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LeMaster C, Schwendinger-Schreck C, Ge B, Cheung W, Johnston JJ, Pastinen T, Smail C. Mapping structural variants to rare disease genes using long-read whole genome sequencing and trait-relevant polygenic scores. medRxiv 2024:2024.03.15.24304216. [PMID: 38562793 PMCID: PMC10984062 DOI: 10.1101/2024.03.15.24304216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Recent studies have revealed the pervasive landscape of rare structural variants (rSVs) present in human genomes. rSVs can have extreme effects on the expression of proximal genes and, in a rare disease context, have been implicated in patient cases where no diagnostic single nucleotide variant (SNV) was found. Approaches for integrating rSVs to date have focused on targeted approaches in known Mendelian rare disease genes. This approach is intractable for rare diseases with many causal loci or patients with complex, multi-phenotype syndromes. We hypothesized that integrating trait-relevant polygenic scores (PGS) would provide a substantial reduction in the number of candidate disease genes in which to assess rSV effects. We further implemented a method for ranking PGS genes to define a set of core/key genes where a rSV has the potential to exert relatively larger effects on disease risk. Among a subset of patients enrolled in the Genomic Answers for Kids (GA4K) rare disease program (N=497), we used PacBio HiFi long-read whole genome sequencing (lrWGS) to identify rSVs intersecting genes in trait-relevant PGSs. Illustrating our approach in Autism (N=54 cases), we identified 1,827 deletions, 158 duplications, 619 insertions, and 14 inversions overlapping putative core/key PGS genes. Additionally, by integrating genomic constraint annotations from gnomAD, we observed that rare duplications overlapping putative core/key PGS genes were frequently in higher constraint regions compared to controls (P = 2×10-04). This difference was not observed in the lowest-ranked gene set (P = 0.18). Overall, our study provides a framework for the annotation of long-read rSVs from lrWGS data and prioritization of disease-linked genomic regions for downstream functional validation of rSV impacts. To enable reuse by other researchers, we have made SV allele frequencies and gene associations freely available.
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Affiliation(s)
- C LeMaster
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
| | - C Schwendinger-Schreck
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
| | - B Ge
- McGill University, Montreal, Quebec, Canada
| | - W Cheung
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
| | - J J Johnston
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
| | - T Pastinen
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
| | - C Smail
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
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2
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Geanes ES, McLennan R, LeMaster C, Bradley T. Autoantibodies to ACE2 and immune molecules are associated with COVID-19 disease severity. Commun Med (Lond) 2024; 4:47. [PMID: 38491326 PMCID: PMC10943194 DOI: 10.1038/s43856-024-00477-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/05/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Increased inflammation caused by SARS-CoV-2 infection can lead to severe coronavirus disease 2019 (COVID-19) and long-term disease manifestations. The mechanisms of this variable long-term immune activation are poorly defined. One feature of this increased inflammation is elevated levels of proinflammatory cytokines and chemokines. Autoantibodies targeting immune factors such as cytokines, as well as the viral host cell receptor, angiotensin-converting enzyme 2 (ACE2), have been observed after SARS-CoV-2 infection. Autoantibodies to immune factors and ACE2 could interfere with normal immune regulation and lead to increased inflammation, severe COVID-19, and long-term complications. METHODS Here, we deeply profiled the features of ACE2, cytokine, and chemokine autoantibodies in samples from patients recovering from severe COVID-19. We measured the levels of immunoglobulin subclasses (IgG, IgA, IgM) in the peripheral blood against ACE2 and 23 cytokines and other immune molecules. We then utilized an ACE2 peptide microarray to map the linear epitopes targeted by ACE2 autoantibodies. RESULTS We demonstrate that ACE2 autoantibody levels are increased in individuals with severe COVID-19 compared with those with mild infection or no prior infection. We identify epitopes near the catalytic domain of ACE2 targeted by these antibodies. Levels of autoantibodies targeting ACE2 and other immune factors could serve as determinants of COVID-19 disease severity, and represent a natural immunoregulatory mechanism in response to viral infection. CONCLUSIONS These results demonstrate that SARS-CoV-2 infection can increase autoantibody levels to ACE2 and other immune factors. The levels of these autoantibodies are associated with COVID-19 disease severity.
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Affiliation(s)
- Eric S Geanes
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Cas LeMaster
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Todd Bradley
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA.
- Department of Pediatrics, University of Missouri, Kansas City, MO, USA.
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, KS, USA.
