1
|
Glass DR, Mayer-Blackwell K, Ramchurren N, Parks KR, Duran GE, Wright AK, Bastidas Torres AN, Islas L, Kim YH, Fling SP, Khodadoust MS, Newell EW. Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma. Cell Rep Med 2024:101527. [PMID: 38670099 DOI: 10.1016/j.xcrm.2024.101527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/14/2023] [Revised: 02/17/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
Cutaneous T cell lymphomas (CTCLs) are skin cancers with poor survival rates and limited treatments. While immunotherapies have shown some efficacy, the immunological consequences of administering immune-activating agents to CTCL patients have not been systematically characterized. We apply a suite of high-dimensional technologies to investigate the local, cellular, and systemic responses in CTCL patients receiving either mono- or combination anti-PD-1 plus interferon-gamma (IFN-γ) therapy. Neoplastic T cells display no evidence of activation after immunotherapy. IFN-γ induces muted endogenous immunological responses, while anti-PD-1 elicits broader changes, including increased abundance of CLA+CD39+ T cells. We develop an unbiased multi-omic profiling approach enabling discovery of immune modules stratifying patients. We identify an enrichment of activated regulatory CLA+CD39+ T cells in non-responders and activated cytotoxic CLA+CD39+ T cells in leukemic patients. Our results provide insights into the effects of immunotherapy in CTCL patients and a generalizable framework for multi-omic analysis of clinical trials.
Collapse
Affiliation(s)
- David R Glass
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| | - Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Nirasha Ramchurren
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - K Rachael Parks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - George E Duran
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna K Wright
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Laura Islas
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Youn H Kim
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven P Fling
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Michael S Khodadoust
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| |
Collapse
|
2
|
Ryu H, Bi TM, Pulliam TH, Sarkar K, Church CD, Kumar N, Mayer-Blackwell K, Jani S, Ramchurren N, Hansen UK, Hadrup SR, Fling SP, Koelle DM, Nghiem P, Newell EW. Merkel cell polyomavirus-specific and CD39 +CLA + CD8 T cells as blood-based predictive biomarkers for PD-1 blockade in Merkel cell carcinoma. Cell Rep Med 2024; 5:101390. [PMID: 38340724 PMCID: PMC10897544 DOI: 10.1016/j.xcrm.2023.101390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/29/2023] [Accepted: 12/21/2023] [Indexed: 02/12/2024]
Abstract
Merkel cell carcinoma is a skin cancer often driven by Merkel cell polyomavirus (MCPyV) with high rates of response to anti-PD-1 therapy despite low mutational burden. MCPyV-specific CD8 T cells are implicated in anti-PD-1-associated immune responses and provide a means to directly study tumor-specific T cell responses to treatment. Using mass cytometry and combinatorial tetramer staining, we find that baseline frequencies of blood MCPyV-specific cells correlated with response and survival. Frequencies of these cells decrease markedly during response to therapy. Phenotypes of MCPyV-specific CD8 T cells have distinct expression patterns of CD39, cutaneous lymphocyte-associated antigen (CLA), and CD103. Correspondingly, overall bulk CD39+CLA+ CD8 T cell frequencies in blood correlate with MCPyV-specific cell frequencies and similarly predicted favorable clinical outcomes. Conversely, frequencies of CD39+CD103+ CD8 T cells are associated with tumor burden and worse outcomes. These cell subsets can be useful as biomarkers and to isolate blood-derived tumor-specific T cells.
Collapse
Affiliation(s)
- Heeju Ryu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Timothy M Bi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Korok Sarkar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Candice D Church
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Nandita Kumar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Saumya Jani
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Nirasha Ramchurren
- Cancer Immunotherapy Trails Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ulla K Hansen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Steven P Fling
- Cancer Immunotherapy Trails Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA; Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Benaroya Research Institute, Seattle, WA, USA
| | - Paul Nghiem
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA.
| |
Collapse
|
3
|
Ford ES, Mayer-Blackwell K, Jing L, Laing KJ, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Greninger AL, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8 + T cells in persons with previous COVID-19. Nat Immunol 2024; 25:166-177. [PMID: 38057617 PMCID: PMC10981451 DOI: 10.1038/s41590-023-01692-x] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hybrid immunity is more protective than vaccination or previous infection alone. To investigate the kinetics of spike-reactive T (TS) cells from SARS-CoV-2 infection through messenger RNA vaccination in persons with hybrid immunity, we identified the T cell receptor (TCR) sequences of thousands of index TS cells and tracked their frequency in bulk TCRβ repertoires sampled longitudinally from the peripheral blood of persons who had recovered from coronavirus disease 2019 (COVID-19). Vaccinations led to large expansions in memory TS cell clonotypes, most of which were CD8+ T cells, while also eliciting diverse TS cell clonotypes not observed before vaccination. TCR sequence similarity clustering identified public CD8+ and CD4+ TCR motifs associated with spike (S) specificity. Synthesis of longitudinal bulk ex vivo single-chain TCRβ repertoires and paired-chain TCRɑβ sequences from droplet sequencing of TS cells provides a roadmap for the rapid assessment of T cell responses to vaccines and emerging pathogens.
