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Fonte C, Jacob P, Vanet A, Ghislin S, Frippiat JP. Hindlimb unloading, a physiological model of microgravity, modifies the murine bone marrow IgM repertoire in a similar manner as aging but less strongly. Immun Ageing 2023; 20:64. [PMID: 37986079 PMCID: PMC10659048 DOI: 10.1186/s12979-023-00393-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/12/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND The spaceflight environment is an extreme environment that affects the immune system of approximately 50% of astronauts. With planned long-duration missions, such as the deployment of the Lunar Gateway and possible interplanetary missions, it is mandatory to determine how all components of the immune system are affected, which will allow the establishment of countermeasures to preserve astronaut health. However, despite being an important component of the immune system, antibody-mediated humoral immunity has rarely been investigated in the context of the effects of the space environment. It has previously been demonstrated that 30 days aboard the BION-M1 satellite and 21 days of hindlimb unloading (HU), a model classically used to mimic the effects of microgravity, decrease murine B lymphopoiesis. Furthermore, modifications in B lymphopoiesis reported in young mice subjected to 21 days of HU were shown to be similar to those observed in aged mice (18-22 months). Since the primary antibody repertoire composed of IgM is created by V(D) J recombination during B lymphopoiesis, the objective of this study was to assess the degree of similarity between changes in the bone marrow IgM repertoire and in the V(D)J recombination process in 2.5-month-old mice subjected to 21 days of HU and aged (18 months) mice. RESULTS We found that in 21 days, HU induced changes in the IgM repertoire that were approximately 3-fold less than those in aged mice, which is a rapid effect. Bone remodeling and epigenetics likely mediate these changes. Indeed, we previously demonstrated a significant decrease in tibial morphometric parameters from day 6 of HU and a progressive reduction in these parameters until day 21 of HU, and it has been shown that age and microgravity induce epigenetic changes. CONCLUSION These data reveal novel immune changes that are akin to advanced aging and underline the importance of studying the effects of spaceflight on antibody-mediated humoral immunity.
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Affiliation(s)
- Coralie Fonte
- Stress Immunity Pathogens Laboratory, UR 7300 SIMPA, Faculty of Medicine, Lorraine University, Vandoeuvre-lès, Nancy, France
| | - Pauline Jacob
- Stress Immunity Pathogens Laboratory, UR 7300 SIMPA, Faculty of Medicine, Lorraine University, Vandoeuvre-lès, Nancy, France
| | - Anne Vanet
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Stéphanie Ghislin
- Stress Immunity Pathogens Laboratory, UR 7300 SIMPA, Faculty of Medicine, Lorraine University, Vandoeuvre-lès, Nancy, France
| | - Jean-Pol Frippiat
- Stress Immunity Pathogens Laboratory, UR 7300 SIMPA, Faculty of Medicine, Lorraine University, Vandoeuvre-lès, Nancy, France.
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Wu H, Zhou Z, Xie S, Yan R, Gong M, Tian X, Wang Z. Similarity measurements of B cell receptor repertoire in baseline mice showed spectrum convergence of IgM. BMC Immunol 2022; 23:11. [PMID: 35246036 PMCID: PMC8895918 DOI: 10.1186/s12865-022-00482-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The B cell receptor (BCR) repertoire is highly diverse among individuals. Poor similarity of the spectrum among inbred baseline mice may limit the ability to discriminate true signals from those involving specific experimental factors. The repertoire similarity of the baseline status lacks intensive measurements. RESULTS We measured the repertoire similarity of IgH in blood and spleen samples from untreated BALB/c and C57BL/6J mice to investigate the baseline status of the two inbred strains. The antibody pool was stratified by the isotype of IgA, IgG and IgM. Between individuals, the results showed better convergence of CDR3 and clonal lineage profiles in IgM than in IgA and IgG, and better robustness of somatic mutation networks in IgM than in IgA and IgG. It also showed that the CDR3 clonotypes and clonal lineages shared better in the spleen samples than in the blood samples. The animal batch differences were detected in CDR3 evenness, mutated clonotype proportions, and maximal network degrees. A cut-off of 95% identity in the CDR3 nucleotide sequences was suitable for clonal lineage establishment. CONCLUSIONS Our findings reveal a natural landscape of BCR repertoire similarities between baseline mice and provide a solid reference for designing studies of mouse BCR repertoires.