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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Evangelous TD, Berry M, Venkatayogi S, LeMaster C, Geanes ES, De Naeyer N, DeMarco T, Shen X, Li H, Hora B, Solomonis N, Misamore J, Lewis MG, Denny TN, Montefiori D, Shaw GM, Wiehe K, Bradley T, Williams WB. Host immunity associated with spontaneous suppression of viremia in therapy-naïve young rhesus macaques following neonatal SHIV infection. J Virol 2023; 97:e0109423. [PMID: 37874153 PMCID: PMC10688376 DOI: 10.1128/jvi.01094-23] [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: 07/20/2023] [Accepted: 09/06/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Despite the advent of highly active anti-retroviral therapy, people are still dying from HIV-related causes, many of whom are children, and a protective vaccine or cure is needed to end the HIV pandemic. Understanding the nature and activation states of immune cell subsets during infection will provide insights into the immunologic milieu associated with viremia suppression that can be harnessed via therapeutic strategies to achieve a functional cure, but these are understudied in pediatric subjects. We evaluated humoral and adaptive host immunity associated with suppression of viremia in rhesus macaques infected soon after birth with a pathogenic SHIV. The results from our study provide insights into the immune cell subsets and functions associated with viremia control in young macaques that may translate to pediatric subjects for the design of future anti-viral strategies in HIV-1-infected infants and children and contribute to an understudied area of HIV-1 pathogenesis in pediatric subjects.
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Affiliation(s)
- Tyler D. Evangelous
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Madison Berry
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Cas LeMaster
- Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Eric S. Geanes
- Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Nicole De Naeyer
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Todd DeMarco
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Division of Surgical Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | | | | | | | - Thomas N. Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - David Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Division of Surgical Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - George M. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Todd Bradley
- Children’s Mercy Kansas City, Kansas City, Missouri, USA
- Department of Pediatrics, UMKC School of Medicine, Kansas City, Missouri, USA
- Departments of Pediatrics and Pathology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Wilton B. Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Division of Surgical Sciences, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
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Bradley T, Geanes E, McLennan R, LeMaster C. Autoantibodies against Angiotensin-converting enzyme 2 and immune molecules are associated with COVID-19 disease severity. Res Sq 2023:rs.3.rs-3304083. [PMID: 37841848 PMCID: PMC10571615 DOI: 10.21203/rs.3.rs-3304083/v1] [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] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Increased inflammation caused by SARS-CoV-2 infection can lead to severe coronavirus disease 2019 (COVID-19) and long-term disease manifestations referred to as post-acute sequalae of COVID (PASC). The mechanisms of this variable long-term immune activation are poorly defined. Autoantibodies targeting immune factors such as cytokines, as well as the viral host cell receptor, angiotensin-converting enzyme 2 (ACE2), have been observed after SARS-CoV-2 infection. Autoantibodies to immune factors and ACE2 could interfere with normal immune regulation and lead to increased inflammation, severe COVID-19, and long-term complications. Here, we deeply pro led the features of ACE2, cytokine, and chemokine autoantibodies in samples from patients recovering from severe COVID-19. We identified epitopes in the catalytic domain of ACE2 targeted by these antibodies, that could inhibit ACE2 function. Levels of autoantibodies targeting ACE2 and other immune factors could serve as determinants of COVID-19 disease severity, and represent a natural immunoregulatory mechanism in response to viral infection.
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LeMaster C, Pierce SH, Geanes ES, Khanal S, Elliott SS, Scott AB, Louiselle DA, McLennan R, Maulik D, Lewis T, Pastinen T, Bradley T. The cellular and immunological dynamics of early and transitional human milk. Commun Biol 2023; 6:539. [PMID: 37202439 DOI: 10.1038/s42003-023-04910-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/03/2023] [Indexed: 05/20/2023] Open
Abstract
Human milk is essential for infant nutrition and immunity, providing protection against infections and other immune-mediated diseases during the lactation period and beyond in later childhood. Milk contains a broad range of bioactive factors such as nutrients, hormones, enzymes, immunoglobulins, growth factors, cytokines, and antimicrobial factors, as well as heterogeneous populations of maternal cells. The soluble and cellular components of milk are dynamic over time to meet the needs of the growing infant. In this study, we utilize systems-approaches to define and characterize 62 analytes of the soluble component, including immunoglobulin isotypes, as well as the cellular component of human milk during the first two weeks postpartum from 36 mothers. We identify soluble immune and growth factors that are dynamic over time and could be utilized to classify milk into different phenotypic groups. We identify 24 distinct populations of both epithelial and immune cells by single-cell transcriptome analysis of 128,016 human milk cells. We found that macrophage populations have shifting inflammatory profiles during the first two weeks of lactation. This analysis provides key insights into the soluble and cellular components of human milk and serves as a substantial resource for future studies of human milk.