Collapse
Affiliation(s)
- Emily S Ford
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kerry J Laing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anton M Sholukh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Russell St Germain
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Emily L Bossard
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Saumya Jani
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Anna Wald
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Brett Eaton
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elizabeth Eudy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elena Postnikova
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | | | | | - Rachel M Gittelman
- Adaptive Biotechnologies, Seattle, WA, USA
- Guardant Health, Redwood City, CA, USA
| | - Matyas Ecsedi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Takeda Oncology, Cambridge, MA, USA
| | - Elise Wilcox
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aude G Chapuis
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Translational Research, Benaroya Research Institute, Seattle, WA, USA.
| |
Collapse
|
4
|
Minot SS, Mayer-Blackwell K, Fiore-Gartland A, Johnson A, Self S, Bhatti P, Yao L, Liu L, Sun X, Jinfa Y, Kublin J. Strain-level characterization of health-associated bacterial consortia that colonize the human gut during infancy. medRxiv 2023:2023.12.16.23300077. [PMID: 38168439 PMCID: PMC10760300 DOI: 10.1101/2023.12.16.23300077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background The human gut microbiome develops rapidly during infancy, a key window of development coinciding with maturation of the adaptive immune system. However, little is known of the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n=94) from a cohort of infants (n=15) at monthly intervals in the first six months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants. Results Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual. Conclusion By augmenting published metagenomic datasets with data from a newly established cohort we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.
Collapse
Affiliation(s)
| | | | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Andrew Johnson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Steven Self
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Parveen Bhatti
- Cancer Control Research, BC Cancer Research Institute, Vancouver, BC, Canada
- Epidemiology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, USA
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Lena Yao
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Lili Liu
- Key Laboratory of Occupational Disease Prevention and Treatment, Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou, China
| | - Xin Sun
- National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Jinfa
- Nanhai Maternity and Child Healthcare Hospital of Foshan, Foshan, China
| | - James Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
- HIV Vaccine Trials Network, Fred Hutchinson Cancer Center, Seattle, USA
| |
Collapse
|
5
|
Johnson AMF, Hager K, Alameh MG, Van P, Potchen N, Mayer-Blackwell K, Fiore-Gartland A, Minot S, Lin PJC, Tam YK, Weissman D, Kublin JG. The Regulation of Nucleic Acid Vaccine Responses by the Microbiome. J Immunol 2023; 211:1680-1692. [PMID: 37850965 PMCID: PMC10656434 DOI: 10.4049/jimmunol.2300196] [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] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
Nucleic acid vaccines, including both RNA and DNA platforms, are key technologies that have considerable promise in combating both infectious disease and cancer. However, little is known about the extrinsic factors that regulate nucleic acid vaccine responses and which may determine their effectiveness. The microbiome is recognized as a significant regulator of immune development and response, whose role in regulating some traditional vaccine platforms has recently been discovered. Using germ-free and specific pathogen-free mouse models in combination with different protein, DNA, and mRNA vaccine regimens, we demonstrate that the microbiome is a significant regulator of nucleic acid vaccine immunogenicity. Although the presence of the microbiome enhances CD8+ T cell responses to mRNA lipid nanoparticle immunization, the microbiome suppresses Ig and CD4+ T cell responses to DNA-prime, DNA-protein-boost immunization, indicating contrasting roles for the microbiome in the regulation of these different nucleic acid vaccine platforms. In the case of mRNA lipid nanoparticle vaccination, germ-free mice display reduced dendritic cell/macrophage activation that may underlie the deficient vaccine response. Our study identifies the microbiome as a relevant determinant of nucleic acid vaccine response with implications for continued therapeutic development and deployment of these vaccines.
