1
|
Gao M, Wang X, Su S, Feng W, Lai Y, Huang K, Cao D, Wang Q. Meningeal lymphatic vessel crosstalk with central nervous system immune cells in aging and neurodegenerative diseases. Neural Regen Res 2025; 20:763-778. [PMID: 38886941 DOI: 10.4103/nrr.nrr-d-23-01595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/22/2023] [Indexed: 06/20/2024] Open
Abstract
Meningeal lymphatic vessels form a relationship between the nervous system and periphery, which is relevant in both health and disease. Meningeal lymphatic vessels not only play a key role in the drainage of brain metabolites but also contribute to antigen delivery and immune cell activation. The advent of novel genomic technologies has enabled rapid progress in the characterization of myeloid and lymphoid cells and their interactions with meningeal lymphatic vessels within the central nervous system. In this review, we provide an overview of the multifaceted roles of meningeal lymphatic vessels within the context of the central nervous system immune network, highlighting recent discoveries on the immunological niche provided by meningeal lymphatic vessels. Furthermore, we delve into the mechanisms of crosstalk between meningeal lymphatic vessels and immune cells in the central nervous system under both homeostatic conditions and neurodegenerative diseases, discussing how these interactions shape the pathological outcomes. Regulation of meningeal lymphatic vessel function and structure can influence lymphatic drainage, cerebrospinal fluid-borne immune modulators, and immune cell populations in aging and neurodegenerative disorders, thereby playing a key role in shaping meningeal and brain parenchyma immunity.
Collapse
Affiliation(s)
- Minghuang Gao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Xinyue Wang
- The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Shijie Su
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Weicheng Feng
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Yaona Lai
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Kongli Huang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Dandan Cao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| |
Collapse
|
2
|
Palladini G, Liedtke M, Zago W, Dolan P, Kinney GG, Gertz MA. The mechanism of action, pharmacological characteristics, and clinical utility of the amyloid depleter birtamimab for the potential treatment of AL amyloidosis. Leuk Lymphoma 2024; 65:1068-1078. [PMID: 38600883 DOI: 10.1080/10428194.2024.2337803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/27/2024] [Indexed: 04/12/2024]
Abstract
Amyloid light chain (AL) amyloidosis is a progressive plasma cell disorder caused by amyloid deposition resulting in organ damage and failure. Current standard-of-care treatments target clonal plasma cells, the source of misfolded light chains (amyloid precursors), yet only half of patients with advanced disease survive ≥6 months. The amyloid depleter birtamimab is an investigational humanized monoclonal antibody that binds misfolded κ and λ light chains with high specificity and was designed to neutralize soluble toxic light chain aggregates and promote phagocytic clearance of deposited amyloid. Post hoc analyses from the Phase 3 VITAL trial suggested birtamimab plus standard of care confers a survival benefit in patients with advanced (Mayo Stage IV) AL amyloidosis. AFFIRM-AL (NCT04973137), a Phase 3 confirmatory trial of birtamimab plus standard of care in patients with Mayo Stage IV AL amyloidosis, is ongoing. This review summarizes birtamimab's mechanism of action, attributes, and potential clinical utility.
Collapse
Affiliation(s)
- Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS, Policlinico San Matteo, Pavia, Italy
| | | | | | - Phil Dolan
- Prothena Biosciences Inc, Brisbane, CA, USA
| | | | - Morie A Gertz
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
3
|
Lê Quý K, Chernigovskaya M, Stensland M, Singh S, Leem J, Revale S, Yadin DA, Nice FL, Povall C, Minns DH, Galson JD, Nyman TA, Snapkow I, Greiff V. Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling. NPJ Syst Biol Appl 2024; 10:73. [PMID: 38997321 PMCID: PMC11245537 DOI: 10.1038/s41540-024-00402-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 07/01/2024] [Indexed: 07/14/2024] Open
Abstract
Immunoglobulins (Ig), which exist either as B-cell receptors (BCR) on the surface of B cells or as antibodies when secreted, play a key role in the recognition and response to antigenic threats. The capability to jointly characterize the BCR and antibody repertoire is crucial for understanding human adaptive immunity. From peripheral blood, bulk BCR sequencing (bulkBCR-seq) currently provides the highest sampling depth, single-cell BCR sequencing (scBCR-seq) allows for paired chain characterization, and antibody peptide sequencing by tandem mass spectrometry (Ab-seq) provides information on the composition of secreted antibodies in the serum. Yet, it has not been benchmarked to what extent the datasets generated by these three technologies overlap and complement each other. To address this question, we isolated peripheral blood B cells from healthy human donors and sequenced BCRs at bulk and single-cell levels, in addition to utilizing publicly available sequencing data. Integrated analysis was performed on these datasets, resolved by replicates and across individuals. Simultaneously, serum antibodies were isolated, digested with multiple proteases, and analyzed with Ab-seq. Systems immunology analysis showed high concordance in repertoire features between bulk and scBCR-seq within individuals, especially when replicates were utilized. In addition, Ab-seq identified clonotype-specific peptides using both bulk and scBCR-seq library references, demonstrating the feasibility of combining scBCR-seq and Ab-seq for reconstructing paired-chain Ig sequences from the serum antibody repertoire. Collectively, our work serves as a proof-of-principle for combining bulk sequencing, single-cell sequencing, and mass spectrometry as complementary methods towards capturing humoral immunity in its entirety.
