Deciphering the antigen specificities of antibodies by clustering their complementarity determining region sequences

Saputri Dianita S., Ismanto Hendra S., Nugraha Dendi K., et al. Deciphering the antigen specificities of antibodies by clustering their complementarity determining region sequences. mSystems 8, e00722-23 (2023); https://doi.org/10.1128/msystems.00722-23.Recent advances in adaptive immune receptor repertoire sequencing have provided abundant B cell receptor (BCR) sequences under various conditions, including vaccination and disease. However, determining target antigen and epitope specificity of the corresponding antibodies is a major challenge due to their exceptional sequence diversity. Here, we introduce a novel method to cluster antibodies sharing antigenic targets based on their complementarity determining region (CDR) sequences. Using the proposed method, we demonstrate that SARS-CoV-2 spike protein receptor-binding domain (RBD) binders and non-RBD binders from publicly available BCR data were classified correctly, with a cluster purity of 95%. These clusters were then leveraged for annotating unlabeled COVID-19 patient BCR data, enabling the discovery of novel anti-RBD antibodies. We further validated the method by clustering BCR repertoires obtained from single-cell immune profiling of diphtheria-tetanus-pertussis (DTP)-vaccinated donors. Antibody expression and antigen-binding assays demonstrated that the clusters exhibited 96% antigen purity, surpassing the apparent 82% purity achieved by assigning antigens to the same B cells using fluorescently labeled DTP antigen probes. Moreover, antibodies within certain clusters were found to possess neutralizing activity, suggesting that CDR clusters contain epitope-level information. Together, this study offers a simple approach for antigen- and epitope-specific BCR discovery that is reproducible, inexpensive, and applicable to a wide range of antigen targets

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Contribution of Viral Mimics of Cellular Genes to KSHV Infection and Disease

Kaposi’s sarcoma-associated herpesvirus (KSHV, also named Human herpesvirus 8 HHV-8) is the cause of Kaposi sarcoma (KS), the most common malignancy in HIV-infected individuals worldwide, primary effusion lymphoma (PEL) and multicentric Castleman disease (MCD). KSHV is a double-stranded DNA virus that encodes several homologues of cellular proteins. The structural similarity between viral and host proteins explains why some viral homologues function as their host counterparts, but sometimes at unusual anatomical sites and inappropriate times. In other cases, structural modification in the viral proteins can suppress or override the function of the host homologue, contributing to KSHV-related diseases. For example, viral IL-6 (vIL-6) is sufficiently different from human IL-6 to activate gp130 signaling independent of the α subunit. As a consequence, vIL-6 can activate many cell types that are unresponsive to cellular IL-6, contributing to MCD disease manifestations. Here, we discuss the molecular biology of KSHV homologues of cellular products as conduits of virus/host interaction with a focus on identifying new strategies for therapy of KS and other KSHV-related diseases

Kaposi's Sarcoma-Associated Herpesvirus (Human Herpesvirus 8) Replication and Transcription Factor Activates the K9 (vIRF) Gene through Two Distinct cis Elements by a Non-DNA-Binding Mechanism

The replication and transcription activator (RTA) of Kaposi's sarcoma-associated herpesvirus (KSHV), or human herpesvirus 8, a homologue of Epstein-Barr virus BRLF1 or Rta, is a strong transactivator and inducer of lytic replication. RTA acting alone can induce lytic replication of KSHV in infected cell lines that originated from primary effusion lymphomas, leading to virus production. During the lytic replication process, RTA activates many kinds of genes, including polyadenylated nuclear RNA, K8, K9 (vIRF), ORF57, and so on. We focused here on the mechanism of how RTA upregulates the K9 (vIRF) promoter and identified two independent cis-acting elements in the K9 (vIRF) promoter that responded to RTA. These elements were finally confined to the sequence 5′-TCTGGGACAGTC-3′ in responsive element (RE) I-2B and the sequence 5′-GTACTTAAAATA-3′ in RE IIC-2, both of which did not share sequence homology. Multiple factors bound specifically with these elements, and their binding was correlated with the RTA-responsive activity. Electrophoretic mobility shift assay with nuclear extract from infected cells and the N-terminal part of RTA expressed in Escherichia coli, however, did not show that RTA interacted directly with these elements, in contrast to the RTA responsive elements in the PAN/K12 promoter region, the ORF57/K8 promoter region. Thus, it was likely that RTA could transactivate several kinds of unique cis elements without directly binding to the responsive elements, probably through cooperation with other DNA-binding factors