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Affiliation(s)
- Cas LeMaster
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Stephen H Pierce
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Eric S Geanes
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Santosh Khanal
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Staci S Elliott
- Division of Neonatology, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Allison B Scott
- Division of Neonatology, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Daniel A Louiselle
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Devika Maulik
- Fetal Health Center, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Tamorah Lewis
- Division of Neonatology, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
- Department of Pediatrics, UMKC School of Medicine, Kansas City, MO, 64108, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
- Department of Pediatrics, UMKC School of Medicine, Kansas City, MO, 64108, USA
| | - Todd Bradley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Department of Pediatrics, UMKC School of Medicine, Kansas City, MO, 64108, USA.
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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LeMaster C, Geanes ES, Fraley ER, Selvarangan R, Bradley T. Vaccination After SARS-CoV-2 Infection Increased Antibody Avidity Against the Omicron Variant Compared to Vaccination Alone. J Infect Dis 2022; 226:1712-1716. [PMID: 35714328 PMCID: PMC9214134 DOI: 10.1093/infdis/jiac247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 01/07/2023] Open
Abstract
The SARS-CoV-2 Omicron variant has caused infections among individuals vaccinated or with prior COVID-19, suggesting immune escape. Here, we showed a decrease in binding and surrogate neutralizing antibody responses to the Omicron variant after 2 doses of the Pfizer COVID-19 mRNA vaccine. Individuals recovered from infection before vaccination had higher antibody levels and avidity to the Omicron variant compared to individuals vaccinated without infection. This suggested that COVID-19 infection before vaccination elicited a higher magnitude and affinity antibody response to the Omicron variant, and repeated exposure through infection or vaccine may be required to improve immunity to emerging SARS-CoV-2 variants.
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Affiliation(s)
- Cas LeMaster
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Eric S Geanes
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Elizabeth R Fraley
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Rangaraj Selvarangan
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children’s Mercy, Kansas City, MO, USA
| | - Todd Bradley
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
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7
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Fraley E, LeMaster C, Khanal S, Banerjee D, Pastinen T, Grundberg E, Selvarangan R, Bradley T. The Impact of Prior Infection and Age on Antibody Persistence After Severe Acute Respiratory Syndrome Coronavirus 2 Messenger RNA Vaccine. Clin Infect Dis 2022; 75:e902-e904. [PMID: 34551091 PMCID: PMC8522412 DOI: 10.1093/cid/ciab850] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Indexed: 01/19/2023] Open
Abstract
Determining the duration of immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines is critical for informing the timing of booster immunization. Many genetic and environmental factors could influence both the magnitude and persistence of the antibody response. Here, we showed that SARS-CoV-2 infection before vaccination and age affected the decay of antibody responses to the SARS-CoV-2 messenger RNA vaccine.
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LeMaster C, Pierce S, Geanes ES, Khanal S, Elliott S, Scott A, Louiselle D, McLennan R, Truog W, Maulik D, Lewis T, Pastinen T, Bradley T. The cellular dynamics of early and transitional human breast milk. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.59.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Breast milk (BM) is a complex fluid containing factors essential for infant nutrition and immunity. Breastfeeding has been shown to be protective against infections and other immune-mediated diseases during the lactation period and beyond in later childhood. This suggests that BM also imprints the neonatal immune system and influences long-term health. BM also contains populations of maternal-derived cells. Which factors in BM that are important for neonatal health and how they change during lactation have not been well-defined. In this study, we used a single-cell transcriptomic approach to identify and define cell types of early and transitional milk. We collected BM samples from mothers of infants 2–5 days (early milk) and 8–12 days (transitional milk) after delivery. We applied single-cell RNA sequencing on over 154,000 BM-derived cells. We identified 25 transcriptionally distinct populations of cells in the BM. As expected, the most abundant cells in BM were mammary epithelial cells and macrophages. Monocytes, T cells, dendritic cells, and neutrophils were also present and had a higher frequency in week 2, suggesting that some immune cells may remain abundant in the early days of lactation and slowly decline as milk matures. We also detected a small number of stem and progenitor, natural killer and B cells in the BM at a higher frequency in week 1. This work provides an atlas of the cellular component in human milk at two timepoints of lactation. In addition to cell identity and frequencies, we have also uncovered unique molecular pathways that are activated in BM cells. This work will lay the foundation for future studies of how these cells influence neonatal health.