Collapse
Grants
- The Leona M. and Harry B. Helmsley Charitable Trust (#2019PG-T1D011, to VG), UiO World-Leading Research Community (to VG), UiO: LifeScience Convergence Environment Immunolingo (to VG), EU Horizon 2020 iReceptorplus (#825821) (to VG), a Norwegian Cancer Society Grant (#215817, to VG), Research Council of Norway projects (#300740, (#311341, #331890 to VG), a Research Council of Norway IKTPLUSS project (#311341, to VG). This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 101007799 (Inno4Vac). This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA (to VG).
- Mass spectrometry-based proteomic analyses were performed by the Proteomics Core Facility, Department of Immunology, University of Oslo/Oslo University Hospital, which is supported by the Core Facilities program of the South-Eastern Norway Regional Health Authority. This core facility is also a member of the National Network of Advanced Proteomics Infrastructure (NAPI), which is funded by the Research Council of Norway INFRASTRUKTUR-program (project number: 295910).
Collapse
Affiliation(s)
- Khang Lê Quý
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Stensland
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Sachin Singh
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | | | | | | | | | | | | | - Tuula A Nyman
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Igor Snapkow
- Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
4
|
Jackson KJ. RAGging on recombination signal sequence strength for diffusion-mediated recombination. Immunol Cell Biol 2024. [PMID: 38973226 DOI: 10.1111/imcb.12803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
In this article, we discuss new insights into the distinct mechanisms for V(D)J recombination for different immunoglobulin loci. This follows the recent revelation that recombination signal sequences (RSS) within the IGKV locus have evolved to be more efficient mediators of recombination activating gene (RAG) recombination compared to the same elements in the IGH locus. This difference in RSS strength is proposed to be driven by different molecular mechanisms for RAG-mediated recombination between the two loci.
Collapse
Affiliation(s)
- Katherine Jl Jackson
- Immunology Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| |
Collapse
|
5
|
Desantis F, Miotto M, Milanetti E, Ruocco G, Di Rienzo L. Computational evidences of a misfolding event in an aggregation-prone light chain preceding the formation of the non-native pathogenic dimer. Proteins 2024; 92:797-807. [PMID: 38314653 DOI: 10.1002/prot.26672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 02/06/2024]
Abstract
Antibody light chain amyloidosis is a disorder in which protein aggregates, mainly composed of immunoglobulin light chains, deposit in diverse tissues impairing the correct functioning of organs. Interestingly, due to the high susceptibility of antibodies to mutations, AL amyloidosis appears to be strongly patient-specific. Indeed, every patient will display their own mutations that will make the proteins involved prone to aggregation thus hindering the study of this disease on a wide scale. In this framework, determining the molecular mechanisms that drive the aggregation could pave the way to the development of patient-specific therapeutics. Here, we focus on a particular patient-derived light chain, which has been experimentally characterized. We investigated the early phases of the aggregation pathway through extensive full-atom molecular dynamics simulations, highlighting a structural rearrangement and the exposure of two hydrophobic regions in the aggregation-prone species. Next, we moved to consider the pathological dimerization process through docking and molecular dynamics simulations, proposing a dimeric structure as a candidate pathological first assembly. Overall, our results shed light on the first phases of the aggregation pathway for a light chain at an atomic level detail, offering new structural insights into the corresponding aggregation process.
