1
|
Pan X, López Acevedo SN, Cuziol C, De Tavernier E, Fahad AS, Longjam PS, Rao SP, Aguilera-Rodríguez D, Rezé M, Bricault CA, Gutiérrez-González MF, de Souza MO, DiNapoli JM, Vigne E, Shahsavarian MA, DeKosky BJ. Large-scale antibody immune response mapping of splenic B cells and bone marrow plasma cells in a transgenic mouse model. Front Immunol 2023; 14:1137069. [PMID: 37346047 PMCID: PMC10280637 DOI: 10.3389/fimmu.2023.1137069] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/30/2023] [Indexed: 06/23/2023] Open
Abstract
Molecular characterization of antibody immunity and human antibody discovery is mainly carried out using peripheral memory B cells, and occasionally plasmablasts, that express B cell receptors (BCRs) on their cell surface. Despite the importance of plasma cells (PCs) as the dominant source of circulating antibodies in serum, PCs are rarely utilized because they do not express surface BCRs and cannot be analyzed using antigen-based fluorescence-activated cell sorting. Here, we studied the antibodies encoded by the entire mature B cell populations, including PCs, and compared the antibody repertoires of bone marrow and spleen compartments elicited by immunization in a human immunoglobulin transgenic mouse strain. To circumvent prior technical limitations for analysis of plasma cells, we applied single-cell antibody heavy and light chain gene capture from the entire mature B cell repertoires followed by yeast display functional analysis using a cytokine as a model immunogen. We performed affinity-based sorting of antibody yeast display libraries and large-scale next-generation sequencing analyses to follow antibody lineage performance, with experimental validation of 76 monoclonal antibodies against the cytokine antigen that identified three antibodies with exquisite double-digit picomolar binding affinity. We observed that spleen B cell populations generated higher affinity antibodies compared to bone marrow PCs and that antigen-specific splenic B cells had higher average levels of somatic hypermutation. A degree of clonal overlap was also observed between bone marrow and spleen antibody repertoires, indicating common origins of certain clones across lymphoid compartments. These data demonstrate a new capacity to functionally analyze antigen-specific B cell populations of different lymphoid organs, including PCs, for high-affinity antibody discovery and detailed fundamental studies of antibody immunity.
Collapse
Affiliation(s)
- Xiaoli Pan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sheila N. López Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Camille Cuziol
- Large Molecule Research, Sanofi, Vitry sur Seine, France
| | | | - Ahmed S. Fahad
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | | | | | - Mathilde Rezé
- Large Molecule Research, Sanofi, Vitry sur Seine, France
| | | | - Matías F. Gutiérrez-González
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Matheus Oliveira de Souza
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | | | | | - Brandon J. DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, United States
| |
Collapse
|
2
|
Efficient human-like antibody repertoire and hybridoma production in trans-chromosomic mice carrying megabase-sized human immunoglobulin loci. Nat Commun 2022; 13:1841. [PMID: 35383174 PMCID: PMC8983744 DOI: 10.1038/s41467-022-29421-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/15/2022] [Indexed: 11/15/2022] Open
Abstract
Trans-chromosomic (Tc) mice carrying mini-chromosomes with megabase-sized human immunoglobulin (Ig) loci have contributed to the development of fully human therapeutic monoclonal antibodies, but mitotic instability of human mini-chromosomes in mice may limit the efficiency of hybridoma production. Here, we establish human antibody-producing Tc mice (TC-mAb mice) that stably maintain a mouse-derived, engineered chromosome containing the entire human Ig heavy and kappa chain loci in a mouse Ig-knockout background. Comprehensive, high-throughput DNA sequencing shows that the human Ig repertoire, including variable gene usage, is well recapitulated in TC-mAb mice. Despite slightly altered B cell development and a delayed immune response, TC-mAb mice have more subsets of antigen-specific plasmablast and plasma cells than wild-type mice, leading to efficient hybridoma production. Our results thus suggest that TC-mAb mice offer a valuable platform for obtaining fully human therapeutic antibodies, and a useful model for elucidating the regulation of human Ig repertoire formation. Trans-chromosomic (Tc) mice have helped the development of therapeutic antibodies, but chromosome instability limits its application. Here the authors develop a new line of Tc mice with full human Ig heavy and kappa loci integrated into the mouse artificial chromosome for stable passage, and confirm efficient generation of B cell responses and specific antibodies.
