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1.
BMC Biol ; 22(1): 151, 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38977974

ABSTRACT

BACKGROUND: RNA-DNA hybrids or R-loops are associated with deleterious genomic instability and protective immunoglobulin class switch recombination (CSR). However, the underlying phenomenon regulating the two contrasting functions of R-loops is unknown. Notably, the underlying mechanism that protects R-loops from classic RNase H-mediated digestion thereby promoting persistence of CSR-associated R-loops during CSR remains elusive. RESULTS: Here, we report that during CSR, R-loops formed at the immunoglobulin heavy (IgH) chain are modified by ribose 2'-O-methylation (2'-OMe). Moreover, we find that 2'-O-methyltransferase fibrillarin (FBL) interacts with activation-induced cytidine deaminase (AID) associated snoRNA aSNORD1C to facilitate the 2'-OMe. Moreover, deleting AID C-terminal tail impairs its association with aSNORD1C and FBL. Disrupting FBL, AID or aSNORD1C expression severely impairs 2'-OMe, R-loop stability and CSR. Surprisingly, FBL, AID's interaction partner and aSNORD1C promoted AID targeting to the IgH locus. CONCLUSION: Taken together, our results suggest that 2'-OMe stabilizes IgH-associated R-loops to enable productive CSR. These results would shed light on AID-mediated CSR and explain the mechanism of R-loop-associated genomic instability.


Subject(s)
Cytidine Deaminase , Immunoglobulin Class Switching , R-Loop Structures , Immunoglobulin Class Switching/genetics , Cytidine Deaminase/metabolism , Cytidine Deaminase/genetics , Cytidine Deaminase/chemistry , Animals , Mice , Methylation , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/metabolism , Recombination, Genetic , RNA/metabolism , RNA/genetics
2.
Nat Commun ; 15(1): 5765, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38982067

ABSTRACT

The ATP-dependent RNA helicase UPF1 plays a crucial role in various mRNA degradation pathways, most importantly in nonsense-mediated mRNA decay (NMD). Here, we show that UPF1 is upregulated during the early stages of B cell development and is important for early B cell development in the bone marrow. B-cell-specific Upf1 deletion in mice severely impedes the early to late LPre-B cell transition, in which VH-DHJH recombination occurs at the Igh gene. Furthermore, UPF1 is indispensable for VH-DHJH recombination, without affecting DH-JH recombination. Intriguingly, the genetic pre-arrangement of the Igh gene rescues the differentiation defect in early LPre-B cells under Upf1 deficient conditions. However, differentiation is blocked again following Ig light chain recombination, leading to a failure in development into immature B cells. Notably, UPF1 interacts with and regulates the expression of genes involved in immune responses, cell cycle control, NMD, and the unfolded protein response in B cells. Collectively, our findings underscore the critical roles of UPF1 during the early LPre-B cell stage and beyond, thus orchestrating B cell development.


Subject(s)
B-Lymphocytes , Cell Differentiation , Nonsense Mediated mRNA Decay , RNA Helicases , Animals , B-Lymphocytes/metabolism , B-Lymphocytes/cytology , Mice , RNA Helicases/metabolism , RNA Helicases/genetics , Mice, Knockout , Mice, Inbred C57BL , Trans-Activators/metabolism , Trans-Activators/genetics , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/metabolism , Unfolded Protein Response/genetics , Humans , Immunoglobulin Light Chains/metabolism , Immunoglobulin Light Chains/genetics
3.
BMC Genomics ; 25(1): 663, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38961347

ABSTRACT

BACKGROUND: The Atlantic cod is a prolific species in the Atlantic, despite its inconsistent specific antibody response. It presents a peculiar case within vertebrate immunology due to its distinct immune system, characterized by the absence of MHCII antigen presentation pathway, required for T cell-dependent antibody responses. Thorough characterisation of immunoglobulin loci and analysis of the antibody repertoire is necessary to further our understanding of the Atlantic cod's immune response on a molecular level. RESULTS: A comprehensive search of the cod genome (gadmor3.0) identified the complete set of IgH genes organized into three sequential translocons on chromosome 2, while IgL genes were located on chromosomes 2 and 5. The Atlantic cod displayed a moderate germline V gene diversity, comprising four V gene families for both IgH and IgL, each with distinct chromosomal locations and organizational structures. 5'RACE sequencing revealed a diverse range of heavy chain CDR3 sequences and relatively limited CDR3 diversity in light chains. The analysis highlighted a differential impact of V-gene germline CDR3 length on receptor CDR3 length between heavy and light chains, underlining different recombination processes. CONCLUSIONS: This study reveals that the Atlantic cod, despite its inconsistent antibody response, maintains a level of immunoglobulin diversity comparable to other fish species. The findings suggest that the extensive recent duplications of kappa light chain genes do not result in increased repertoire diversity. This research provides a comprehensive view of the Atlantic cod's immunoglobulin gene organization and repertoire, necessary for future studies of antibody responses at the molecular level.