Supported by funding from Children's Mercy Kansas City
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Affiliation(s)
- Cas LeMaster
- 1Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City
| | - Stephen Pierce
- 1Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City
- 2Department of Pathology and Laboratory Medicine, university of kansas medical center
| | - Eric S Geanes
- 1Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City
| | - Santosh Khanal
- 1Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City
| | - Staci Elliott
- 3Department of Neonatology, Children’s Mercy Kansas City
| | - Allison Scott
- 3Department of Neonatology, Children’s Mercy Kansas City
| | - Daniel Louiselle
- 1Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City
| | - Rebecca McLennan
- 1Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City
| | - William Truog
- 4Center for Infant Pulmonary Disorders, Children’s Mercy Kansas City
| | - Devika Maulik
- 5Department of Obstetrics and Gynecology, University of Missouri Kansas City
- 6Maternal Fetal Medicine, Children’s Mercy Kansas City
| | - Tamorah Lewis
- 4Center for Infant Pulmonary Disorders, Children’s Mercy Kansas City
| | - Tomi Pastinen
- 1Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City
| | - Todd Bradley
- 1Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City
- 2Department of Pathology and Laboratory Medicine, university of kansas medical center
- 7Department of Pediatrics, University of Missouri Kansas City
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Bradley T, Geanes E, LeMaster C, Fraley ER, Khanal S, McLennan R, Grundberg E, Selvarangan R. Identification of conserved coronavirus epitopes targeted by antibodies after SARS-CoV-2 infection or vaccination. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.65.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
SARS-CoV-2 is a novel betacoronavirus that causes coronavirus disease 2019 and has resulted in millions of deaths worldwide. Novel coronavirus infections in humans have steadily become more common. Understanding antibody responses to SARS-CoV-2, and identifying conserved, cross-reactive epitopes among coronavirus strains could inform the design of vaccines and therapeutics with broad application. Here, we determined that individuals with previous SARS-CoV-2 infection or vaccinated with the Pfizer-BioNTech BNT162b2 vaccine produced antibody responses that cross-reacted with related betacoronaviruses. Moreover, we designed a peptide-conjugate vaccine with a conserved SARS-CoV-2 S2 spike epitope, immunized mice and determined cross-reactive antibody binding to SARS-CoV-2 and other related coronaviruses. This conserved spike epitope also shared sequence homology to proteins in commensal gut microbiota and antibodies targeting this region reacted with proteins in human fecal protein extracts. This indicated that the composition of the gut microbiota could prime immune responses in humans. Thus, SARS-CoV-2 conserved epitopes elicited cross-reactive immune responses to both related coronaviruses and host bacteria that could serve as future targets for broad coronavirus therapeutics and vaccines.
This work was supported through internal institutional funds from Children’s Mercy Research Institute and Children’s Mercy Kansas City.
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Fraley ER, Khanal S, LeMaster C, Pierce S, Pastinen T, Bradley T. B cell receptor repertoire dynamics and convergent evolution following SARS-CoV-2 vaccination. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.65.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel betacoronavirus causing Coronavirus disease 2019 (COVID-19). B cell receptors (BCRs) are expressed at the surface of the B cell and are secreted as soluble antibodies. These antibodies can block viral infection by neutralizing the virus, are critical for resolution of SARS-CoV-2 infection, and may be correlates of protection for COVID-19 vaccines. We have previously shown that SARS-CoV-2 immunization elicits a robust antibody response that is significantly higher in individuals who recovered from COVID-19. Moreover, recovered individuals had slower antibody decay in their levels seven months after vaccination. Here, we sequenced the BCR repertoire of individuals undergoing vaccination by SARS-CoV-2 mRNA vaccine (Pfizer, BNT162b2) with (seropositive) or without (seronegative) previous laboratory confirmed COVID-19 infection. We identified genetic differences in the BCR repertoire between groups including V gene usage, CD3R length, percentage of somatic hypermutation, and clonotype diversity. We then focused our analyses to vaccine-expanded clonotypes in both groups to further analyze the differences in BCR repertoire on candidate SARS-CoV-2-specific clonotypes. We determined the frequency of pre-existing clones present after infection that were engaged by the vaccine in the seropositive group. Moreover, in both groups we identified clonotypes that were shared among individuals that could be a result of convergent evolution. Defining the characteristics and evolution of the BCR repertoire during vaccination of individuals with different histories of viral infection will aid in understanding SARS-CoV-2 humoral response dynamics.