Collapse
|
3
|
Schmitz S, Soto C, Crowe JE, Meiler J. Human-likeness of antibody biologics determined by back-translation and comparison with large antibody variable gene repertoires. MAbs 2021; 12:1758291. [PMID: 32397786 PMCID: PMC8648325 DOI: 10.1080/19420862.2020.1758291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The antibody (Ab) germline gene rearrangement of variable (V), diversity (D), and joining (J) gene segments, as well as somatic hypermutation, give rise to the human Ab variable gene sequence repertoire. It is common to characterize single nucleotide frequencies of the variable region by alignment to species-specific wildtype germline genes. The increasing application of next-generation sequencing to immune repertoire studies has led to the compilation of increasing large adaptive immunome receptor repertoire datasets. We have developed a method that maps the sequence of a target Ab onto an immunome dataset of 326 million human Ab sequences. For this purpose, we created a position- and gene-specific scoring matrix (PGSSM) and its corresponding antibody similarity score. We characterized our PGSSM score and found that it strongly correlated with the phylogenetic distance of 181,355 Ab sequences from GenBank across 20 species. The most likely human nucleotide back-translation was obtained given only PGSSMs and the amino acid sequence of an Ab achieving a nucleotide sequence recovery of 95.9% and 97.2% for human heavy and light chains, respectively. In conclusion, the scoring of our back-translation is a valuable estimate for the similarity of an Ab sequence to the natural human repertoire. As expected, Ab therapeutic molecules developed from a human source showed a higher similarity to the repertoire than engineered Abs. Thus, the PGSSM metric introduced here can be used to engineer human-like Ab therapeutics.
Collapse
Affiliation(s)
- Samuel Schmitz
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Cinque Soto
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.,The Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James E Crowe
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.,The Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.,Institute for Drug Development, Leipzig University Medical School, Leipzig, SAC, Germany
| |
Collapse
|
4
|
Liao H, Li S, Yu Y, Yue Y, Su K, Zheng Q, Jiang N, Zhang Z. Characteristics of Plasmablast Repertoire in Chronically HIV-Infected Individuals for Immunoglobulin H and L Chain Profiled by Single-Cell Analysis. Front Immunol 2020; 10:3163. [PMID: 32117215 PMCID: PMC7026028 DOI: 10.3389/fimmu.2019.03163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/31/2019] [Indexed: 02/05/2023] Open
Abstract
Characterization of the diversified immunoglobulin (Ig) repertoire may provide insight into pathways that shape an efficient antibody (Ab) repertoire for immune response against human immunodeficiency virus (HIV) infection. This study aimed to profile characteristics of the plasmablast repertoire during chronic HIV infection. Ig variable regions of plasmablasts from both chronically HIV-infected donors (HIVDs) previously treated with antiretroviral therapy (ART) and healthy donors (HDs) were amplified by single-cell PCR to establish the basis for further repertoire analysis. We compared the plasmablast repertoires expressed in multiple chronically HIVDs after ART treatment cessation and HDs. We also examined the non-productive repertoire to identify the indication of the immediate products of the rearrangement machinery without an impact of selection during HIV infection. We found multiple differences between the productive repertoires of HIVD and HD subjects, including biased usages of VH3-49, VH1-2, VH3-33, VH3-74, and VH5-51 in VH and D1-7, D1-14, D1-20, and D5-5/18 in D segments in the HIVD group, as well as shorter and preferential glycine usages in CDRH3 regions. Gene selections were also detected in light chains. Notably, differences between productive rearrangements of HIVDs and HDs outnumbered those between productive and non-productive rearrangements within HIVDs. HIV infection may exert a dominant impact on the development of the plasmablast repertoire. The impact of selection is of limited significance in shaping the plasmablast repertoire. Overall, the data indicate that the environment in which the plasmablasts live can affect the distribution of the VH and VL genes in the repertoire and the amino acid compositions of the expressed Abs.