Subject(s)
Gadus morhua , High-Throughput Nucleotide Sequencing , Animals , Gadus morhua/genetics , Immunoglobulin Heavy Chains/genetics , Immunoglobulins/genetics , Genetic Loci , Genes, Immunoglobulin , Immunoglobulin Variable Region/genetics
4.
Cell Rep ; 43(7): 114456, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-38990722

ABSTRACT

The rearrangement and expression of the immunoglobulin µ heavy chain (Igh) gene require communication of the intragenic Eµ and 3' regulatory region (RR) enhancers with the variable (VH) gene promoter. Eµ binding of the transcription factor YY1 has been implicated in enhancer-promoter communication, but the YY1 protein network remains obscure. By analyzing the comprehensive proteome of the 1-kb Eµ wild-type enhancer and that of Eµ lacking the YY1 binding site, we identified the male-specific lethal (MSL)/MOF complex as a component of the YY1 protein network. We found that MSL2 recruitment depends on YY1 and that gene knockout of Msl2 in primary pre-B cells reduces µ gene expression and chromatin looping of Eµ to the 3' RR enhancer and VH promoter. Moreover, Mof heterozygosity in mice impaired µ expression and early B cell differentiation. Together, these data suggest that the MSL/MOF complex regulates Igh gene expression by augmenting YY1-mediated enhancer-promoter communication.


Subject(s)
Enhancer Elements, Genetic , Promoter Regions, Genetic , YY1 Transcription Factor , YY1 Transcription Factor/metabolism , YY1 Transcription Factor/genetics , Promoter Regions, Genetic/genetics , Animals , Enhancer Elements, Genetic/genetics , Mice , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/metabolism , Male , Humans , Mice, Inbred C57BL , Cell Differentiation , Transcription Factors/metabolism , Transcription Factors/genetics
5.
Mol Biol Evol ; 41(7)2024 Jul 03.
Article in English | MEDLINE | ID: mdl-39011558

ABSTRACT

Immunoglobulins (Igs) have a crucial role in humoral immunity. Two recent studies have reported a high-frequency Neanderthal-introgressed haplotype throughout Eurasia and a high-frequency Neanderthal-introgressed haplotype specific to southern East Asia at the immunoglobulin heavy-chain (IGH) gene locus on chromosome 14q32.33. Surprisingly, we found the previously reported high-frequency Neanderthal-introgressed haplotype does not exist throughout Eurasia. Instead, our study identified two distinct high-frequency haplotypes of putative Neanderthal origin in East Asia and Europe, although they shared introgressed alleles. Notably, the alleles of putative Neanderthal origin reduced the expression of IGHG1 and increased the expression of IGHG2 and IGHG3 in various tissues. These putatively introgressed alleles also affected the production of IgG1 upon antigen stimulation and increased the risk of systemic lupus erythematosus. Additionally, the greatest genetic differentiation across the whole genome between southern and northern East Asians was observed for the East Asian haplotype of putative Neanderthal origin. The frequency decreased from southern to northern East Asia and correlated positively with the genome-wide proportion of southern East Asian ancestry, indicating that this putative positive selection likely occurred in the common ancestor of southern East Asian populations before the admixture with northern East Asian populations.


Subject(s)
Haplotypes , Neanderthals , Neanderthals/genetics , Animals , Humans , Europe , Asia, Eastern , Asian People/genetics , Immunoglobulin Heavy Chains/genetics , White People/genetics , Evolution, Molecular , Genetic Introgression , Selection, Genetic , East Asian People
6.
Nat Cell Biol ; 26(6): 991-1002, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38866970

ABSTRACT

The contribution of three-dimensional genome organization to physiological ageing is not well known. Here we show that large-scale chromatin reorganization distinguishes young and old bone marrow progenitor (pro-) B cells. These changes result in increased interactions at the compartment level and reduced interactions within topologically associated domains (TADs). The gene encoding Ebf1, a key B cell regulator, switches from compartment A to B with age. Genetically reducing Ebf1 recapitulates some features of old pro-B cells. TADs that are most reduced with age contain genes important for B cell development, including the immunoglobulin heavy chain (Igh) locus. Weaker intra-TAD interactions at Igh correlate with altered variable (V), diversity (D) and joining (J) gene recombination. Our observations implicate three-dimensional chromatin reorganization as a major driver of pro-B cell phenotypes that impair B lymphopoiesis with age.


