crude antigen ELISA (overall seropositivity of 9.4% [14/149]). Seropositive patients had higher absolute eosinophil counts (AECs) than seronegative patients (P = .004). AEC was positively correlated to the levels of eosinophil granule proteins eosinophil cationic protein (ECP) and eosinophil peroxidase (EPO) (P < .05), while IFABP was positively related to the 2 other eosinophil granule proteins (major basic protein [MBP] and eosinophil-derived neurotoxin [EDN]; Spearman's r = 0.3090 and 0.3778, respectively; P < .05; multivariate analyses slopes = 0.70 and 2.83, respectively). CONCLUSIONS This study suggests that, in SOT patients, strongyloidiasis triggers both eosinophilia and eosinophil activation, the latter being associated with intestinal inflammation. These data provide insight into the pathogenesis of S. stercoralis infection in the immunocompromised population at high risk of severe strongyloidiasis syndromes.
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Affiliation(s)
- Eva Clark
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston Texas, USA.,Department of Medicine, Section of Health Services Research, Baylor College of Medicine, Houston Texas, USA.,Houston Health Services Research & Development, Innovations in Quality, Effectiveness and Safety (IQuESt), Baylor College of Medicine Michael E. DeBakey VA Medical Center, Houston, Texas, USA
| | - Haley Pritchard
- Department of Medicine, Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Vagish Hemmige
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston Texas, USA.,Department of Medicine, Division of Infectious Diseases, Montefiore Medical Center, Bronx, New York, USA.,Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Alejandro Restrepo
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston Texas, USA
| | - Karla Bautista
- Laboratory of Clinical Parasitology and Diagnostics, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Ashish Damania
- Laboratory of Clinical Parasitology and Diagnostics, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Alessandra Ricciardi
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas B Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rojelio Mejia
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston Texas, USA.,Laboratory of Clinical Parasitology and Diagnostics, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, USA
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10
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Cruz-Chan JV, Villanueva-Lizama LE, Versteeg L, Damania A, Villar MJ, González-López C, Keegan B, Pollet J, Gusovsky F, Hotez PJ, Bottazzi ME, Jones KM. Vaccine-linked chemotherapy induces IL-17 production and reduces cardiac pathology during acute Trypanosoma cruzi infection. Sci Rep 2021; 11:3222. [PMID: 33547365 PMCID: PMC7865072 DOI: 10.1038/s41598-021-82930-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023] Open
Abstract
Chagas disease resulting from Trypanosoma cruzi infection leads to a silent, long-lasting chronic neglected tropical disease affecting the poorest and underserved populations around the world. Antiparasitic treatment with benznidazole does not prevent disease progression or death in patients with established cardiac disease. Our consortium is developing a therapeutic vaccine based on the T. cruzi flagellar—derived antigen Tc24-C4 formulated with a Toll-like receptor 4 agonist adjuvant, to complement existing chemotherapy and improve treatment efficacy. Here we demonstrate that therapeutic treatment of acutely infected mice with a reduced dose of benznidazole concurrently with vaccine treatment – also known as “vaccine-linked chemotherapy”—induced a TH17 like immune response, with significantly increased production of antigen specific IL-17A, IL-23 and IL-22, and CD8 + T lymphocytes, as well as significantly increased T. cruzi specific IFNγ-producing CD4 + T lymphocytes. Significantly reduced cardiac inflammation, fibrosis, and parasite burdens and improved survival were achieved by vaccine-linked chemotherapy and individual treatments. Importantly, low dose treatments were comparably efficacious to high dose treatments, demonstrating potential dose sparing effects. We conclude that through induction of TH17 immune responses vaccine-linked chemotherapeutic strategies could bridge the tolerability and efficacy gaps of current drug treatment in Chagasic patients.