Collapse
Affiliation(s)
- Andrew M. F. Johnson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Kevin Hager
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | | | - Phuong Van
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Nicole Potchen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | | | | | - Samuel Minot
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | | | | | - Drew Weissman
- Penn Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| |
Collapse
|
6
|
Mayer-Blackwell K, Ryu H, Codd AS, Parks KR, MacMillan HR, Cohen KW, Stewart TL, Seese A, Lemos MP, De Rosa SC, Czartoski JL, Moodie Z, Nguyen LT, McGuire DJ, Ahmed R, Fiore-Gartland A, McElrath MJ, Newell EW. mRNA vaccination boosts S-specific T cell memory and promotes expansion of CD45RA int T EMRA-like CD8 + T cells in COVID-19 recovered individuals. Cell Rep Med 2023; 4:101149. [PMID: 37552991 PMCID: PMC10439252 DOI: 10.1016/j.xcrm.2023.101149] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/01/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023]
Abstract
SARS-CoV-2 infection and mRNA vaccination both elicit spike (S)-specific T cell responses. To analyze how T cell memory from prior infection influences T cell responses to vaccination, we evaluated functional T cell responses in naive and previously infected vaccine recipients. Pre-vaccine S-specific responses are predictive of subsequent CD8+ T cell vaccine-response magnitudes. Comparing baseline with post-vaccination TCRβ repertoires, we observed large clonotypic expansions correlated with the frequency of spike-specific T cells. Epitope mapping the largest CD8+ T cell responses confirms that an HLA-A∗03:01 epitope was highly immunodominant. Peptide-MHC tetramer staining together with mass cytometry and single-cell sequencing permit detailed phenotyping and clonotypic tracking of these S-specific CD8+ T cells. Our results demonstrate that infection-induced S-specific CD8+ T cell memory plays a significant role in shaping the magnitude and clonal composition of the circulating T cell repertoire after vaccination, with mRNA vaccination promoting CD8+ memory T cells to a TEMRA-like phenotype.
Collapse
Affiliation(s)
- Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Heeju Ryu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Amy S Codd
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - K Rachael Parks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Hugh R MacMillan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kristen W Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Terri L Stewart
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Aaron Seese
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Maria P Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julie L Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Long T Nguyen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Donald J McGuire
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| |
Collapse
|
7
|
Johnson AMF, Hager K, Alameh MG, Van P, Potchen N, Mayer-Blackwell K, Fiore-Gartland A, Minot S, Lin PJC, Tam YK, Weissman D, Kublin JG. The Regulation of Nucleic Acid Vaccine Responses by the Microbiome. bioRxiv 2023:2023.02.18.529093. [PMID: 36824851 PMCID: PMC9949122 DOI: 10.1101/2023.02.18.529093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Nucleic acid vaccines, including both RNA and DNA platforms, are key technologies that have considerable promise in combating both infectious disease and cancer. However, little is known about the extrinsic factors that regulate nucleic acid vaccine responses and which may determine their effectiveness. The microbiome is recognized as a significant regulator of immune development and response, whose role in regulating some traditional vaccine platforms has recently been discovered. Using germ-free and specific-pathogen-free mouse models in combination with different protein, DNA, and mRNA vaccine regimens, we demonstrate that the microbiome is a significant regulator of nucleic acid vaccine immunogenicity. While the presence of the microbiome enhances CD8+ T cell responses to mRNA lipid nanoparticle (LNP) immunization, the microbiome suppresses immunoglobulin and CD4+ T cell responses to DNA-prime, DNA-protein-boost immunization, indicating contrasting roles for the microbiome in the regulation of these different nucleic acid vaccine platforms. In the case of mRNA-LNP vaccination, germ-free mice display reduced dendritic cell/macrophage activation that may underlie the deficient vaccine response. Our study identifies the microbiome as a relevant determinant of nucleic acid vaccine response with implications for their continued therapeutic development and deployment.
Collapse
|
8
|
Mayer-Blackwell K, Johnson AM, Potchen N, Minot SS, Heptinstall J, Seaton K, Sawant S, Shen X, Tomaras GD, Fiore-Gartland A, Kublin JG. Multi-trial analysis of HIV-1 envelope gp41-reactive antibodies among global recipients of candidate HIV-1 vaccines. Front Immunol 2022; 13:983313. [PMID: 36311720 PMCID: PMC9597301 DOI: 10.3389/fimmu.2022.983313] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Many participants in HIV-1 vaccine trials, who have not previously been exposed to or vaccinated against HIV-1, display serum immunoglobulin antibodies that bind the gp41 region of HIV-1 envelope prior to vaccination. Previous studies have hypothesized that these pre-existing antibodies may be cross-reactive and may skew future vaccine responses. In 12 large studies conducted by the HIV Vaccine Trial Network (HVTN) (n=1470 individuals), we find wide variation among participants in the pre-vaccine levels of gp41-reactive antibodies as measured by the binding antibody multiplex assay (BAMA). In the absence of exposure to the gp41 immunogen, anti-gp41 IgG levels were temporally stable over 26-52 weeks in repeated measures of placebo recipients. The analysis revealed that the geometric mean of pre-vaccine anti-gp41 IgG response was greater among participants in South Africa compared with participants in the United States. With gene-level metagenomic sequencing of pre-vaccination fecal samples collected from participants in one trial (HVTN 106), we detected positive associations between pre-vaccine anti-gp41 IgG and abundance of genes from multiple taxa in the Eubacteriales order. The genes most strongly associated with higher baseline anti-gp41 IgG mapped to a clade containing Blautia wexlerae and closely related strains. In trials with vaccine products containing the full or partial portion of gp41 immunogen alongside a gp120 immunogen, we did not find evidence that individuals with higher baseline anti-gp41 IgG had different levels of anti-gp120 IgG after vaccination compared to individuals with lower pre-vaccine anti-gp41 levels (pooled estimate of standardized mean difference -0.01 with a 95% CI [-0.37; 0.34]).