Subject(s)
Aging , B-Lymphocytes , Chromatin Assembly and Disassembly , Immunoglobulin Heavy Chains , Lymphopoiesis , Animals , Aging/genetics , Aging/metabolism , B-Lymphocytes/metabolism , Lymphopoiesis/genetics , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/metabolism , Trans-Activators/metabolism , Trans-Activators/genetics , Chromatin/metabolism , Chromatin/genetics , Precursor Cells, B-Lymphoid/metabolism , Precursor Cells, B-Lymphoid/cytology , Precursor Cells, B-Lymphoid/immunology , Mice, Inbred C57BL , Mice , Cell Differentiation , Mice, Knockout
7.
Nat Commun ; 15(1): 4728, 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38830864

ABSTRACT

Due to their exceptional solubility and stability, nanobodies have emerged as powerful building blocks for research tools and therapeutics. However, their generation in llamas is cumbersome and costly. Here, by inserting an engineered llama immunoglobulin heavy chain (IgH) locus into IgH-deficient mice, we generate a transgenic mouse line, which we refer to as 'LamaMouse'. We demonstrate that LamaMice solely express llama IgH molecules without association to Igκ or λ light chains. Immunization of LamaMice with AAV8, the receptor-binding domain of the SARS-CoV-2 spike protein, IgE, IgG2c, and CLEC9A enabled us to readily select respective target-specific nanobodies using classical hybridoma and phage display technologies, single B cell screening, and direct cloning of the nanobody-repertoire into a mammalian expression vector. Our work shows that the LamaMouse represents a flexible and broadly applicable platform for a facilitated selection of target-specific nanobodies.


Subject(s)
Camelids, New World , Immunoglobulin Heavy Chains , Mice, Transgenic , Single-Domain Antibodies , Spike Glycoprotein, Coronavirus , Animals , Single-Domain Antibodies/genetics , Single-Domain Antibodies/immunology , Camelids, New World/immunology , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/immunology , Mice , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/chemistry , Lectins, C-Type/metabolism , Lectins, C-Type/immunology , Lectins, C-Type/genetics , SARS-CoV-2/immunology , SARS-CoV-2/genetics , Immunoglobulin E/immunology , Humans , Dependovirus/genetics , Dependovirus/immunology , Immunoglobulin G/immunology , COVID-19/immunology , B-Lymphocytes/immunology
8.
Viral Immunol ; 37(5): 259-265, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38848306

ABSTRACT

Cytomegalovirus (CMV) has long been thought to have an association with glioblastoma multiforme (GBM), although the exact role of CMV and any subsequent implications for treatment have yet to be fully understood. This study addressed whether IGH complementarity determining region-3 (CDR3)-CMV protein chemical complementarity, with IGH CDR3s representing both tumor resident and blood-sourced IGH recombinations, was associated with overall survival (OS) distinctions. IGH recombination sequencing reads were obtained from (a) the Clinical Proteomic Tumor Analysis Consortium, tumor RNAseq files; and (b) the cancer genome atlas, blood exome-derived files. The Adaptive Match web tool was used to calculate chemical complementarity scores (CSs) based on hydrophobic interactions, and those scores were used to group GBM cases and assess survival probabilities. We found a higher OS probability for cases whose hydrophobic IGH CDR3-CMV protein chemical complementarity scores (Hydro CSs) were in the upper 50th percentile for several CMV proteins, including UL99 and UL123, as well as for CSs based on known B cell epitopes representing these proteins. We also identified multiple immune signature genes, including CD79A and TNFRSF17, for which higher RNA expression was associated with higher Hydro CSs. Results were consistent with the idea that stronger immunoglobulin responses to CMV are associated with better OS probabilities for GBM.