Collapse
Affiliation(s)
- Fausta Desantis
- The Open University Affiliated Research Centre at Istituto Italiano di Tecnologia, Genova, Italy
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano & Neuro Science, Roma, Italy
| | - Mattia Miotto
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano & Neuro Science, Roma, Italy
| | - Edoardo Milanetti
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano & Neuro Science, Roma, Italy
- Department of Physics, Sapienza University of Rome, Rome, Italy
| | - Giancarlo Ruocco
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano & Neuro Science, Roma, Italy
- Department of Physics, Sapienza University of Rome, Rome, Italy
| | - Lorenzo Di Rienzo
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano & Neuro Science, Roma, Italy
| |
Collapse
|
6
|
Bhattacharyya P, Christopherson RI, Skarratt KK, Fuller SJ. Method for B Cell Receptor Enrichment in Malignant B Cells. Cancers (Basel) 2024; 16:2341. [PMID: 39001403 PMCID: PMC11240526 DOI: 10.3390/cancers16132341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
B cells are central to the adaptive immune response and provide long-lasting immunity after infection. B cell activation is mediated by the surface membrane-bound B cell receptor (BCR) following recognition of a specific antigen. The BCR has been challenging to analyse using mass spectrometry (MS) due to the difficulty of isolating and enriching this membrane-bound protein complex. There are approximately 120,000 BCRs on the B cell surface; however, depending on the B cell activation state, there may be hundreds-of-millions to billions of proteins in a B cell. Consequently, advanced proteomic techniques such as MS workflows that use purified proteins to yield structural and protein-interaction information have not been published for the BCR complex. This paper describes a method for enriching the BCR complex that is MS-compatible. The method involves a Protein G pull down on agarose beads using an intermediary antibody to each of the BCR complex subcomponents (CD79a, CD79b, and membrane immunoglobulin). The enrichment process is shown to pull down the entire BCR complex and has the advantage of being readily compatible with further proteomic study including MS analysis. Using intermediary antibodies has the potential to enrich all isotypes of the BCR, unlike previous methods described in the literature that use protein G-coated beads to directly pull down the membrane IgG (mIgG) but cannot be used for other mIg isotypes.
Collapse
Affiliation(s)
- Puja Bhattacharyya
- Sydney Medical School Nepean, Faculty of Medicine and Health, The University of Sydney, Penrith, NSW 2750, Australia; (P.B.); (K.K.S.)
- Blacktown Hospital, Blacktown Rd., Blacktown, NSW 2148, Australia
| | | | - Kristen K. Skarratt
- Sydney Medical School Nepean, Faculty of Medicine and Health, The University of Sydney, Penrith, NSW 2750, Australia; (P.B.); (K.K.S.)
- Nepean Hospital, Derby Str., Kingswood, NSW 2747, Australia
| | - Stephen J. Fuller
- Sydney Medical School Nepean, Faculty of Medicine and Health, The University of Sydney, Penrith, NSW 2750, Australia; (P.B.); (K.K.S.)
- Nepean Hospital, Derby Str., Kingswood, NSW 2747, Australia
| |
Collapse
|
7
|
Paparoditis P, Shulman Z. The tumor-driven antibody-mediated immune response in cancer. Curr Opin Immunol 2024:102431. [PMID: 38866666 DOI: 10.1016/j.coi.2024.102431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/14/2024]
Abstract
Immune cells in the tumor microenvironment play a crucial role in cancer prognosis and response to immunotherapy. Recent studies highlight the significance of tumor-infiltrating B cells and tertiary lymphoid structures as markers of favorable prognosis and patient-positive response to immune checkpoint blockers in some types of cancer. Although the presence of germinal center B cells and plasma cells in the tumor microenvironment has been established, determining their tumor reactivity remains challenging. The few known tumor targets range from viral proteins to self and altered self-proteins. The emergence of self-reactive antibodies in patients with cancer, involves the opposing forces of antigen-driven affinity increase and peripheral tolerance mechanisms. Here, B cell tumor antigen specificity and affinity maturation in tumor-directed immune responses in cancer are discussed.