Collapse
Affiliation(s)
- Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Andrew M. Johnson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Nicole Potchen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Simon S. Minot
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Jack Heptinstall
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Kelly Seaton
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Sheetal Sawant
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Xiaoying Shen
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Georgia D. Tomaras
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| |
Collapse
|
9
|
Ford ES, Mayer-Blackwell K, Jing L, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. CD8 + T cell clonotypes from prior SARS-CoV-2 infection predominate during the cellular immune response to mRNA vaccination. Res Sq 2022:rs.3.rs-2146712. [PMID: 36263073 PMCID: PMC9580387 DOI: 10.21203/rs.3.rs-2146712/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Almost three years into the SARS-CoV-2 pandemic, hybrid immunity is highly prevalent worldwide and more protective than vaccination or prior infection alone. Given emerging resistance of variant strains to neutralizing antibodies (nAb), it is likely that T cells contribute to this protection. To understand how sequential SARS-CoV-2 infection and mRNA-vectored SARS-CoV-2 spike (S) vaccines affect T cell clonotype-level expansion kinetics, we identified and cross-referenced TCR sequences from thousands of S-reactive single cells against deeply sequenced peripheral blood TCR repertoires longitudinally collected from persons during COVID-19 convalescence through booster vaccination. Successive vaccinations recalled memory T cells and elicited antigen-specific T cell clonotypes not detected after infection. Vaccine-related recruitment of novel clonotypes and the expansion of S-specific clones were most strongly observed for CD8+ T cells. Severe COVID-19 illness was associated with a more diverse CD4+ T cell response to SARS-CoV-2 both prior to and after mRNA vaccination, suggesting imprinting of CD4+ T cells by severe infection. TCR sequence similarity search algorithms revealed myriad public TCR clusters correlating with human leukocyte antigen (HLA) alleles. Selected TCRs from distinct clusters functionally recognized S in the predicted HLA context, with fine viral peptide requirements differing between TCRs. Most subjects tested had S-specific T cells in the nasal mucosa after a 3rd mRNA vaccine dose. The blood and nasal T cell responses to vaccination revealed by clonal tracking were more heterogeneous than nAb boosts. Analysis of bulk and single cell TCR sequences reveals T cell kinetics and diversity at the clonotype level, without requiring prior knowledge of T cell epitopes or HLA restriction, providing a roadmap for rapid assessment of T cell responses to emerging pathogens.
Collapse
|
10
|
Jani S, Pulliam TH, Mayer-Blackwell K, Bradley P, Koelle DM, Nghiem P. Development of a Merkel polyomavirus-specific T cell receptor analysis tool to guide cancer immunotherapy. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
11
|
James CA, Yu KKQ, Mayer-Blackwell K, Fiore-Gartland A, Smith MT, Layton ED, Johnson JL, Hanekom WA, Scriba TJ, Seshadri C. Durable Expansion of TCR-δ Meta-Clonotypes After BCG Revaccination in Humans. Front Immunol 2022; 13:834757. [PMID: 35432299 PMCID: PMC9005636 DOI: 10.3389/fimmu.2022.834757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium bovis bacille Calmette-Guérin (BCG) has been used for 100 years and prevents disseminated tuberculosis and death in young children. However, it shows only partial efficacy against pulmonary tuberculosis (TB) in adults, so new vaccines are urgently needed. The protective efficacy of BCG depends on T cells, which are typically activated by pathogen-derived protein antigens that bind to highly polymorphic major histocompatibility complex (MHC) molecules. Some T cells recognize non-protein antigens via antigen presenting systems that are independent of genetic background, leading to their designation as donor-unrestricted T (DURT) cells. Whether live whole cell vaccines, like BCG, can induce durable expansions of DURT cells in humans is not known. We used combinatorial tetramer staining, multi-parameter flow cytometry, and immunosequencing to comprehensively characterize the effect of BCG on activation and expansion of DURT cell subsets. We examined peripheral blood mononuclear cells (PBMC) derived from a Phase I study of South African adults in which samples were archived at baseline, 3 weeks, and 52 weeks post-BCG revaccination. We did not observe a change in the frequency of total mucosal-associated invariant T (MAIT) cells, invariant natural killer T (iNKT) cells, germline encoded mycolyl-reactive (GEM) T cells, or γδ T cells at 52 weeks post-BCG. However, immunosequencing revealed a set of TCR-δ clonotypes that were expanded at 52 weeks post-BCG revaccination. These expanded clones expressed the Vδ2 gene segment and could be further defined on the basis of biochemical similarity into several 'meta-clonotypes' that likely recognize similar epitopes. Our data reveal that BCG vaccination leads to durable expansion of DURT cell clonotypes despite a limited effect on total circulating frequencies in the blood and have implications for defining the immunogenicity of candidate whole cell TB vaccines.