Subject(s)
Complementarity Determining Regions , Cytomegalovirus Infections , Cytomegalovirus , Glioblastoma , Viral Proteins , Humans , Glioblastoma/mortality , Glioblastoma/genetics , Glioblastoma/virology , Cytomegalovirus/genetics , Cytomegalovirus/immunology , Complementarity Determining Regions/genetics , Complementarity Determining Regions/immunology , Cytomegalovirus Infections/mortality , Cytomegalovirus Infections/immunology , Cytomegalovirus Infections/virology , Viral Proteins/genetics , Viral Proteins/immunology , Immunoglobulin Heavy Chains/genetics , Female , Middle Aged , Male , Survival Analysis , Aged , Epitopes, B-Lymphocyte/immunology , Epitopes, B-Lymphocyte/genetics
9.
Science ; 384(6697): eadj8321, 2024 May 17.
Article in English | MEDLINE | ID: mdl-38753769

ABSTRACT

Germline-targeting immunogens hold promise for initiating the induction of broadly neutralizing antibodies (bnAbs) to HIV and other pathogens. However, antibody-antigen recognition is typically dominated by heavy chain complementarity determining region 3 (HCDR3) interactions, and vaccine priming of HCDR3-dominant bnAbs by germline-targeting immunogens has not been demonstrated in humans or outbred animals. In this work, immunization with N332-GT5, an HIV envelope trimer designed to target precursors of the HCDR3-dominant bnAb BG18, primed bnAb-precursor B cells in eight of eight rhesus macaques to substantial frequencies and with diverse lineages in germinal center and memory B cells. We confirmed bnAb-mimicking, HCDR3-dominant, trimer-binding interactions with cryo-electron microscopy. Our results demonstrate proof of principle for HCDR3-dominant bnAb-precursor priming in outbred animals and suggest that N332-GT5 holds promise for the induction of similar responses in humans.


Subject(s)
AIDS Vaccines , Broadly Neutralizing Antibodies , Complementarity Determining Regions , Germinal Center , HIV Antibodies , Animals , Humans , AIDS Vaccines/immunology , B-Lymphocytes/immunology , Broadly Neutralizing Antibodies/immunology , Complementarity Determining Regions/immunology , Cryoelectron Microscopy , env Gene Products, Human Immunodeficiency Virus/immunology , Germinal Center/immunology , HIV Antibodies/immunology , HIV Infections/immunology , HIV Infections/prevention & control , HIV-1/immunology , Immunoglobulin Heavy Chains/immunology , Immunoglobulin Heavy Chains/genetics , Macaca mulatta , Memory B Cells/immunology
10.
Nature ; 630(8015): 189-197, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38811728

ABSTRACT

In developing B cells, V(D)J recombination assembles exons encoding IgH and Igκ variable regions from hundreds of gene segments clustered across Igh and Igk loci. V, D and J gene segments are flanked by conserved recombination signal sequences (RSSs) that target RAG endonuclease1. RAG orchestrates Igh V(D)J recombination upon capturing a JH-RSS within the JH-RSS-based recombination centre1-3 (RC). JH-RSS orientation programmes RAG to scan upstream D- and VH-containing chromatin that is presented in a linear manner by cohesin-mediated loop extrusion4-7. During Igh scanning, RAG robustly utilizes only D-RSSs or VH-RSSs in convergent (deletional) orientation with JH-RSSs4-7. However, for Vκ-to-Jκ joining, RAG utilizes Vκ-RSSs from deletional- and inversional-oriented clusters8, inconsistent with linear scanning2. Here we characterize the Vκ-to-Jκ joining mechanism. Igk undergoes robust primary and secondary rearrangements9,10, which confounds scanning assays. We therefore engineered cells to undergo only primary Vκ-to-Jκ rearrangements and found that RAG scanning from the primary Jκ-RC terminates just 8 kb upstream within the CTCF-site-based Sis element11. Whereas Sis and the Jκ-RC barely interacted with the Vκ locus, the CTCF-site-based Cer element12 4 kb upstream of Sis interacted with various loop extrusion impediments across the locus. Similar to VH locus inversion7, DJH inversion abrogated VH-to-DJH joining; yet Vκ locus or Jκ inversion allowed robust Vκ-to-Jκ joining. Together, these experiments implicated loop extrusion in bringing Vκ segments near Cer for short-range diffusion-mediated capture by RC-based RAG. To identify key mechanistic elements for diffusional V(D)J recombination in Igk versus Igh, we assayed Vκ-to-JH and D-to-Jκ rearrangements in hybrid Igh-Igk loci generated by targeted chromosomal translocations, and pinpointed remarkably strong Vκ and Jκ RSSs. Indeed, RSS replacements in hybrid or normal Igk and Igh loci confirmed the ability of Igk-RSSs to promote robust diffusional joining compared with Igh-RSSs. We propose that Igk evolved strong RSSs to mediate diffusional Vκ-to-Jκ joining, whereas Igh evolved weaker RSSs requisite for modulating VH joining by RAG-scanning impediments.