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Affiliation(s)
- Julio V Cruz-Chan
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Laboratorio de Parasitología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Liliana E Villanueva-Lizama
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Laboratorio de Parasitología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Leroy Versteeg
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Cell Biology and Immunology Group, Wageningen University & Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Ashish Damania
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Maria José Villar
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Cristina González-López
- Laboratorio de Parasitología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Brian Keegan
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jeroen Pollet
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Peter J Hotez
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,James A. Baker III Institute for Public Policy, Rice University, Houston, TX, USA
| | - Maria Elena Bottazzi
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kathryn M Jones
- Texas Children's Hospital Center for Vaccine Development, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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11
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Mejia R, Damania A, Jeun R, Bryan PE, Vargas P, Juarez M, Cajal PS, Nasser J, Krolewiecki A, Lefoulon E, Long C, Drake E, Cimino RO, Slatko B. Impact of intestinal parasites on microbiota and cobalamin gene sequences: a pilot study. Parasit Vectors 2020; 13:200. [PMID: 32306993 PMCID: PMC7168842 DOI: 10.1186/s13071-020-04073-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/10/2020] [Indexed: 01/10/2023] Open
Abstract
Background Approximately 30% of children worldwide are infected with gastrointestinal parasites. Depending on the species, parasites can disrupt intestinal bacterial microbiota affecting essential vitamin biosynthesis. Methods Stool samples were collected from 37 asymptomatic children from a previous cross-sectional Argentinian study. A multi-parallel real-time quantitative PCR was implemented for Ascaris lumbricoides, Ancylostoma duodenale, Necator americanus, Strongyloides stercoralis, Trichuris trichiura, Cryptosporidium spp., Entamoeba histolytica and Giardia duodenalis. In addition, whole-genome sequencing analysis was conducted for bacterial microbiota on all samples and analyzed using Livermore Metagenomic Analysis Toolkit and DIAMOND software. Separate analyses were carried out for uninfected, Giardia-only, Giardia + helminth co-infections, and helminth-only groups. Results For Giardia-only infected children compared to uninfected children, DNA sequencing data showed a decrease in microbiota biodiversity that correlated with increasing Giardia burden and was statistically significant using Shannonʼs alpha diversity (Giardia-only > 1 fg/µl 2.346; non-infected group 3.253, P = 0.0317). An increase in diversity was observed for helminth-only infections with a decrease in diversity for Giardia + helminth co-infections (P = 0.00178). In Giardia-only infections, microbiome taxonomy changed from Firmicutes towards increasing proportions of Prevotella, with the degree of change related to the intensity of infection compared to uninfected (P = 0.0317). The abundance of Prevotella bacteria was decreased in the helminths-only group but increased for Giardia + helminth co-infections (P = 0.0262). Metagenomic analysis determined cobalamin synthesis was decreased in the Giardia > 1 fg/µl group compared to both the Giardia < 1 fg/µl and the uninfected group (P = 0.0369). Giardia + helminth group also had a decrease in cobalamin CbiM genes from helminth-only infections (P = 0.000754). Conclusion The study results may provide evidence for an effect of parasitic infections enabling the permissive growth of anaerobic bacteria such as Prevotella, suggesting an altered capacity of vitamin B12 (cobalamin) biosynthesis and potential impact on growth and development in children .
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Affiliation(s)
- Rojelio Mejia
- National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA. .,Universidad Nacional de Salta, Salta, Argentina.
| | - Ashish Damania
- National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Rebecca Jeun
- National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Patricia E Bryan
- National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | | | | | | | - Evan Drake
- New England Biolabs, Inc, Ipswich, MA, USA
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12
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Iyer R, Damania A, Iken B. Genome data of Stenotrophomonas maltophilia DF07 collected from polluted river sediment reveals an opportunistic pathogen and a potential antibiotic reservoir. Data Brief 2019; 25:104137. [PMID: 31304216 PMCID: PMC6600701 DOI: 10.1016/j.dib.2019.104137] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/21/2019] [Accepted: 06/03/2019] [Indexed: 12/02/2022] Open
Abstract
Stenotrophomonas maltophilia DF07 is a gram negative bacterium isolated from polluted San Jacinto River sediment near Moncrief Park in Channelview, Texas. The genome of strain DF07 (chromosome and plasmid) was compiled at the scaffold level and can be accessed through the National Center for Biotechnology Information database under accession NZ_NJGC00000000. The DF07 genome consists of a total of 4,801,842 bp encoding for approximately 4,351 functional proteins. Approximately 86 proteins are associated with broad-spectrum antibiotic resistance, 11 are associated with bacteriocin production, and a total of 17 proteins encode for an assortment of Mycobacterium-like virulence and invasion operons. S. maltophilia DF07 is genetically similar to the nosocomial S. maltophilia strain AU12-09, but also harbors an unusually large plasmid that encodes for over 150 proteins of unknown function. Taken together, this strain is potentially an important antibiotic reservoir and its origin within a recreational park merits further study of the area.