Collapse
Affiliation(s)
- Philipp Paparoditis
- Department of Systems Immunology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ziv Shulman
- Department of Systems Immunology, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|
8
|
Sawamura J, Morishita S, Ishigooka J. Several supplementary concepts for applied category-theoretical states over an extended Petri net using an example relating to genetic coding: Toward an abstract algebraic formulation of molecular/genetic biology. PLoS One 2024; 19:e0302710. [PMID: 38848321 PMCID: PMC11161097 DOI: 10.1371/journal.pone.0302710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/09/2024] [Indexed: 06/09/2024] Open
Abstract
algebraic concepts such as category are considered cornerstones on which logical consistency relies in any sophisticated study of natural phenomena. However, to the best of our knowledge, in molecular/genetic biology, their application is still severely limited because they capture neither the dynamics nor provide a visual form. The Petri net (PN) has often been used to illustrate visually parallel, asynchronous dynamic events in small data systems. A prototypal hybrid model combining both category theory and extended PNs may instead be indispensable for that purpose. This hybrid model incorporates 1) token-like elements of a group, 2) object-like places of a category, 3) square poles (rather than pentagon poles) that enable unique identifications of single-strand DNA sequences from the shape of its polygonal line, 4) creation/annihilation morphisms that generate/erase tokens, 5) Cartesian products 'Z5×Z2×…' that enable conversions between DNA and RNA sequences, 6) somatic recombinations (VDJ recombinations) for antibodies displayed concretely in category-theoretic form, 7) 'identity protein Δ' translated from a triplet of identity bases 'EEE' as an advanced concept from our previous display of the canonical central dogma, 8) illustrations of an incidence-matrix-like matrix A that includes operators as coordinates, and 9) basic topics concerning the canonical central dogma being displayed concretely using concepts of conventional category theory such as 'adjoint', 'adjoint functor', 'natural transformation', 'Yoneda's lemma' and 'Kan extension'. These ideas provide more advanced tools that expand our previous model concerning nucleic-acid-base sequences. Despite the nascent nature of our methodology, our hybrid model has potential in a variety of applications, illustrated using molecular/genetic sequences, in particular providing a simple dynamic/visual representation. With further improvements, this approach may prove effective in reducing the need for large data-storing systems.
Collapse
Affiliation(s)
| | - Shigeru Morishita
- Depression Prevention Medical Center, Inariyama Takeda Hospital, Kyoto, Japan
| | | |
Collapse
|
9
|
Hyrien O, Yanev NM. A branching stochastic evolutionary model of the B-cell repertoire. J Math Biol 2024; 89:10. [PMID: 38847854 PMCID: PMC11161549 DOI: 10.1007/s00285-024-02102-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 09/15/2023] [Accepted: 03/13/2024] [Indexed: 06/10/2024]
Abstract
We propose a stochastic framework to describe the evolution of the B-cell repertoire during germinal center (GC) reactions. Our model is formulated as a multitype age-dependent branching process with time-varying immigration. The immigration process captures the mechanism by which founder B cells initiate clones by gradually seeding GC over time, while the branching process describes the temporal evolution of the composition of these clones. The model assigns a type to each cell to represent attributes of interest. Examples of attributes include the binding affinity class of the B cells, their clonal family, or the nucleotide sequence of the heavy and light chains of their receptors. The process is generally non-Markovian. We present its properties, including as t → ∞ when the process is supercritical, the most relevant case to study expansion of GC B cells. We introduce temporal alpha and beta diversity indices for multitype branching processes. We focus on the dynamics of clonal dominance, highlighting its non-stationarity, and the accumulation of somatic hypermutations in the context of sequential immunization. We evaluate the impact of the ongoing seeding of GC by founder B cells on the dynamics of the B-cell repertoire, and quantify the effect of precursor frequency and antigen availability on the timing of GC entry. An application of the model illustrates how it may help with interpretation of BCR sequencing data.
Collapse
Affiliation(s)
- Ollivier Hyrien
- Biostatistics, Bioinformatics, Epidemiology Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Nikolay M Yanev
- Department of Operations Research, Probability and Statistics, Institute of Mathematics and Informatics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| |
Collapse
|
10
|
Vu MH, Robert PA, Akbar R, Swiatczak B, Sandve GK, Haug DTT, Greiff V. Linguistics-based formalization of the antibody language as a basis for antibody language models. NATURE COMPUTATIONAL SCIENCE 2024; 4:412-422. [PMID: 38877120 DOI: 10.1038/s43588-024-00642-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 05/13/2024] [Indexed: 06/16/2024]
Abstract
Apparent parallels between natural language and antibody sequences have led to a surge in deep language models applied to antibody sequences for predicting cognate antigen recognition. However, a linguistic formal definition of antibody language does not exist, and insight into how antibody language models capture antibody-specific binding features remains largely uninterpretable. Here we describe how a linguistic formalization of the antibody language, by characterizing its tokens and grammar, could address current challenges in antibody language model rule mining.