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Geanes ES, LeMaster C, Fraley ER, Khanal S, McLennan R, Grundberg E, Selvarangan R, Bradley T. Cross-reactive antibodies elicited to conserved epitopes on SARS-CoV-2 spike protein after infection and vaccination. Sci Rep 2022; 12:6496. [PMID: 35444221 PMCID: PMC9019795 DOI: 10.1038/s41598-022-10230-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/05/2022] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 is a novel betacoronavirus that caused coronavirus disease 2019 and has resulted in millions of deaths worldwide. Novel coronavirus infections in humans have steadily become more common. Understanding antibody responses to SARS-CoV-2, and identifying conserved, cross-reactive epitopes among coronavirus strains could inform the design of vaccines and therapeutics with broad application. Here, we determined that individuals with previous SARS-CoV-2 infection or vaccinated with the Pfizer-BioNTech BNT162b2 vaccine produced antibody responses that cross-reacted with related betacoronaviruses. Moreover, we designed a peptide-conjugate vaccine with a conserved SARS-CoV-2 S2 spike epitope, immunized mice and determined cross-reactive antibody binding to SARS-CoV-2 and other related coronaviruses. This conserved spike epitope also shared sequence homology to proteins in commensal gut microbiota and could prime immune responses in humans. Thus, SARS-CoV-2 conserved epitopes elicit cross-reactive immune responses to both related coronaviruses and host bacteria that could serve as future targets for broad coronavirus therapeutics and vaccines.
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Affiliation(s)
- Eric S Geanes
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Cas LeMaster
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Elizabeth R Fraley
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Santosh Khanal
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Rangaraj Selvarangan
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA
| | - Todd Bradley
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA. .,Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA. .,Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA. .,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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Fraley E, LeMaster C, Geanes E, Banerjee D, Khanal S, Grundberg E, Selvarangan R, Bradley T. Humoral immune responses during SARS-CoV-2 mRNA vaccine administration in seropositive and seronegative individuals. BMC Med 2021; 19:169. [PMID: 34304742 PMCID: PMC8310732 DOI: 10.1186/s12916-021-02055-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/07/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The global pandemic of coronavirus disease 2019 (COVID-19) is caused by infection with the SARS-CoV-2 virus. Currently, there are three approved vaccines against SARS-CoV-2 in the USA, including two based on messenger RNA (mRNA) technology that has demonstrated high vaccine efficacy. We sought to characterize humoral immune responses, at high resolution, during immunization with the BNT162b2 (Pfizer-BioNTech) vaccine in individuals with or without prior history of natural SARS-CoV-2 infection. METHODS We determined antibody responses after each dose of the BNT162b2 SARS-CoV-2 vaccine in individuals who had no prior history of SARS-CoV-2 infection (seronegative) and individuals that had previous viral infection 30-60 days prior to first vaccination (seropositive). To do this, we used both an antibody isotype-specific multiplexed bead-based binding assays targeting multiple SARS-CoV-2 viral protein antigens and an assay that identified potential SARS-CoV-2 neutralizing antibody levels. Moreover, we mapped antibody epitope specificity after immunization using SARS-CoV-2 spike protein peptide arrays. RESULTS Antibody levels were significantly higher after a single dose in seropositive individuals compared to seronegative individuals and were comparable to levels observed in seronegative individuals after two doses. While IgG was boosted by vaccination for both seronegative and seropositive individuals, only seronegative individuals had increased IgA or IgM antibody titers after primary immunization. We identified immunodominant peptides targeted on both SARS-CoV-2 spike S1 and S2 subunits after vaccination. CONCLUSION These findings demonstrated the antibody responses to SARS-CoV-2 immunization in seropositive and seronegative individuals and provide support for the concept of using prior infection history as a guide for the consideration of future vaccination regimens. Moreover, we identified key epitopes on the SARS-CoV-2 spike protein that are targeted by antibodies after vaccination that could guide future vaccine and immune correlate development.
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Affiliation(s)
- Elizabeth Fraley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Cas LeMaster
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Eric Geanes
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Dithi Banerjee
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Santosh Khanal
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Department of Pediatrics, UMKC School of Medicine, Kansas City, MO, 64108, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA. .,Department of Pediatrics, UMKC School of Medicine, Kansas City, MO, 64108, USA.
| | - Todd Bradley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, 64108, USA. .,Department of Pediatrics, UMKC School of Medicine, Kansas City, MO, 64108, USA. .,Departments of Pediatrics and Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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Bradley T, Grundberg E, Selvarangan R, LeMaster C, Fraley E, Banerjee D, Belden B, Louiselle D, Nolte N, Biswell R, Pastinen T, Myers A, Schuster J. Antibody Responses after a Single Dose of SARS-CoV-2 mRNA Vaccine. N Engl J Med 2021; 384:1959-1961. [PMID: 33755375 PMCID: PMC8008753 DOI: 10.1056/nejmc2102051] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Nick Nolte
- Children's Mercy Kansas City, Kansas City, MO
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