Collapse
Affiliation(s)
- Hongyan Liao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Song Li
- Department of Chemotherapy, Cancer Center, Qilu Hospital of Shandong University, Jinan, China
| | - Yangsheng Yu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Yinshi Yue
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Kaihong Su
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States.,Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States.,Eppley Research Institute, University of Nebraska Medical Center, Omaha, NE, United States
| | - Qin Zheng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Nenggang Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Zhixin Zhang
- State Key Laboratory of Biotherapy, Ministry of Education Key Laboratory of Birth Defects, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
5
|
Joyce C, Burton DR, Briney B. Comparisons of the antibody repertoires of a humanized rodent and humans by high throughput sequencing. Sci Rep 2020; 10:1120. [PMID: 31980672 PMCID: PMC6981180 DOI: 10.1038/s41598-020-57764-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 12/12/2019] [Indexed: 11/10/2022] Open
Abstract
The humanization of animal model immune systems by genetic engineering has shown great promise for antibody discovery, tolerance studies and for the evaluation of vaccines. Assessment of the baseline antibody repertoires of unimmunized model animals will be useful as a benchmark for future immunization experiments. We characterized the heavy chain and kappa light chain antibody repertoires of a model animal, the OmniRat, by high throughput antibody sequencing and made use of two novel datasets for comparison to human repertoires. Intra-animal and inter-animal repertoire comparisons reveal a high level of conservation in antibody diversity between the lymph node and spleen and between members of the species. Multiple differences were found in both the heavy and kappa chain repertoires between OmniRats and humans including gene segment usage, CDR3 length distributions, class switch recombination, somatic hypermutation levels and in features of V(D)J recombination. The Inference and Generation of Repertoires (IGoR) software tool was used to model recombination in VH regions which allowed for the quantification of some of these differences. Diversity estimates of the OmniRat heavy chain repertoires almost reached that of humans, around two orders of magnitude less. Despite variation between the species repertoires, a high frequency of OmniRat clonotypes were also found in the human repertoire. These data give insights into the development and selection of humanized animal antibodies and provide actionable information for use in vaccine studies.
Collapse
Affiliation(s)
- Collin Joyce
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Human Vaccines Project, New York, NY, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Human Vaccines Project, New York, NY, USA.
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
6
|
Collins AM, Watson CT. Immunoglobulin Light Chain Gene Rearrangements, Receptor Editing and the Development of a Self-Tolerant Antibody Repertoire. Front Immunol 2018; 9:2249. [PMID: 30349529 PMCID: PMC6186787 DOI: 10.3389/fimmu.2018.02249] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/13/2022] Open
Abstract
Discussion of the antibody repertoire usually emphasizes diversity, but a conspicuous feature of the light chain repertoire is its lack of diversity. The diversity of reported allelic variants of germline light chain genes is also limited, even in well-studied species. In this review, the implications of this lack of diversity are considered. We explore germline and rearranged light chain genes in a variety of species, with a particular focus on human and mouse genes. The importance of the number, organization and orientation of the genes for the control of repertoire development is discussed, and we consider how primary rearrangements and receptor editing together shape the expressed light chain repertoire. The resulting repertoire is dominated by just a handful of IGKV and IGLV genes. It has been hypothesized that an important function of the light chain is to guard against self-reactivity, and the role of secondary rearrangements in this process could explain the genomic organization of the light chain genes. It could also explain why the light chain repertoire is so limited. Heavy and light chain genes may have co-evolved to ensure that suitable light chain partners are usually available for each heavy chain that forms early in B cell development. We suggest that the co-evolved loci of the house mouse often became separated during the inbreeding of laboratory mice, resulting in new pairings of loci that are derived from different sub-species of the house mouse. A resulting vulnerability to self-reactivity could explain at least some mouse models of autoimmune disease.