Collapse
Affiliation(s)
- Mai Ha Vu
- Department of Linguistics and Scandinavian Studies, University of Oslo, Oslo, Norway.
| | - Philippe A Robert
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, Hefei, China
| | | | | | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
11
|
Durrant MG, Perry NT, Pai JJ, Jangid AR, Athukoralage JS, Hiraizumi M, McSpedon JP, Pawluk A, Nishimasu H, Konermann S, Hsu PD. Bridge RNAs direct programmable recombination of target and donor DNA. Nature 2024; 630:984-993. [PMID: 38926615 PMCID: PMC11208160 DOI: 10.1038/s41586-024-07552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 05/09/2024] [Indexed: 06/28/2024]
Abstract
Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes that are involved in fundamental DNA repair processes, such as homologous recombination, or in the transposition of foreign genetic material by viruses and mobile genetic elements1,2. Here we report that IS110 insertion sequences, a family of minimal and autonomous mobile genetic elements, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and the donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables the insertion of DNA into genomic target sites, as well as programmable DNA excision and inversion. The IS110 bridge recombination system expands the diversity of nucleic-acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements-insertion, excision and inversion-that are required for genome design.
Collapse
Affiliation(s)
- Matthew G Durrant
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T Perry
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | | | - Aditya R Jangid
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Masahiro Hiraizumi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | | | | | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
- Structural Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Inamori Research Institute for Science, Kyoto, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Saitama, Japan
| | - Silvana Konermann
- Arc Institute, Palo Alto, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick D Hsu
- Arc Institute, Palo Alto, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
| |
Collapse
|
12
|
Burbach SM, Briney B. Improving antibody language models with native pairing. PATTERNS (NEW YORK, N.Y.) 2024; 5:100967. [PMID: 38800360 PMCID: PMC11117052 DOI: 10.1016/j.patter.2024.100967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/25/2024] [Accepted: 03/08/2024] [Indexed: 05/29/2024]
Abstract
Existing antibody language models are limited by their use of unpaired antibody sequence data. A recently published dataset of ∼1.6 × 106 natively paired human antibody sequences offers a unique opportunity to evaluate how antibody language models are improved by training with native pairs. We trained three baseline antibody language models (BALM), using natively paired (BALM-paired), randomly-paired (BALM-shuffled), or unpaired (BALM-unpaired) sequences from this dataset. To address the paucity of paired sequences, we additionally fine-tuned ESM (evolutionary scale modeling)-2 with natively paired antibody sequences (ft-ESM). We provide evidence that training with native pairs allows the model to learn immunologically relevant features that span the light and heavy chains, which cannot be simulated by training with random pairs. We additionally show that training with native pairs improves model performance on a variety of metrics, including the ability of the model to classify antibodies by pathogen specificity.
Collapse
Affiliation(s)
- Sarah M Burbach
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Multi-Omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Multi-Omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- San Diego Center for AIDS Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
13
|
Weyrich A, Hecht W, Köhler K, Herden C, Henrich M. Comparative analysis of primer sets for the assessment of clonality in feline lymphomas. Front Vet Sci 2024; 11:1356330. [PMID: 38774911 PMCID: PMC11106357 DOI: 10.3389/fvets.2024.1356330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Introduction Lymphomas are among the most important and common malignant tumors in cats. Differentiating lymphomas from reactive lymphoid proliferations can be challenging, so additional tools such as clonality assessment by PCR are important in diagnosis finding. Several PCR assays have been developed to assess clonality in feline lymphomas. For T-cell lymphomas TRG (T-cell receptor gamma) genes are the preferred target whereas for B-cell lymphomas most primer sets target immunoglobulin heavy chain (IGH) genes. Here we compare commonly used diagnostic primer sets for the assessment of clonality in feline lymphomas under controlled conditions (i.e., identical sample set, PCR setup, amplicon detection system). Methods Formalin-fixed and paraffin-embedded samples from 31 feline T-cell lymphomas, 29 B-cell lymphomas, and 11 non-neoplastic controls were analyzed by PCR combined with capillary electrophoresis. Results and discussion We show that the combination of the primer sets published by Weiss et al. and Mochizuki et al. provided the best results for T-cell clonality, i.e., correctly assigns most populations as clonal or polyclonal. For B-cell clonality, the combination of the primer sets by Mochizuki et al. and Rout et al. gave the best results when omitting the Kde gene rearrangement due to its low specificity. This study rigorously evaluated various primer sets under uniform experimental conditions to improve accuracy of lymphoma diagnostic and provides a recommendation for achieving the highest diagnostic precision in lymphoma clonality analysis.