Subject(s)
Immunoglobulin Heavy Chains , Immunoglobulin Joining Region , Immunoglobulin Variable Region , Immunoglobulin kappa-Chains , V(D)J Recombination , Animals , Female , Male , Mice , Alleles , B-Lymphocytes/immunology , B-Lymphocytes/metabolism , Chromatin/genetics , Chromatin/metabolism , Chromatin/chemistry , Cohesins/metabolism , Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Joining Region/genetics , Immunoglobulin kappa-Chains/genetics , Immunoglobulin Variable Region/genetics , V(D)J Recombination/genetics
11.
Protein Expr Purif ; 220: 106499, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38703798

ABSTRACT

Monoclonal antibodies (mAbs) are a driving force in the biopharmaceutical industry. Therapeutic mAbs are usually produced in mammalian cells, but there has been a push towards the use of alternative production hosts, such as Escherichia coli. When the genes encoding for a mAb heavy and light chains are codon-optimized for E. coli expression, a truncated form of the heavy chain can form along with the full-length product. In this work, the role of codon optimization in the formation of a truncated product was investigated. This study used the amino acid sequences of several therapeutic mAbs and multiple optimization algorithms. It was found that several algorithms incorporate sequences that lead to a truncated product. Approaches to avoid this truncated form are discussed.


Subject(s)
Antibodies, Monoclonal , Escherichia coli , Antibodies, Monoclonal/genetics , Antibodies, Monoclonal/biosynthesis , Antibodies, Monoclonal/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Codon/genetics , Algorithms , Amino Acid Sequence , Recombinant Proteins/genetics , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Humans , Gene Expression , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/chemistry
12.
Protein Sci ; 33(6): e5017, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38747382

ABSTRACT

Biparatopic antibodies (bpAbs) are engineered antibodies that bind to multiple different epitopes within the same antigens. bpAbs comprise diverse formats, including fragment-based formats, and choosing the appropriate molecular format for a desired function against a target molecule is a challenging task. Moreover, optimizing the design of constructs requires selecting appropriate antibody modalities and adjusting linker length for individual bpAbs. Therefore, it is crucial to understand the characteristics of bpAbs at the molecular level. In this study, we first obtained single-chain variable fragments and camelid heavy-chain variable domains targeting distinct epitopes of the metal binding protein MtsA and then developed a novel format single-chain bpAb connecting these fragment antibodies with various linkers. The physicochemical properties, binding activities, complex formation states with antigen, and functions of the bpAb were analyzed using multiple approaches. Notably, we found that the assembly state of the complexes was controlled by a linker and that longer linkers tended to form more compact complexes. These observations provide detailed molecular information that should be considered in the design of bpAbs.


Subject(s)
Single-Chain Antibodies , Single-Chain Antibodies/chemistry , Single-Chain Antibodies/genetics , Single-Chain Antibodies/immunology , Animals , Humans , Protein Engineering/methods , Epitopes/chemistry , Epitopes/immunology , Immunoglobulin Heavy Chains/chemistry , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/immunology
13.
Cell Rep ; 43(5): 114211, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38722741

ABSTRACT

Multiple myeloma (MM) remains an incurable hematological malignancy demanding innovative therapeutic strategies. Targeting MYC, the notorious yet traditionally undruggable oncogene, presents an appealing avenue. Here, using a genome-scale CRISPR-Cas9 screen, we identify the WNK lysine-deficient protein kinase 1 (WNK1) as a regulator of MYC expression in MM cells. Genetic and pharmacological inhibition of WNK1 reduces MYC expression and, further, disrupts the MYC-dependent transcriptional program. Mechanistically, WNK1 inhibition attenuates the activity of the immunoglobulin heavy chain (IgH) enhancer, thus reducing MYC transcription when this locus is translocated near the MYC locus. WNK1 inhibition profoundly impacts MM cell behaviors, leading to growth inhibition, cell-cycle arrest, senescence, and apoptosis. Importantly, the WNK inhibitor WNK463 inhibits MM growth in primary patient samples as well as xenograft mouse models and exhibits synergistic effects with various anti-MM compounds. Collectively, our study uncovers WNK1 as a potential therapeutic target in MM.