Gene Regulation and Functional Alterations Induced by Kaposi's Sarcoma-Associated Herpesvirus-Encoded ORFK13/vFLIP in Endothelial Cells▿ †

Kaposi's sarcoma (KS) is an angioproliferative inflammatory disorder induced by endothelial cell infection with the KS-associated herpesvirus (KSHV). ORFK13/vFLIP, one of the KSHV genes expressed in KS, encodes a 188-amino-acid protein which binds to the Iκb kinase (IKK) complex to activate NF-κB. We examined ORFK13/vFLIP contribution to KS phenotype and potential for therapeutic targeting. Retroviral transduction of ORFK13/vFLIP into primary human endothelial cells induces the spindle morphology distinctive of KS cells and promotes the formation of abnormal vascular networks typical of KS vasculature; upregulates the expression of proinflammatory cytokines, chemokines, and interferon-responsive genes; and stimulates the adhesion of inflammatory cells characteristic of KS lesions. Thymidine phosphorylase, a cellular enzyme markedly induced by ORFK13/vFLIP, can metabolize the prodrug 5-fluoro-5-deoxyuridine (5-dFUrd) to 5-fluouridine (5-FU), a potent thymidine synthase inhibitor, which blocks DNA and RNA synthesis. When tested for cytotoxicity, 5-dFUrd (0.1 to 1 μM) selectively killed ORFK13/vFLIP-expressing endothelial cells while sparing control cells. These results demonstrate that ORFK13/vFLIP directly and indirectly contributes to the inflammatory and vascular phenotype of KS and identify 5-dFUrd as a potential new drug that targets KSHV latency for the treatment of KS and other KSHV-associated malignancies

External stimulation induces the secretion of autophagosome-like vesicles by B cells

Macroautophagy/autophagy is a cellular degradation and recycling process that supports cellular homeostasis. Since an autophagosome marker, microtubule-associated protein 1A/1B-light chain 3 (LC3)-II, was found in cell-derived extracellular vesicles (EVs), autophagy may cooperate with EV secretion pathways to control unconventional secretion of intracellular molecules. Several studies have demonstrated that pharmacological inhibition of autophagic turnover and pathogen-induced endolysosomal dysfunction enhanced the secretion of autophagosome-like EVs (ALVs). However, whether external stimulation induces ALV secretion is unclear. Here we showed that co-stimulation with IL-4 and anti-CD40 antibody (IL-4:CD40) enhanced the secretion of LC3-II+ALVs compared to co-stimulation by IL-4 and lipopolysaccharide (IL-4:LPS) or by IL4 and anti-IgM antibody in B cells. While IL-4:LPS stimulation accelerated autophagic flux, IL-4:CD40 stimulation reduced autophagosome-lysosome fusion without affecting lysosomal function. Although both IL-4:LPS and IL-4:CD40 induced the expression of similar genes involved in vesicle fusion or transportation, IL-4:CD40 preferentially enhanced the expression of the small GTPase RAB27a compared to IL-4:LPS. Genetic disruption by the CRISPR-Cas9 system revealed that loss of RAB27a membrane-binding ability impaired LC3-II+ALV secretion but not ALIX+EV secretion in B-lymphoma A20 cells. Additionally, reconstitution of human wild-type RAB27A in RAB27a mutant A20 cells restored LC3-II+ALV secretion, indicating that RAB27a controls autophagosome secretion. Furthermore, LC3-II+ALVs were found in the sera of tumor-bearing mice and the plasma of healthy human donors. Our findings may provide a role for B-cell secretory autophagy in regulating intercellular communication under various physiological conditions, such as vaccination, pathogen infection, and B-cell lymphoma progression. Abbreviations: ALVs: autophagosome-like vesicles; ATG: autophagy-related; Baf A1: bafilomycin A1; CNX: calnexin; EVs: extracellular vesicles; Ig: immunoglobulin; IL: Interleukin; LC3: microtubule-associated protein 1A/1B-light; LPS: Lipopolysaccharides; MVs: microvesicles; RAB: member RAS oncogene family; TLR: toll-like recepto