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Affiliation(s)
- Rupa Iyer
- Center for Life Sciences Technology, Engineering Technology, University of Houston, Houston, USA
- Corresponding author.
| | - Ashish Damania
- Department of Pediatrics-Tropical Medicine, Baylor College of Medicine, Houston, USA
| | - Brian Iken
- Center for Life Sciences Technology, Engineering Technology, University of Houston, Houston, USA
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13
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Briggs N, Wei J, Versteeg L, Zhan B, Keegan B, Damania A, Pollet J, Hayes KS, Beaumier C, Seid CA, Leong J, Grencis RK, Bottazzi ME, Sastry KJ, Hotez PJ. Trichuris muris whey acidic protein induces type 2 protective immunity against whipworm. PLoS Pathog 2018; 14:e1007273. [PMID: 30153307 PMCID: PMC6130879 DOI: 10.1371/journal.ppat.1007273] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 05/17/2018] [Revised: 09/10/2018] [Accepted: 08/09/2018] [Indexed: 12/13/2022] Open
Abstract
Human whipworm (Trichuris trichiura) infects approximately 1 in 15 people worldwide, representing the leading infectious cause of colitis and subsequent, inflammatory bowel disease (IBD). Current control measures focused on mass deworming have had limited success due to low drug efficacies. Vaccination would be an ideal, cost-effective strategy to induce protective immunity, leading to control of infection and transmission. Here we report the identification of whey acidic protein, a whipworm secretory protein, as a strong immunogen for inducing protective efficacy in a surrogate mouse T. muris infection model. The recombinant WAP protein (rTm-WAP49), as well as a single, highly conserved repeat within WAP (fragment 8) expressed as an Na-GST-1 fusion protein (rTm-WAP-F8+Na-GST-1), generate a strong T helper type 2 (Th2) immune response when delivered as subcutaneous vaccines formulated with Montanide ISA 720. Oral challenge with T. muris infective eggs following vaccination led to a significant reduction in worm burden of 48% by rTm-WAP49 and 33% by rTm-WAP-F8+Na-GST-1. The cellular immune correlates of protection included significant antigen-specific production of Th2 cytokines IL-4, IL-9, and IL-13 by cells isolated from the vaccine-draining inguinal lymph nodes, parasite-draining mesenteric lymph nodes, and spleen in mice vaccinated with either rTm-WAP49 or rTm-WAP-F8+Na-GST-1. The humoral immune correlates included a high antigen-specific ratio of IgG1 to IgG2a, without eliciting an IgE-mediated allergic response. Immunofluorescent staining of adult T. muris with WAP antisera identified the worm's pathogenic stichosome organ as the site of secretion of native Tm-WAP protein into the colonic mucosa. Given the high sequence conservation for the WAP proteins from T. muris and T. trichiura, the results presented here support the WAP protein to be further evaluated as a potential human whipworm vaccine candidate.