Collapse
Affiliation(s)
- Charlotte A James
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Krystle K Q Yu
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Malisa T Smith
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Erik D Layton
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - John L Johnson
- Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Willem A Hanekom
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Chetan Seshadri
- Department of Medicine, University of Washington, Seattle, WA, United States
- Tuberculosis Research and Training Center, University of Washington, Seattle, WA, United States
| |
Collapse
|
12
|
Mayer-Blackwell K, Fiore-Gartland A, Thomas PG. Flexible Distance-Based TCR Analysis in Python with tcrdist3. Methods Mol Biol 2022; 2574:309-366. [PMID: 36087210 PMCID: PMC9719034 DOI: 10.1007/978-1-0716-2712-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Paired- and single-chain T cell receptor (TCR) sequencing are now commonly used techniques for interrogating adaptive immune responses. TCRs targeting the same epitope frequently share motifs consisting of critical contact residues. Here we illustrate the key features of tcrdist3, a new Python package for distance-based TCR analysis through a series of three interactive examples. In the first example, we illustrate how tcrdist3 can integrate sequence similarity networks, gene-usage plots, and background-adjusted CDR3 logos to identify TCR sequence features conferring antigen specificity among sets of peptide-MHC-multimer sorted receptors. In the second example, we show how the TCRjoin feature in tcrdist3 can be used to flexibly query receptor sequences of interest against bulk repertoires or libraries of previously annotated TCRs based on matching of similar sequences. In the third example, we show how the TCRdist metric can be leveraged to identify candidate polyclonal receptors under antigenic selection in bulk repertoires based on sequence neighbor enrichment testing, a statistical approach similar to TCRNET and ALICE algorithms, but with added flexibility in how the neighborhood can be defined.
Collapse
Affiliation(s)
- Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Paul G. Thomas
- Immunology Department, St. Jude Children’s Research Hospital, Memphis, USA,Corresponding author: Paul G. Thomas,
| |
Collapse
|
13
|
Mayer-Blackwell K, Schattgen S, Cohen-Lavi L, Crawford JC, Souquette A, Gaevert JA, Hertz T, Thomas PG, Bradley P, Fiore-Gartland A. TCR meta-clonotypes for biomarker discovery with tcrdist3 enabled identification of public, HLA-restricted clusters of SARS-CoV-2 TCRs. eLife 2021; 10:e68605. [PMID: 34845983 PMCID: PMC8631793 DOI: 10.7554/elife.68605] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [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] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 11/11/2021] [Indexed: 01/04/2023] Open
Abstract
T-cell receptors (TCRs) encode clinically valuable information that reflects prior antigen exposure and potential future response. However, despite advances in deep repertoire sequencing, enormous TCR diversity complicates the use of TCR clonotypes as clinical biomarkers. We propose a new framework that leverages experimentally inferred antigen-associated TCRs to form meta-clonotypes - groups of biochemically similar TCRs - that can be used to robustly quantify functionally similar TCRs in bulk repertoires across individuals. We apply the framework to TCR data from COVID-19 patients, generating 1831 public TCR meta-clonotypes from the SARS-CoV-2 antigen-associated TCRs that have strong evidence of restriction to patients with a specific human leukocyte antigen (HLA) genotype. Applied to independent cohorts, meta-clonotypes targeting these specific epitopes were more frequently detected in bulk repertoires compared to exact amino acid matches, and 59.7% (1093/1831) were more abundant among COVID-19 patients that expressed the putative restricting HLA allele (false discovery rate [FDR]<0.01), demonstrating the potential utility of meta-clonotypes as antigen-specific features for biomarker development. To enable further applications, we developed an open-source software package, tcrdist3, that implements this framework and facilitates flexible workflows for distance-based TCR repertoire analysis.