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Affiliation(s)
- Hongkai Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Shi Xie
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong Yan
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mingxing Gong
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xingui Tian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
| | - Zhanhui Wang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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3
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Lai Polo SH, Saravia-Butler AM, Boyko V, Dinh MT, Chen YC, Fogle H, Reinsch SS, Ray S, Chakravarty K, Marcu O, Chen RB, Costes SV, Galazka JM. RNAseq Analysis of Rodent Spaceflight Experiments Is Confounded by Sample Collection Techniques. iScience 2020; 23:101733. [PMID: 33376967 PMCID: PMC7756143 DOI: 10.1016/j.isci.2020.101733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/04/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
To understand the physiological changes that occur in response to spaceflight, mice are transported to the International Space Station (ISS) and housed for variable periods of time before euthanasia on-orbit or return to Earth. Sample collection under such difficult conditions introduces confounding factors that need to be identified and addressed. We found large changes in the transcriptome of mouse tissues dissected and preserved on-orbit compared with tissues from mice euthanized on-orbit, preserved, and dissected after return to Earth. Changes due to preservation method eclipsed those between flight and ground samples, making it difficult to identify spaceflight-specific changes. Follow-on experiments to interrogate the roles of euthanasia methods, tissue and carcass preservation protocols, and library preparation methods suggested that differences due to preservation protocols are exacerbated when coupled with polyA selection. This has important implications for the interpretation of existing datasets and the design of future experiments. Experimentation is necessary to understand how organisms respond to space Specialized protocols are used for preserving biological samples on the ISS RNAseq datasets are impacted by preservation protocols used on the ISS Impacts can be alleviated with improved carcass preservation protocols
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Affiliation(s)
- San-Huei Lai Polo
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Amanda M Saravia-Butler
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,Logyx, LLC, Mountain View, CA 94043, USA
| | - Valery Boyko
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,The Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Marie T Dinh
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,Logyx, LLC, Mountain View, CA 94043, USA
| | - Yi-Chun Chen
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Homer Fogle
- NASA Ames Research Center, Moffett Field, CA 94035, USA.,The Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Shayoni Ray
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | | | - Oana Marcu
- Carl Sagan Center, SETI Institute, Mountain View, CA 94043, USA
| | - Rick B Chen
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,NASA Ames Research Center, Moffett Field, CA 94035, USA
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Buchheim JI, Ghislin S, Ouzren N, Albuisson E, Vanet A, Matzel S, Ponomarev S, Rykova M, Choukér A, Frippiat JP. Plasticity of the human IgM repertoire in response to long-term spaceflight. FASEB J 2020; 34:16144-16162. [PMID: 33047384 DOI: 10.1096/fj.202001403rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022]
Abstract
Immune dysregulation is among the main adverse outcomes of spaceflight. Despite the crucial role of the antibody repertoire in host protection, the effects of spaceflight on the human antibody repertoire are unknown. Consequently, using high-throughput sequencing, we examined the IgM repertoire of five cosmonauts 25 days before launch, after 64 ± 11 and 129 ± 20 days spent on the International Space Station (ISS), and at 1, 7, and 30 days after landing. This is the first study of this kind in humans. Our data revealed that the IgM repertoire of the cosmonauts was different from that of control subjects (n = 4) prior to launch and that two out the five analyzed cosmonauts presented significant changes in their IgM repertoire during the mission. These modifications persisted up to 30 days after landing, likely affected the specificities of IgM binding sites, correlated with changes in the V(D)J recombination process responsible for creating antibody genes, and coincided with a higher stress response. These data confirm that the immune system of approximately half of the astronauts who spent 6 months on the ISS is sensitive to spaceflight conditions, and reveal individual responses indicating that personalized approaches should be implemented during future deep-space exploration missions that will be of unprecedented durations.