Collapse
Affiliation(s)
| | | | | | | | - Manfred Henrich
- Institut für Veterinär-Pathologie, Justus-Liebig-Universität Giessen, Giessen, Germany
| |
Collapse
|
14
|
Rückert T, Romagnani C. Extrinsic and intrinsic drivers of natural killer cell clonality. Immunol Rev 2024; 323:80-106. [PMID: 38506411 DOI: 10.1111/imr.13324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Clonal expansion of antigen-specific lymphocytes is the fundamental mechanism enabling potent adaptive immune responses and the generation of immune memory. Accompanied by pronounced epigenetic remodeling, the massive proliferation of individual cells generates a critical mass of effectors for the control of acute infections, as well as a pool of memory cells protecting against future pathogen encounters. Classically associated with the adaptive immune system, recent work has demonstrated that innate immune memory to human cytomegalovirus (CMV) infection is stably maintained as large clonal expansions of natural killer (NK) cells, raising questions on the mechanisms for clonal selection and expansion in the absence of re-arranged antigen receptors. Here, we discuss clonal NK cell memory in the context of the mechanisms underlying clonal competition of adaptive lymphocytes and propose alternative selection mechanisms that might decide on the clonal success of their innate counterparts. We propose that the integration of external cues with cell-intrinsic sources of heterogeneity, such as variegated receptor expression, transcriptional states, and somatic variants, compose a bottleneck for clonal selection, contributing to the large size of memory NK cell clones.
Collapse
Affiliation(s)
- Timo Rückert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
| | - Chiara Romagnani
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
| |
Collapse
|
15
|
Vuscan P, Kischkel B, Joosten LAB, Netea MG. Trained immunity: General and emerging concepts. Immunol Rev 2024; 323:164-185. [PMID: 38551324 DOI: 10.1111/imr.13326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/11/2024] [Indexed: 05/18/2024]
Abstract
Over the past decade, compelling evidence has unveiled previously overlooked adaptive characteristics of innate immune cells. Beyond their traditional role in providing short, non-specific protection against pathogens, innate immune cells can acquire antigen-agnostic memory, exhibiting increased responsiveness to secondary stimulation. This long-term de-facto innate immune memory, also termed trained immunity, is mediated through extensive metabolic rewiring and epigenetic modifications. While the upregulation of trained immunity proves advantageous in countering immune paralysis, its overactivation contributes to the pathogenesis of autoinflammatory and autoimmune disorders. In this review, we present the latest advancements in the field of innate immune memory followed by a description of the fundamental mechanisms underpinning trained immunity generation and different cell types that mediate it. Furthermore, we explore its implications for various diseases and examine current limitations and its potential therapeutic targeting in immune-related disorders.
Collapse
Affiliation(s)
- Patricia Vuscan
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Brenda Kischkel
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| |
Collapse
|
16
|
Crow RS, Shaw CG, Grayfer L, Smith LC. Recombinant SpTransformer proteins are functionally diverse for binding and phagocytosis by three subtypes of sea urchin phagocytes. Front Immunol 2024; 15:1372904. [PMID: 38742116 PMCID: PMC11089230 DOI: 10.3389/fimmu.2024.1372904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/29/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction The California purple sea urchin, Strongylocentrotus purpuratus, relies solely on an innate immune system to combat the many pathogens in the marine environment. One aspect of their molecular defenses is the SpTransformer (SpTrf) gene family that is upregulated in response to immune challenge. The gene sequences are highly variable both within and among animals and likely encode thousands of SpTrf isoforms within the sea urchin population. The native SpTrf proteins bind foreign targets and augment phagocytosis of a marine Vibrio. A recombinant (r)SpTrf-E1-Ec protein produced by E. coli also binds Vibrio but does not augment phagocytosis. Methods To address the question of whether other rSpTrf isoforms function as opsonins and augment phagocytosis, six rSpTrf proteins were expressed in insect cells. Results The rSpTrf proteins are larger than expected, are glycosylated, and one dimerized irreversibly. Each rSpTrf protein cross-linked to inert magnetic beads (rSpTrf::beads) results in different levels of surface binding and phagocytosis by phagocytes. Initial analysis shows that significantly more rSpTrf::beads associate with cells compared to control BSA::beads. Binding specificity was verified by pre-incubating the rSpTrf::beads with antibodies, which reduces the association with phagocytes. The different rSpTrf::beads show significant differences for cell surface binding and phagocytosis by phagocytes. Furthermore, there are differences among the three distinct types of phagocytes that show specific vs. constitutive binding and phagocytosis. Conclusion These findings illustrate the complexity and effectiveness of the sea urchin innate immune system driven by the natSpTrf proteins and the phagocyte cell populations that act to neutralize a wide range of foreign pathogens.