Collapse
Affiliation(s)
- Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Stefan Schattgen
- Department of Immunology, St Jude Children's Research HospitalMemphisUnited States
| | - Liel Cohen-Lavi
- Department of Industrial Engineering and Management, Ben-Gurion University of the NegevBe'er ShevaIsrael
| | - Jeremy C Crawford
- Department of Immunology, St Jude Children's Research HospitalMemphisUnited States
| | | | - Jessica A Gaevert
- Department of Immunology, St Jude Children's Research HospitalMemphisUnited States
| | - Tomer Hertz
- Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the NegevBe'er ShevaUnited States
| | - Paul G Thomas
- St Jude Children's Research HospitalMemphisUnited States
| | - Philip Bradley
- Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| |
Collapse
|
14
|
Mayer-Blackwell K, Schattgen S, Cohen-Lavi L, Crawford JC, Souquette A, Gaevert JA, Hertz T, Thomas PG, Bradley P, Fiore-Gartland A. TCR meta-clonotypes for biomarker discovery with tcrdist3: identification of public, HLA-restricted SARS-CoV-2 associated TCR features. bioRxiv 2021. [PMID: 33398288 PMCID: PMC7781332 DOI: 10.1101/2020.12.24.424260] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
As the mechanistic basis of adaptive cellular antigen recognition, T cell receptors (TCRs) encode clinically valuable information that reflects prior antigen exposure and potential future response. However, despite advances in deep repertoire sequencing, enormous TCR diversity complicates the use of TCR clonotypes as clinical biomarkers. We propose a new framework that leverages antigen-enriched repertoires to form meta-clonotypes - groups of biochemically similar TCRs - that can be used to robustly identify and quantify functionally similar TCRs in bulk repertoires. We apply the framework to TCR data from COVID-19 patients, generating 1831 public TCR meta-clonotypes from the 17 SARS-CoV-2 antigen-enriched repertoires with the strongest evidence of HLA-restriction. Applied to independent cohorts, meta-clonotypes targeting these specific epitopes were more frequently detected in bulk repertoires compared to exact amino acid matches, and 59.7% (1093/1831) were more abundant among COVID-19 patients that expressed the putative restricting HLA allele (FDR < 0.01), demonstrating the potential utility of meta-clonotypes as antigen-specific features for biomarker development. To enable further applications, we developed an open-source software package, tcrdist3, that implements this framework and facilitates flexible workflows for distance-based TCR repertoire analysis.
Collapse
Affiliation(s)
- Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Stefan Schattgen
- Immunology Department, St. Jude Children's Research Hospital, Memphis, USA
| | - Liel Cohen-Lavi
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | | | - Aisha Souquette
- Immunology Department, St. Jude Children's Research Hospital, Memphis, USA
| | - Jessica A Gaevert
- Immunology Department, St. Jude Children's Research Hospital, Memphis, USA.,St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, USA
| | - Tomer Hertz
- Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Paul G Thomas
- Immunology Department, St. Jude Children's Research Hospital, Memphis, USA
| | - Philip Bradley
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| |
Collapse
|
15
|
Grembi JA, Mayer-Blackwell K, Luby SP, Spormann AM. High-Throughput Multiparallel Enteropathogen Detection via Nano-Liter qPCR. Front Cell Infect Microbiol 2020; 10:351. [PMID: 32766166 PMCID: PMC7381150 DOI: 10.3389/fcimb.2020.00351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 01/17/2020] [Accepted: 06/08/2020] [Indexed: 11/13/2022] Open
Abstract
Quantitative molecular diagnostic methods can effectively detect pathogen-specific nucleic acid sequences, but costs associated with multi-pathogen panels hinder their widespread use in research trials. Nano-liter qPCR (nL-qPCR) is a miniaturized tool for quantification of multiple targets in large numbers of samples based on assay parallelization on a single chip, with potentially significant cost-savings due to rapid throughput and reduced reagent volumes. We evaluated a suite of novel and published assays to detect 17 enteric pathogens using a commercially available nL-qPCR technology. Amplification efficiencies ranged from 88 to 98% (mean 91%) and were reproducible across four operators at two separate facilities. When applied to fecal material, assays were sensitive and selective (99.8% of DNA amplified were genes from the target organism). Due to nanofluidic volumes, detection limits were 1-2 orders of magnitude less sensitive for nL-qPCR than an enteric TaqMan Array Card (TAC). However, higher detection limits do not hinder detection of diarrhea-causing pathogen concentrations. Compared to TAC, nL-qPCR displayed 99% (95% CI 0.98, 0.99) negative percent agreement and 62% (95% CI 0.59, 0.65) overall positive percent agreement for presence of pathogens across diarrheal and non-diarrheal fecal samples. Positive percent agreement was 89% among samples with concentrations above the nL-qPCR detection limits. nL-qPCR assays showed an underestimation bias of 0.34 log10 copies/gram of stool [IQR -0.40, -0.28] compared with TAC. With 12 times higher throughput for a sixth of the per-sample cost of the enteric TAC, the nL-qPCR chip is a viable alternative for enteropathogen quantification for studies where other technologies are cost-prohibitive.