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Affiliation(s)
- Judith-Irina Buchheim
- Laboratory of Translational Research "Stress and Immunity", Department of Anesthesiology, Hospital of the Ludwig-Maximilians-University, Munich, Germany
| | - Stéphanie Ghislin
- Stress Immunity Pathogens Laboratory, EA 7300 Faculty of Medicine, Lorraine University, Vandoeuvre-lès-Nancy, France
| | - Nassima Ouzren
- Stress Immunity Pathogens Laboratory, EA 7300 Faculty of Medicine, Lorraine University, Vandoeuvre-lès-Nancy, France
| | - Eliane Albuisson
- DRCI, MPI Department, Methodology Unit, Data Management and Statistics UMDS, Nancy University Hospital, Vandoeuvre-lès-Nancy, France
| | - Anne Vanet
- University of Paris, Paris, France.,Genoinformatics Center, Jacques Monod Institute, UMR7592, CNRS, Paris, France
| | - Sandra Matzel
- Laboratory of Translational Research "Stress and Immunity", Department of Anesthesiology, Hospital of the Ludwig-Maximilians-University, Munich, Germany
| | - Sergey Ponomarev
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, Russia
| | - Marina Rykova
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Choukér
- Laboratory of Translational Research "Stress and Immunity", Department of Anesthesiology, Hospital of the Ludwig-Maximilians-University, Munich, Germany
| | - Jean-Pol Frippiat
- Stress Immunity Pathogens Laboratory, EA 7300 Faculty of Medicine, Lorraine University, Vandoeuvre-lès-Nancy, France
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Rettig TA, Bye BA, Nishiyama NC, Hlavacek S, Ward C, Pecaut MJ, Chapes SK. Effects of skeletal unloading on the antibody repertoire of tetanus toxoid and/or CpG treated C57BL/6J mice. PLoS One 2019; 14:e0210284. [PMID: 30653556 PMCID: PMC6336310 DOI: 10.1371/journal.pone.0210284] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/19/2018] [Indexed: 01/26/2023] Open
Abstract
Spaceflight affects the immune system, but the effects on the antibody repertoire, responsible for humoral immunity, has not been well explored. In particular, the complex gene assembly and expression process; including mutations, might make this process vulnerable. Complementarity determining region 3 (CDR3), composed of parts of the V-(D-)J-gene segments, is very important for antigen binding and can be used as an important measure of variability. Skeletal unloading, and the physiological effects of it, parallel many impacts of space flight. Therefore, we explored the impact of skeletal unloading using the antiorthostatic suspension (AOS) model. Animals were experimentally challenged with tetanus toxoid (TT) and/or the adjuvant CpG. Blood was analyzed for anti-TT antibody and corticosterone concentrations. Whole spleen tissue was prepared for repertoire characterization. AOS animals showed higher levels of corticosterone levels, but AOS alone did not affect anti-TT serum antibody levels. Administration of CpG significantly increased the circulating anti-TT antibody concentrations. AOS did alter constant gene usage resulting in higher levels of IgM and lower levels of IgG. CpG also altered constant gene region usage increasing usage of IgA. Significant changes could be detected in multiple V-, D-, and J-gene segments in both the heavy and light chains in response to AOS, TT, and CpG treatments. Analysis of class-switched only transcripts revealed a different pattern of V-gene segment usage than detected in the whole repertoire and also showed significant alterations in gene segment usage after challenge. Alterations in V/J pairing were also detected in response to challenge. CDR3 amino acid sequence overlaps were similar among treatment groups, though the addition of CpG lowered overlap in the heavy chain. We isolated 3,045 whole repertoire and 98 potentially TT-specific CDR3 sequences for the heavy chain and 569 for the light chain. Our results demonstrate that AOS alters the repertoire response to challenge with TT and/or CpG.
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Affiliation(s)
- Trisha A. Rettig
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Bailey A. Bye
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Nina C. Nishiyama
- Division of Biomedical Engineering Sciences, Loma Linda University, Loma Linda, California, United States of America
| | - Savannah Hlavacek
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Claire Ward
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Michael J. Pecaut
- Division of Biomedical Engineering Sciences, Loma Linda University, Loma Linda, California, United States of America
| | - Stephen K. Chapes
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
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Rettig TA, Pecaut MJ, Chapes SK. A comparison of unamplified and massively multiplexed PCR amplification for murine antibody repertoire sequencing. FASEB Bioadv 2019; 1:6-17. [PMID: 32123808 PMCID: PMC6996338 DOI: 10.1096/fba.1017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/09/2018] [Accepted: 08/17/2018] [Indexed: 11/26/2022] Open
Abstract
Sequencing antibody repertoires has steadily become cheaper and easier. Sequencing methods usually rely on some form of amplification, often a massively multiplexed PCR prior to sequencing. To eliminate potential biases and create a data set that could be used for other studies, our laboratory compared unamplified sequencing results from the splenic heavy-chain repertoire in the mouse to those processed through two commercial applications. We also compared the use of mRNA vs total RNA, reverse transcriptase, and primer usage for cDNA synthesis and submission. The use of mRNA for cDNA synthesis resulted in higher read counts but reverse transcriptase and primer usage had no statistical effects on read count. Although most of the amplified data sets contained more antibody reads than the unamplified data set, we detected more unique variable (V)-gene segments in the unamplified data set. Although unique CDR3 detection was much lower in the unamplified data set, RNASeq detected 98% of the high-frequency CDR3s. We have shown that unamplified profiling of the antibody repertoire is possible, detects more V-gene segments, and detects high-frequency clones in the repertoire.