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Affiliation(s)
- Neima Briggs
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, United States of America
- Department of Immunology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Junfei Wei
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
| | - Leroy Versteeg
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
| | - Bin Zhan
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
| | - Brian Keegan
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
| | - Ashish Damania
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
| | - Jeroen Pollet
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
| | - Kelly S. Hayes
- School of Biological Sciences, FBMH, MAHSC, University of Manchester, Manchester, United Kingdom
- Wellcome Trust Centre for Cell Matrix Research, University of Manchester, Manchester, United Kingdom
- The Lydia Becker Institute for Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - Coreen Beaumier
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
| | - Christopher A. Seid
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
| | - Jamie Leong
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
| | - Richard K. Grencis
- School of Biological Sciences, FBMH, MAHSC, University of Manchester, Manchester, United Kingdom
- Wellcome Trust Centre for Cell Matrix Research, University of Manchester, Manchester, United Kingdom
- The Lydia Becker Institute for Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - Maria Elena Bottazzi
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - K. Jagannadha Sastry
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, United States of America
- Department of Immunology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Peter J. Hotez
- Texas Children’s Hospital Center for Vaccine Development, Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States of America
- Department of Biology, Baylor University, Waco, Texas, United States of America
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Olive JK, Hotez PJ, Damania A, Nolan MS. Correction: The state of the antivaccine movement in the United States: A focused examination of nonmedical exemptions in states and counties. PLoS Med 2018; 15:e1002616. [PMID: 29979682 PMCID: PMC6034910 DOI: 10.1371/journal.pmed.1002616] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pmed.1002578.].
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15
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Iyer R, Iken B, Damania A, Krieger J. Whole genome analysis of six organophosphate-degrading rhizobacteria reveals putative agrochemical degradation enzymes with broad substrate specificity. Environ Sci Pollut Res Int 2018; 25:13660-13675. [PMID: 29502257 DOI: 10.1007/s11356-018-1435-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/30/2018] [Indexed: 06/08/2023]
Abstract
Six organophosphate-degrading bacterial strains collected from farm and ranch soil rhizospheres across the Houston-metropolitan area were identified as strains of Pseudomonas putida (CBF10-2), Pseudomonas stutzeri (ODKF13), Ochrobactrum anthropi (FRAF13), Stenotrophomonas maltophilia (CBF10-1), Achromobacter xylosoxidans (ADAF13), and Rhizobium radiobacter (GHKF11). Whole genome sequencing data was assessed for relevant genes, proteins, and pathways involved in the breakdown of agrochemicals. For comparative purposes, this analysis was expanded to also include data from deposited strains in the National Center for Biotechnology Information's (NCBI) database. This study revealed Zn-dependent metallo-β-lactamase (MBL)-fold proteins similar to OPHC2 first identified in P. pseudoalcaligenes as the likely agents of organophosphate (OP) hydrolysis in A. xylosoxidans ADAF13, S. maltophilia CBF10-1, O. anthropi FRAF13, and R. radiobacter GHKF11. A search of similar proteins within NCBI identified over 200 hits for bacterial genera and species with a similar OPHC2 domain. Taken together, we conclude from this data that intrinsic low-level OP hydrolytic activity is likely prevalent across the rhizosphere stemming from widespread OPHC2-like metalloenzymes. In addition, P. stutzeri ODKF13, P. putida CBF10-2, O. anthropi FRAF13, and R. radiobacter GHKF11 were found to harbor glycine oxidase (GO) enzymes that putatively possess low-level activity against the herbicide glyphosate. These bacterial GOs are reported to catalyze the degradation of glyphosate to α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and suggest a possible link to AMPA that can be found in glyphosate-contaminated agricultural soil. The presence of aromatic degradation proteins were also detected in five of six study strains, but are attributed primarily to components of the widely distributed β-ketoadipate pathway found in many soil bacteria.
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Affiliation(s)
- Rupa Iyer
- Center for Life Sciences Technology, Engineering Technology, University of Houston, 300 Technology Building, Houston, TX, 77204, USA.