Collapse
Affiliation(s)
- Jessica A Grembi
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
| | - Koshlan Mayer-Blackwell
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
| | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, United States
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States.,Department of Chemical Engineering, Stanford University, Stanford, CA, United States
| |
Collapse
|
16
|
Mayer-Blackwell K, Azizian MF, Green JK, Spormann AM, Semprini L. Survival of Vinyl Chloride Respiring Dehalococcoides mccartyi under Long-Term Electron Donor Limitation. Environ Sci Technol 2017; 51:1635-1642. [PMID: 28002948 DOI: 10.1021/acs.est.6b05050] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In anoxic groundwater aquifers, the long-term survival of Dehalococcoides mccartyi populations expressing the gene vcrA (or bvcA) encoding reductive vinyl chloride dehalogenases are important to achieve complete dechlorination of tetrachloroethene (PCE) and trichloroethene (TCE) to nonchlorinated ethene. The absence or inactivity of vcrA-containing Dehalococcoides results in the accumulation of the harmful chlorinated intermediates dichloroethene (DCE) and vinyl chloride (VC). Although vcrA-containing Dehalococcoides subpopulations depend on synergistic interaction with other organohalide-respiring populations generating their metabolic electron acceptors (DCE and VC), their survival requires successful competition for electron donor within the entire organohalide-respiring microbial community. To understand this dualism of synergy and competition under growth conditions relevant in contaminated aquifers, we investigated Dehalococcoides-level population structure when subjected to a change in the ratio of electron donor to chlorinated electron acceptor in continuously stirred tank reactors (CSTRs) operated over 7 years. When the electron donor formate was supplied in stoichiometric excess to TCE, both tceA-containing and vcrA-containing Dehalococcoides populations persisted, and near-complete dechlorination to ethene was stably maintained. When the electron donor formate was supplied at substoichiometric concentrations, the interactions between tceA-containing and vcrA-containing populations shifted toward direct competition for the same limiting catabolic electron donor substrate with subsequent niche exclusion of the vcrA-containing population. After more than 2000 days of operation under electron donor limitation, increasing the electron donor to TCE ratio facilitated a recovery of the vcrA-containing Dehalococoides population to its original frequency. We demonstrate that electron donor scarcity alone, in the absence of competing metabolic processes or inhibitory dechlorination intermediate products, is sufficient to alter the Dehalococcoides population structure. These results underscore the importance of electron donor and chloroethene stoichiometry in maintaining balanced functional performance within consortia composed of multiple D. mccartyi subpopulations, even when other competing electron acceptor processes are absent.
Collapse
Affiliation(s)
| | - Mohammad F Azizian
- Chemical, Biological and Environmental Engineering, Oregon State University , Corvallis, Oregon 97331, United States
| | - Jennifer K Green
- Chemical, Biological and Environmental Engineering, Oregon State University , Corvallis, Oregon 97331, United States
| | | | - Lewis Semprini
- Chemical, Biological and Environmental Engineering, Oregon State University , Corvallis, Oregon 97331, United States
| |
Collapse
|
17
|
Mayer-Blackwell K, Fincker M, Molenda O, Callahan B, Sewell H, Holmes S, Edwards EA, Spormann AM. 1,2-Dichloroethane Exposure Alters the Population Structure, Metabolism, and Kinetics of a Trichloroethene-Dechlorinating Dehalococcoides mccartyi Consortium. Environ Sci Technol 2016; 50:12187-12196. [PMID: 27809491 DOI: 10.1021/acs.est.6b02957] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Bioremediation of groundwater contaminated with chlorinated aliphatic hydrocarbons such as perchloroethene and trichloroethene can result in the accumulation of the undesirable intermediate vinyl chloride. Such accumulation can either be due to the absence of specific vinyl chloride respiring Dehalococcoides mccartyi or to the inhibition of such strains by the metabolism of other microorganisms. The fitness of vinyl chloride respiring Dehalococcoides mccartyi subpopulations is particularly uncertain in the presence of chloroethene/chloroethane cocontaminant mixtures, which are commonly found in contaminated groundwater. Therefore, we investigated the structure of Dehalococcoides populations in a continuously fed reactor system under changing chloroethene/ethane influent conditions. We observed that increasing the influent ratio of 1,2-dichloroethane to trichloroethene was associated with ecological selection of a tceA-containing Dehalococcoides population relative to a vcrA-containing Dehalococcoides population. Although both vinyl chloride and 1,2-dichloroethane could be simultaneously transformed to ethene, prolonged exposure to 1,2-dichloroethane diminished the vinyl chloride transforming capacity of the culture. Kinetic tests revealed that dechlorination of 1,2-dichloroethane by the consortium was strongly inhibited by cis-dichloroethene but not vinyl chloride. Native polyacrylamide gel electrophoresis and mass spectrometry revealed that a trichloroethene reductive dehalogenase (TceA) homologue was the most consistently expressed of four detectable reductive dehalogenases during 1,2-dichloroethane exposure, suggesting that it catalyzes the reductive dihaloelimination of 1,2-dichloroethane to ethene.