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Affiliation(s)
| | - Michael J. Pecaut
- Division of Biomedical Engineering Sciences (BMES)Loma Linda UniversityLoma LindaCalifornia
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Ward C, Rettig TA, Hlavacek S, Bye BA, Pecaut MJ, Chapes SK. Effects of spaceflight on the immunoglobulin repertoire of unimmunized C57BL/6 mice. LIFE SCIENCES IN SPACE RESEARCH 2018; 16:63-75. [PMID: 29475521 PMCID: PMC5826609 DOI: 10.1016/j.lssr.2017.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/20/2017] [Accepted: 11/27/2017] [Indexed: 05/25/2023]
Abstract
Spaceflight has been shown to suppress the adaptive immune response, altering the distribution and function of lymphocyte populations. B lymphocytes express highly specific and highly diversified receptors, known as immunoglobulins (Ig), that directly bind and neutralize pathogens. Ig diversity is achieved through the enzymatic splicing of gene segments within the genomic DNA of each B cell in a host. The collection of Ig specificities within a host, or Ig repertoire, has been increasingly characterized in both basic research and clinical settings using high-throughput sequencing technology (HTS). We utilized HTS to test the hypothesis that spaceflight affects the B-cell repertoire. To test this hypothesis, we characterized the impact of spaceflight on the unimmunized Ig repertoire of C57BL/6 mice that were flown aboard the International Space Station (ISS) during the Rodent Research One validation flight in comparison to ground controls. Individual gene segment usage was similar between ground control and flight animals, however, gene segment combinations and the junctions in which gene segments combine was varied among animals within and between treatment groups. We also found that spontaneous somatic mutations in the IgH and Igκ gene loci were not increased. These data suggest that space flight did not affect the B cell repertoire of mice flown and housed on the ISS over a short period of time.
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Affiliation(s)
- Claire Ward
- Division of Biology, Kansas State University, 1717 Claflin Rd, 116 Ackert Hall, Manhattan, KS 66502, United States
| | - Trisha A Rettig
- Division of Biology, Kansas State University, 1717 Claflin Rd, 116 Ackert Hall, Manhattan, KS 66502, United States
| | - Savannah Hlavacek
- Division of Biology, Kansas State University, 1717 Claflin Rd, 116 Ackert Hall, Manhattan, KS 66502, United States
| | - Bailey A Bye
- Division of Biology, Kansas State University, 1717 Claflin Rd, 116 Ackert Hall, Manhattan, KS 66502, United States
| | - Michael J Pecaut
- Department of Basic Sciences, Division of Radiation Research, Loma Linda University, 11021 Campus St. Rm 101, Loma Linda, CA 92350, United States
| | - Stephen K Chapes
- Division of Biology, Kansas State University, 1717 Claflin Rd, 116 Ackert Hall, Manhattan, KS 66502, United States.
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Characterization of the naive murine antibody repertoire using unamplified high-throughput sequencing. PLoS One 2018; 13:e0190982. [PMID: 29320559 PMCID: PMC5761896 DOI: 10.1371/journal.pone.0190982] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/22/2017] [Indexed: 12/22/2022] Open
Abstract
Antibody specificity and diversity are generated through the enzymatic splicing of genomic gene segments within each B cell. Antibodies are heterodimers of heavy- and light-chains encoded on separate loci. We studied the antibody repertoire from pooled, splenic tissue of unimmunized, adult female C57BL/6J mice, using high-throughput sequencing (HTS) without amplification of antibody transcripts. We recovered over 90,000 heavy-chain and over 135,000 light-chain immunoglobulin sequences. Individual V-, D-, and J-gene segment usage was uniform among the three mouse pools, particularly in highly abundant gene segments, with low frequency V-gene segments not being detected in all pools. Despite the similar usage of individual gene segments, the repertoire of individual B-cell CDR3 amino acid sequences in each mouse pool was highly varied, affirming the combinatorial diversity in the B-cell pool that has been previously demonstrated. There also was some skewing in the V-gene segments that were detected depending on chromosomal location. This study presents a unique, non-primer biased glimpse of the conventionally housed, unimmunized antibody repertoire of the C57BL6/J mouse.
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