Collapse
Affiliation(s)
- Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| |
Collapse
|
7
|
Adler AS, Bedinger D, Adams MS, Asensio MA, Edgar RC, Leong R, Leong J, Mizrahi RA, Spindler MJ, Bandi SR, Huang H, Tawde P, Brams P, Johnson DS. A natively paired antibody library yields drug leads with higher sensitivity and specificity than a randomly paired antibody library. MAbs 2018; 10:431-443. [PMID: 29376776 PMCID: PMC5916548 DOI: 10.1080/19420862.2018.1426422] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Deep sequencing and single-chain variable fragment (scFv) yeast display methods are becoming more popular for discovery of therapeutic antibody candidates in mouse B cell repertoires. In this study, we compare a deep sequencing and scFv display method that retains native heavy and light chain pairing with a related method that randomly pairs heavy and light chain. We performed the studies in a humanized mouse, using interleukin 21 receptor (IL-21R) as a test immunogen. We identified 44 high-affinity binder scFv with the native pairing method and 100 high-affinity binder scFv with the random pairing method. 30% of the natively paired scFv binders were also discovered with the randomly paired method, and 13% of the randomly paired binders were also discovered with the natively paired method. Additionally, 33% of the scFv binders discovered only in the randomly paired library were initially present in the natively paired pre-sort library. Thus, a significant proportion of “randomly paired” scFv were actually natively paired. We synthesized and produced 46 of the candidates as full-length antibodies and subjected them to a panel of binding assays to characterize their therapeutic potential. 87% of the antibodies were verified as binding IL-21R by at least one assay. We found that antibodies with native light chains were more likely to bind IL-21R than antibodies with non-native light chains, suggesting a higher false positive rate for antibodies from the randomly paired library. Additionally, the randomly paired method failed to identify nearly half of the true natively paired binders, suggesting a higher false negative rate. We conclude that natively paired libraries have critical advantages in sensitivity and specificity for antibody discovery programs.
Collapse
Affiliation(s)
- Adam S Adler
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Daniel Bedinger
- b Carterra Inc. , 825 N 300 W, Suite C309, Salt Lake City , UT USA
| | - Matthew S Adams
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Michael A Asensio
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Robert C Edgar
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Renee Leong
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Jackson Leong
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Rena A Mizrahi
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Matthew J Spindler
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | | | - Haichun Huang
- c Bristol-Myers Squibb , 700 Bay Road, Redwood City , CA USA
| | - Pallavi Tawde
- c Bristol-Myers Squibb , 700 Bay Road, Redwood City , CA USA
| | - Peter Brams
- c Bristol-Myers Squibb , 700 Bay Road, Redwood City , CA USA
| | - David S Johnson
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| |
Collapse
|
8
|
Liao H, Yu Y, Li S, Yue Y, Tao C, Su K, Zhang Z. Circulating Plasmablasts from Chronically Human Immunodeficiency Virus-Infected Individuals Predominantly Produce Polyreactive/Autoreactive Antibodies. Front Immunol 2017; 8:1691. [PMID: 29270169 PMCID: PMC5723652 DOI: 10.3389/fimmu.2017.01691] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/16/2017] [Indexed: 02/05/2023] Open
Abstract
Understanding the B-cell response during chronic human immunodeficiency virus (HIV) infection is essential for eliciting broad and potent neutralizing antibodies (Abs). In this study, we analyzed the plasmablast repertoire of chronically HIV-infected individuals in combination with antiretroviral therapy (ART). Among the obtained 72 recombinant monoclonal antibodies (mAbs), 27.8% weakly bound to HIV gp140 and were non-neutralizing. Remarkably, 56.9% were polyreactive and 55.6% were autoreactive. The prominent feature of being polyreactive/autoreactive is not limited to anti-gp140 Abs. Furthermore, these polyreactive/autoreactive Abs displayed striking cross-reactivity with DWEYS in the N-methyl-d-aspartate receptor (NMDAR), and this binding induced SH-SY5Y cell apoptosis. We also found higher frequencies of VH4-34 utilization and VH replacement in the plasmablast repertoire of chronically HIV-infected individuals, which may contribute to the generation of poly/autoreactive Abs. Taken together, these data demonstrate that circulating plasmablasts in chronically HIV-infected individuals experienced with ART predominantly produce poly/autoreactive Abs with minimal anti-HIV neutralizing capacity and potential cross-reactivity with autoantigens. This may represent another dysfunction of B cells during chronic HIV infection.