Collapse
Affiliation(s)
- Koshlan Mayer-Blackwell
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Maeva Fincker
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Olivia Molenda
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Benjamin Callahan
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Holly Sewell
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Susan Holmes
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A Edwards
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Alfred M Spormann
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| |
Collapse
|
18
|
Mayer-Blackwell K, Azizian MF, Machak C, Vitale E, Carpani G, de Ferra F, Semprini L, Spormann AM. Nanoliter qPCR platform for highly parallel, quantitative assessment of reductive dehalogenase genes and populations of dehalogenating microorganisms in complex environments. Environ Sci Technol 2014; 48:9659-9667. [PMID: 25046033 DOI: 10.1021/es500918w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Idiosyncratic combinations of reductive dehalogenase (rdh) genes are a distinguishing genomic feature of closely related organohalogen-respiring bacteria. This feature can be used to deconvolute the population structure of organohalogen-respiring bacteria in complex environments and to identify relevant subpopulations, which is important for tracking interspecies dynamics needed for successful site remediation. Here we report the development of a nanoliter qPCR platform to identify organohalogen-respiring bacteria and populations by quantifying major orthologous reductive dehalogenase gene groups. The qPCR assays can be operated in parallel within a 5184-well nanoliter qPCR (nL-qPCR) chip at a single annealing temperature and buffer condition. We developed a robust bioinformatics approach to select from thousands of computationally proposed primer pairs those that are specific to individual rdh gene groups and compatible with a single amplification condition. We validated hundreds of the most selective qPCR assays and examined their performance in a trichloroethene-degrading bioreactor, revealing population structures as well as their unexpected shifts in abundance and community dynamics.
Collapse
Affiliation(s)
- Koshlan Mayer-Blackwell
- Civil and Environmental Engineering, §Geological and Environmental Sciences, and ⊥Chemical Engineering, Stanford University , Stanford, California 94305, United States
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Kaster AK, Mayer-Blackwell K, Pasarelli B, Spormann AM. Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin. ISME J 2014; 8:1831-42. [PMID: 24599070 DOI: 10.1038/ismej.2014.24] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/27/2014] [Accepted: 02/03/2014] [Indexed: 11/09/2022]
Abstract
The phylum Chloroflexi is one of the most frequently detected phyla in the subseafloor of the Pacific Ocean margins. Dehalogenating Chloroflexi (Dehalococcoidetes) was originally discovered as the key microorganisms mediating reductive dehalogenation via their key enzymes reductive dehalogenases (Rdh) as sole mode of energy conservation in terrestrial environments. The frequent detection of Dehalococcoidetes-related 16S rRNA and rdh genes in the marine subsurface implies a role for dissimilatory dehalorespiration in this environment; however, the two genes have never been linked to each other. To provide fundamental insights into the metabolism, genomic population structure and evolution of marine subsurface Dehalococcoidetes sp., we analyzed a non-contaminated deep-sea sediment core sample from the Peruvian Margin Ocean Drilling Program (ODP) site 1230, collected 7.3 m below the seafloor by a single cell genomic approach. We present for the first time single cell genomic data on three deep-sea Chloroflexi (Dsc) single cells from a marine subsurface environment. Two of the single cells were considered to be part of a local Dehalococcoidetes population and assembled together into a 1.38-Mb genome, which appears to be at least 85% complete. Despite a high degree of sequence-level similarity between the shared proteins in the Dsc and terrestrial Dehalococcoidetes, no evidence for catabolic reductive dehalogenation was found in Dsc. The genome content is however consistent with a strictly anaerobic organotrophic or lithotrophic lifestyle.
Collapse
Affiliation(s)
| | | | - Ben Pasarelli
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Alfred M Spormann
- 1] Department of Chemical Engineering, Stanford University, Stanford, CA, USA [2] Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| |
Collapse
|