| | - Brian Iken
- Center for Life Sciences Technology, Engineering Technology, University of Houston, 300 Technology Building, Houston, TX, 77204, USA
| | - Ashish Damania
- Department of Pediatrics-Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jerry Krieger
- Center for Life Sciences Technology, Engineering Technology, University of Houston, 300 Technology Building, Houston, TX, 77204, USA
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16
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Affiliation(s)
- Peter J. Hotez
- Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Biology, Baylor University, Waco, Texas, United States of America
- * E-mail:
| | - Ashish Damania
- Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, United States of America
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17
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Iyer R, Iken B, Damania A. Genome of Pseudomonas nitroreducens DF05 from dioxin contaminated sediment downstream of the San Jacinto River waste pits reveals a broad array of aromatic degradation gene determinants. Genom Data 2017; 14:40-43. [PMID: 28856100 PMCID: PMC5565767 DOI: 10.1016/j.gdata.2017.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/13/2017] [Accepted: 07/19/2017] [Indexed: 12/03/2022]
Abstract
P. nitroreducens DF05 is a Gram negative, motile, aerobic, rod-shaped and psychrotrophic bacterium that was isolated from contaminated San Jacinto River sediment near River Terrace Park in Channelview, Texas. The draft genome of strain DF05 consists of a total of 192 contigs assembled at the scaffold level totaling 6,487,527 bp and encoding for 5862 functional proteins, 1116 of which are annotated as hypothetical proteins. The bacterial chromosome has a GC content of 65.15% and contains 22 rRNA and 70 tRNA loci. In addition, approximately 142 proteins localized on the bacterial chromosome are associated with metabolism of aromatic compounds. A single plasmid approximately 95 kb in size was also detected carrying copies of RNA genes and multiple phage assembly proteins.
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Affiliation(s)
- Rupa Iyer
- Center for Life Sciences Technology, Engineering Technology, University of Houston, 300 Technology Building, Houston, TX 77204, USA
| | - Brian Iken
- Center for Life Sciences Technology, Engineering Technology, University of Houston, 300 Technology Building, Houston, TX 77204, USA
| | - Ashish Damania
- Department of Pediatrics-Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
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18
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Iyer R, Damania A, Iken B. Whole genome sequencing of Microbacterium sp. AISO3 from polluted San Jacinto River sediment reveals high bacterial mobility, metabolic versatility and heavy metal resistance. Genom Data 2017; 14:10-13. [PMID: 28794988 PMCID: PMC5542380 DOI: 10.1016/j.gdata.2017.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 11/18/2022]
Abstract
The genus Microbacterium is composed of high GC content, Gram-positive bacteria of the phylum Acintobacteria known for their antibiotic production. Microbacterium species commonly colonize agricultural rhizospheres and more infrequently have been found to colonize and infect human tissues as well. Here we report the 3,696,310 bp draft genome (chromosome and plasmids) sequence assembled at the scaffold level from 232 contigs of Microbacterium sp. strain AISO3, isolated from polluted San Jacinto River sediment in Channelview, Texas. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession NHRF00000000.
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Affiliation(s)
- Rupa Iyer
- Center for Life Sciences Technology, Department of Engineering Technology, University of Houston, Houston, TX, USA
- Corresponding author.
| | - Ashish Damania
- Department of Tropical Medicine-Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Brian Iken
- Center for Life Sciences Technology, Department of Engineering Technology, University of Houston, Houston, TX, USA
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Affiliation(s)
- Peter J. Hotez
- Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine at Baylor College of Medicine, Houston, Texas, United States of America
- Department of Biology, Baylor University, Waco, Texas, United States of America
- Center for Health and Biosciences, James A Baker III Institute for Public Policy, Rice University, Houston, Texas, United States of America
- Scowcroft Institute of International Affairs, Bush School of Government and Public Service, College Station, Texas, United States of America
- * E-mail:
| | - Ashish Damania
- Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine at Baylor College of Medicine, Houston, Texas, United States of America
| | | | - Jeffrey Stanaway
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
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20
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Abstract
Although approximately one-half of the global disease burden due to the major helminthic infections occurs among the poor living in rich economies, almost all of the public support for helminth control and research and development comes out of the United States and Europe.