Subject(s)
Multiple Myeloma , Proto-Oncogene Proteins c-myc , WNK Lysine-Deficient Protein Kinase 1 , Multiple Myeloma/genetics , Multiple Myeloma/drug therapy , Multiple Myeloma/pathology , Multiple Myeloma/metabolism , WNK Lysine-Deficient Protein Kinase 1/metabolism , WNK Lysine-Deficient Protein Kinase 1/genetics , Humans , Animals , Mice , Cell Line, Tumor , Proto-Oncogene Proteins c-myc/metabolism , Proto-Oncogene Proteins c-myc/genetics , Gene Expression Regulation, Neoplastic/drug effects , Immunoglobulin Heavy Chains/genetics , Cell Proliferation/drug effects , Apoptosis/drug effects , Xenograft Model Antitumor Assays
14.
Genes (Basel) ; 15(4)2024 04 08.
Article in English | MEDLINE | ID: mdl-38674401

ABSTRACT

The variable domain of a heavy-chain antibody (VHH) has the potential to be used to redirect the cell tropism of adenoviral vectors. Here, we attempted to establish platforms to simplify the screening of VHHs for their specific targeting function when being incorporated into the fiber of adenovirus. Both fowl adenovirus 4 (FAdV-4) and simian adenovirus 1 (SAdV-1) have two types of fiber, one of which is dispensable for virus propagation and is a proper site for VHH display. An intermediate plasmid, pMD-FAV4Fs, was constructed as the start plasmid for FAdV-4 fiber2 modification. Foldon from phage T4 fibritin, a trigger for trimerization, was employed to bridge the tail/shaft domain of fiber2 and VHHs against human CD16A, a key membrane marker of natural killer (NK) cells. Through one step of restriction-assembly, the modified fiber2 was transferred to the adenoviral plasmid, which was linearized and transfected to packaging cells. Five FAdV-4 viruses carrying the GFP gene were finally rescued and amplified, with three VHHs being displayed. One recombinant virus, FAdV4FC21-EG, could hardly transduce human 293 or Jurkat cells. In contrast, when it was used at a multiplicity of infection of 1000 viral particles per cell, the transduction efficiency reached 51% or 34% for 293 or Jurkat cells expressing exogenous CD16A. Such a strategy of fiber modification was transplanted to the SAdV-1 vector to construct SAdV1FC28H-EG, which moderately transduced primary human NK cells while the parental virus transduced none. Collectively, we reformed the strategy of integrating VHH to fiber and established novel platforms for screening VHHs to construct adenoviral vectors with a specific tropism.


Subject(s)
Genetic Vectors , Viral Tropism , Humans , Genetic Vectors/genetics , HEK293 Cells , Immunoglobulin Heavy Chains/genetics , Aviadenovirus/genetics , Aviadenovirus/immunology , Animals , Capsid Proteins/genetics , Capsid Proteins/immunology , Capsid Proteins/metabolism
15.
J Immunol ; 212(11): 1744-1753, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38629917

ABSTRACT

H chain-only Igs are naturally produced in camelids and sharks. Because these Abs lack the L chain, the Ag-binding domain is half the size of a traditional Ab, allowing this type of Ig to bind to targets in novel ways. Consequently, the H chain-only single-domain Ab (sdAb) structure has the potential to increase the repertoire and functional range of an active humoral immune system. The majority of vertebrates use the standard heterodimeric (both H and L chains) structure and do not produce sdAb format Igs. To investigate if other animals are able to support sdAb development and function, transgenic chickens (Gallus gallus) were designed to produce H chain-only Abs by omitting the L chain V region and maintaining only the LC region to serve as a chaperone for Ab secretion from the cell. These birds produced 30-50% normal B cell populations within PBMCs and readily expressed chicken sequence sdAbs. Interestingly, the H chains contained a spontaneous CH1 deletion. Although no isotype switching to IgY or IgA occurred, the IgM repertoire was diverse, and immunization with a variety of protein immunogens rapidly produced high and specific serum titers. mAbs of high affinity were efficiently recovered by single B cell screening. In in vitro functional assays, the sdAbs produced by birds immunized against SARS-CoV-2 were also able to strongly neutralize and prevent viral replication. These data suggest that the truncated L chain design successfully supported sdAb development and expression in chickens.