Collapse
Affiliation(s)
- Hongyan Liao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Yangsheng Yu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Song Li
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States.,Qilu Hospital of Shandong University, Jinan, China
| | - Yinshi Yue
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Chuanmin Tao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Kaihong Su
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States.,Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States.,Eppley Research Institute, University of Nebraska Medical Center, Omaha, NE, United States
| | - Zhixin Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Ministry of Education Key Laboratory of Birth Defects, Sichuan University, Chengdu, China
| |
Collapse
|
9
|
Khavrutskii IV, Chaudhury S, Stronsky SM, Lee DW, Benko JG, Wallqvist A, Bavari S, Cooper CL. Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses. Front Immunol 2017; 8:910. [PMID: 28855898 PMCID: PMC5557726 DOI: 10.3389/fimmu.2017.00910] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/17/2017] [Indexed: 12/15/2022] Open
Abstract
Recent advances in the next-generation sequencing of B-cell receptors (BCRs) enable the characterization of humoral responses at a repertoire-wide scale and provide the capability for identifying unique features of immune repertoires in response to disease, vaccination, or infection. Immunosequencing now readily generates 103–105 sequences per sample; however, statistical analysis of these repertoires is challenging because of the high genetic diversity of BCRs and the elaborate clonal relationships among them. To date, most immunosequencing analyses have focused on reporting qualitative trends in immunoglobulin (Ig) properties, such as usage or somatic hypermutation (SHM) percentage of the Ig heavy chain variable (IGHV) gene segment family, and on reducing complex Ig property distributions to simple summary statistics. However, because Ig properties are typically not normally distributed, any approach that fails to assess the distribution as a whole may be inadequate in (1) properly assessing the statistical significance of repertoire differences, (2) identifying how two repertoires differ, and (3) determining appropriate confidence intervals for assessing the size of the differences and their potential biological relevance. To address these issues, we have developed a technique that uses Wilcox’ robust statistics toolbox to identify statistically significant vaccine-specific differences between Ig repertoire properties. The advantage of this technique is that it can determine not only whether but also where the distributions differ, even when the Ig repertoire properties are non-normally distributed. We used this technique to characterize murine germinal center (GC) B-cell repertoires in response to a complex Ebola virus-like particle (eVLP) vaccine candidate with known protective efficacy. The eVLP-mediated GC B-cell responses were highly diverse, consisting of thousands of clonotypes. Despite this staggering diversity, we identified statistically significant differences between non-immunized, vaccine only, and vaccine-plus-adjuvant groups in terms of Ig properties, including IGHV-family usage, SHM percentage, and characteristics of the BCR complementarity-determining region. Most notably, our analyses identified a robust eVLP-specific feature—enhanced IGHV8-family usage in B-cell repertoires. These findings demonstrate the utility of our technique in identifying statistically significant BCR repertoire differences following vaccination. More generally, our approach is potentially applicable to a wide range of studies in infection, vaccination, auto-immunity, and cancer.
Collapse
Affiliation(s)
- Ilja V Khavrutskii
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Sidhartha Chaudhury
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Sabrina M Stronsky
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
| | - Donald W Lee
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Jacqueline G Benko
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Sina Bavari
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
| | - Christopher L Cooper
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
| |
Collapse
|