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Affiliation(s)
- Peter J Hotez
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine at Baylor College of Medicine, Houston, Texas, United States of America.,Department of Biology, Baylor University, Waco, Texas, United States of America.,Center for Health and Biosciences, James A Baker III Institute for Public Policy, Rice University, Houston, Texas, United States of America
| | - Ashish Damania
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine at Baylor College of Medicine, Houston, Texas, United States of America
| | - Mohsen Naghavi
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, United States of America
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21
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Affiliation(s)
- Peter J Hotez
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine at Baylor College of Medicine, Houston, Texas, USA
- Department of Biology, Baylor University, Waco, Texas, USA
- Center for Health and Biosciences, James A Baker III Institute for Public Policy, Rice University, Houston, Texas, USA
- * E-mail:
| | - Ashish Damania
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine at Baylor College of Medicine, Houston, Texas, USA
| | - Mohsen Naghavi
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington, USA
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22
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Wei J, Damania A, Gao X, Liu Z, Mejia R, Mitreva M, Strych U, Bottazzi ME, Hotez PJ, Zhan B. The hookworm Ancylostoma ceylanicum intestinal transcriptome provides a platform for selecting drug and vaccine candidates. Parasit Vectors 2016; 9:518. [PMID: 27677574 PMCID: PMC5039805 DOI: 10.1186/s13071-016-1795-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/12/2016] [Indexed: 12/02/2022] Open
Abstract
Background The intestine of hookworms contains enzymes and proteins involved in the blood-feeding process of the parasite and is therefore a promising source of possible vaccine antigens. One such antigen, the hemoglobin-digesting intestinal aspartic protease known as Na-APR-1 from the human hookworm Necator americanus, is currently a lead candidate antigen in clinical trials, as is Na-GST-1 a heme-detoxifying glutathione S-transferase. Methods In order to discover additional hookworm vaccine antigens, messenger RNA was obtained from the intestine of male hookworms, Ancylostoma ceylanicum, maintained in hamsters. RNA-seq was performed using Illumina high-throughput sequencing technology. The genes expressed in the hookworm intestine were compared with those expressed in the whole worm and those genes overexpressed in the parasite intestine transcriptome were further analyzed. Results Among the lead transcripts identified were genes encoding for proteolytic enzymes including an A. ceylanicum APR-1, but the most common proteases were cysteine-, serine-, and metallo-proteases. Also in abundance were specific transporters of key breakdown metabolites, including amino acids, glucose, lipids, ions and water; detoxifying and heme-binding glutathione S-transferases; a family of cysteine-rich/antigen 5/pathogenesis-related 1 proteins (CAP) previously found in high abundance in parasitic nematodes; C-type lectins; and heat shock proteins. These candidates will be ranked for downstream antigen target selection based on key criteria including abundance, uniqueness in the parasite versus the vertebrate host, as well as solubility and yield of expression. Conclusion The intestinal transcriptome of A. ceylanicum provides useful information for the identification of proteins involved in the blood-feeding process, representing a first step towards a reverse vaccinology approach to a human hookworm vaccine. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1795-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junfei Wei
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ashish Damania
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xin Gao
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Zhuyun Liu
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rojelio Mejia
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.,Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Ulrich Strych
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maria Elena Bottazzi
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Biology, Baylor University, Waco, TX, 76706, USA
| | - Peter J Hotez
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Biology, Baylor University, Waco, TX, 76706, USA
| | - Bin Zhan
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
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Iyer R, Iken B, Damania A. A comparison of organophosphate degradation genes and bioremediation applications. Environ Microbiol Rep 2013; 5:787-798. [PMID: 24249287 DOI: 10.1111/1758-2229.12095] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 08/11/2013] [Accepted: 08/13/2013] [Indexed: 06/02/2023]
Abstract
Organophosphates (OPs) form the bulk of pesticides that are currently in use around the world accounting for more than 30% of the world market. They also form the core for many nerve-based warfare agents including sarin and soman. The widespread use and the resultant build-up of OP pesticides and chemical nerve agents has led to the development of major health problems due to their extremely toxic interaction with any biological system that encounters them. Growing concern over the accumulation of OP compounds in our food products, in the soils from which they are harvested and in wastewater run-off has fuelled a growing interest in microbial biotechnology that provides cheap, efficient OP detoxification to supplement expensive chemical methods. In this article, we review the current state of knowledge of OP pesticide and chemical agent degradation and attempt to clarify confusion over identification and nomenclature of two major families of OP-degrading enzymes through a comparison of their structure and function. The isolation, characterization, utilization and manipulation of the major detoxifying enzymes and the molecular basis of degradation of OP pesticides and chemical nerve agents are discussed as well as the achievements and technological advancements made towards the bioremediation of such compounds.
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Affiliation(s)
- Rupa Iyer
- College of Technology, University of Houston, 300 Technology Building Houston, TX 77204-4021, USA
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