Subject(s)
Animals, Genetically Modified , Chickens , Immunoglobulin Heavy Chains , Single-Domain Antibodies , Animals , Chickens/immunology , Single-Domain Antibodies/immunology , Single-Domain Antibodies/genetics , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/immunology , SARS-CoV-2/immunology , SARS-CoV-2/genetics , COVID-19/immunology , Transgenes/genetics , B-Lymphocytes/immunology , Antibodies, Viral/immunology , Immunoglobulin Light Chains/genetics , Immunoglobulin Light Chains/immunology , Humans
16.
J Immunol ; 212(12): 1913-1921, 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38647373

ABSTRACT

Using an Ig H chain conferring specificity for N-acetyl-d-glucosamine (GlcNAc), we developed transgenic (VHHGAC39 TG) mice to study the role of self-antigens in GlcNAc-reactive B-1 B cell development. In VHHGAC39 TG mice, GlcNAc-reactive B-1 B cell development during ontogeny and in adult bone marrow was normal. However, adult TG mice exhibited a block at transitional-2 immature B cell stages, resulting in impaired allelic exclusion and accumulation of a B cell subset coexpressing endogenous Ig gene rearrangements. Similarly, VHHGAC39 B cell fitness was impeded compared with non-self-reactive VHJ558 B TG cells in competitive mixed bone marrow chimeras. Nonetheless, adult VHHGAC39 mice immunized with Streptococcus pyogenes produce anti-GlcNAc Abs. Peritoneal cavity B cells transferred from VHHGAC39 TG mice into RAG-/- mice also exhibited robust expansion and anti-GlcNAc Ab production. However, chronic treatment of young VHHGAC39 mice with GlcNAc-specific mAbs leads to lower GlcNAc-binding B cell frequencies while increasing the proportion of GlcNAc-binding B1-a cells, suggesting that Ag masking or clearance of GlcNAc Ags impedes maturation of newly formed GlcNAc-reactive B cells. Finally, BCR H chain editing promotes expression of endogenous nontransgenic BCR alleles, allowing potentially self-reactive TG B cells to escape anergy or deletion at the transitional stage of precursor B cell development. Collectively, these observations indicate that GlcNAc-reactive B cell development is sensitive to the access of autologous Ags.


Subject(s)
Acetylglucosamine , Mice, Transgenic , Animals , Mice , Acetylglucosamine/immunology , Cell Differentiation/immunology , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/immunology , Immunity, Innate/immunology , B-Lymphocyte Subsets/immunology , Mice, Inbred C57BL , Autoantigens/immunology , Streptococcus pyogenes/immunology , B-Lymphocytes/immunology
17.
J Immunol ; 212(10): 1579-1588, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38557795

ABSTRACT

Abs are vital to human immune responses and are composed of genetically variable H and L chains. These structures are initially expressed as BCRs. BCR diversity is shaped through somatic hypermutation and selection during immune responses. This evolutionary process produces B cell clones, cells that descend from a common ancestor but differ by mutations. Phylogenetic trees inferred from BCR sequences can reconstruct the history of mutations within a clone. Until recently, BCR sequencing technologies separated H and L chains, but advancements in single-cell sequencing now pair H and L chains from individual cells. However, it is unclear how these separate genes should be combined to infer B cell phylogenies. In this study, we investigated strategies for using paired H and L chain sequences to build phylogenetic trees. We found that incorporating L chains significantly improved tree accuracy and reproducibility across all methods tested. This improvement was greater than the difference between tree-building methods and persisted even when mixing bulk and single-cell sequencing data. However, we also found that many phylogenetic methods estimated significantly biased branch lengths when some L chains were missing, such as when mixing single-cell and bulk BCR data. This bias was eliminated using maximum likelihood methods with separate branch lengths for H and L chain gene partitions. Thus, we recommend using maximum likelihood methods with separate H and L chain partitions, especially when mixing data types. We implemented these methods in the R package Dowser: https://dowser.readthedocs.io.


Subject(s)
B-Lymphocytes , Phylogeny , Receptors, Antigen, B-Cell , Humans , Receptors, Antigen, B-Cell/genetics , Receptors, Antigen, B-Cell/immunology , B-Lymphocytes/immunology , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Light Chains/genetics , Immunoglobulin Light Chains/immunology , Single-Cell Analysis/methods , Mutation
18.
Leuk Lymphoma ; 65(8): 1100-1109, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38608254

ABSTRACT

We describe two types of IGH::BCL2 breakpoints involving the 5' region of BCL2 (5' BCL2). One was ins(14;18)(q32;q21q21) observed in 2 follicular lymphoma (FL) cases, in which IGH was cleaved at 3' of IGHD and 5' of IGHJ and BCL2 was cleaved at 5' BCL2 and downstream regions, and a 281- or 201-kilobase pair fragment containing the BCL2 protein-coding sequences was invertedly inserted into IGH. In another type observed in 2 FL and 2 chronic lymphocytic leukemia (CLL) cases, breakage and reunion occurred within the switch region associated with IGHM (Sµ) and 5' BCL2, creating IGH Sµ::5' BCL2 fusion sequences on der(18)t(14;18)(q32;q21). The former is considered to be mediated by VDJ-recombination, while the latter by the class switch recombination process. There were no particular features in FL or CLL cases with IGH::5' BCL2 breakpoints compared with those with t(14;18)(q32;q21)/IGH::BCL2 involving the 3' breakpoint cluster regions.


Subject(s)
Chromosome Breakpoints , Chromosomes, Human, Pair 14 , Chromosomes, Human, Pair 18 , Immunoglobulin Heavy Chains , Proto-Oncogene Proteins c-bcl-2 , Translocation, Genetic , Humans , Chromosomes, Human, Pair 14/genetics , Chromosomes, Human, Pair 18/genetics , Immunoglobulin Heavy Chains/genetics , Proto-Oncogene Proteins c-bcl-2/genetics , Immunoglobulin Class Switching/genetics , V(D)J Recombination/genetics , Lymphoma, Follicular/genetics , Lymphoma, Follicular/pathology , Middle Aged , Male , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis , Leukemia, Lymphocytic, Chronic, B-Cell/pathology , Female , In Situ Hybridization, Fluorescence , Aged
19.
Int J Hematol ; 119(6): 686-696, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38492198

ABSTRACT

Chronic lymphocytic leukemia (CLL) is rare in Japan. We conducted the nationwide, prospective observational study CLLRSG-01 to clarify the current state of CLL in Japan and to make accurate international comparisons by preparing naturally air-dried smears like those used in other countries. Of the 201 untreated patients enrolled and evaluated, 119 were diagnosed with CLL and 82 with non-CLL mature B-cell neoplasms, based on the WHO classification. Of the 119 CLL patients, 90 were classified as typical and 29 as atypical according to FAB classification morphology, with the proportion of atypical CLL consistent with reports from other countries. Immunophenotypic analyses by flow cytometry showed that 55% of Japanese CLL patients had a Matutes score of 4 or higher, which is lower than the rate of about 90% in Europeans. Mutated IGHV was identified in 80% of Japanese CLL patients, which is a higher rate than in Western patients. The most frequent IGHV gene was VH3-30 (15%), followed by VH3-23 (12%) and VH4-34 (10%). VH1-69, the most common gene in Western countries, was identified in only one patient. These results indicate that the pattern of immunophenotypes and IGHV gene usage in Japanese CLL patients differs from that in Western patients.


Subject(s)
Immunophenotyping , Leukemia, Lymphocytic, Chronic, B-Cell , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Leukemia, Lymphocytic, Chronic, B-Cell/epidemiology , Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis , Humans , Japan/epidemiology , Aged , Male , Female , Middle Aged , Aged, 80 and over , Prospective Studies , Adult , Mutation , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Variable Region/genetics
20.
Sci Rep ; 14(1): 7370, 2024 03 28.
Article in English | MEDLINE | ID: mdl-38548819

ABSTRACT

Class switch recombination (CSR) plays an important role in adaptive immune response by enabling mature B cells to replace the initial IgM by another antibody class (IgG, IgE or IgA). CSR is preceded by transcription of the IgH constant genes and is controlled by the super-enhancer 3' regulatory region (3'RR) in an activation-specific manner. The 3'RR is composed of four enhancers (hs3a, hs1-2, hs3b and hs4). In mature B cells, 3'RR activity correlates with transcription of its enhancers. CSR can also occur in primary developing B cells though at low frequency, but in contrast to mature B cells, the transcriptional elements that regulate the process in developing B cells are ill-known. In particular, the role of the 3'RR in the control of constant genes' transcription and CSR has not been addressed. Here, by using a mouse line devoid of the 3'RR and a culture system that highly enriches in pro-B cells, we show that the 3'RR activity is indeed required for switch transcription and CSR, though its effect varies in an isotype-specific manner and correlates with transcription of hs4 enhancer only.


Subject(s)
Immunoglobulin Heavy Chains , Super Enhancers , Immunoglobulin Heavy Chains/genetics , Regulatory Sequences, Nucleic Acid/genetics , Immunoglobulin Class Switching/genetics , B-Lymphocytes , Immunoglobulin Isotypes/genetics , Enhancer Elements, Genetic
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