Collapse
Affiliation(s)
| | | | | | - L Courtney Smith
- Department of Biological Sciences, George Washington University, Washington, DC, United States
| |
Collapse
|
17
|
Stork EM, van Rijswijck DMH, van Schie KA, Hoek M, Kissel T, Scherer HU, Huizinga TWJ, Heck AJR, Toes REM, Bondt A. Antigen-specific Fab profiling achieves molecular-resolution analysis of human autoantibody repertoires in rheumatoid arthritis. Nat Commun 2024; 15:3114. [PMID: 38600082 PMCID: PMC11006680 DOI: 10.1038/s41467-024-47337-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
The presence of autoantibodies is a defining feature of many autoimmune diseases. The number of unique autoantibody clones is conceivably limited by immune tolerance mechanisms, but unknown due to limitations of the currently applied technologies. Here, we introduce an autoantigen-specific liquid chromatography-mass spectrometry-based IgG1 Fab profiling approach using the anti-citrullinated protein antibody (ACPA) repertoire in rheumatoid arthritis (RA) as an example. We show that each patient harbors a unique and diverse ACPA IgG1 repertoire dominated by only a few antibody clones. In contrast to the total plasma IgG1 antibody repertoire, the ACPA IgG1 sub-repertoire is characterised by an expansion of antibodies that harbor one, two or even more Fab glycans, and different glycovariants of the same clone can be detected. Together, our data indicate that the autoantibody response in a prominent human autoimmune disease is complex, unique to each patient and dominated by a relatively low number of clones.
Collapse
Affiliation(s)
- Eva Maria Stork
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Danique M H van Rijswijck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, the Netherlands
| | - Karin A van Schie
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Max Hoek
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, the Netherlands
| | - Theresa Kissel
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Hans Ulrich Scherer
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Tom W J Huizinga
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, the Netherlands
| | - Rene E M Toes
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Albert Bondt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, The Netherlands.
- Netherlands Proteomics Center, Padualaan 8, Utrecht, the Netherlands.
| |
Collapse
|
18
|
Beaulaurier J, Ly L, Duty JA, Tyer C, Stevens C, Hung CT, Sookdeo A, Drong AW, Kowdle S, Turner DJ, Juul S, Hickey S, Lee B. De novo antibody discovery in human blood from full-length single B cell transcriptomics and matching haplotyped-resolved germline assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586834. [PMID: 38585716 PMCID: PMC10996687 DOI: 10.1101/2024.03.26.586834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Immunoglobulin (IGH, IGK, IGL) loci in the human genome are highly polymorphic regions that encode the building blocks of the light and heavy chain IG proteins that dimerize to form antibodies. The processes of V(D)J recombination and somatic hypermutation in B cells are responsible for creating an enormous reservoir of highly specific antibodies capable of binding a vast array of possible antigens. However, the antibody repertoire is fundamentally limited by the set of variable (V), diversity (D), and joining (J) alleles present in the germline IG loci. To better understand how the germline IG haplotypes contribute to the expressed antibody repertoire, we combined genome sequencing of the germline IG loci with single-cell transcriptome sequencing of B cells from the same donor. Sequencing and assembly of the germline IG loci captured the IGH locus in a single fully-phased contig where the maternal and paternal contributions to the germline V, D, and J repertoire can be fully resolved. The B cells were collected following a measles, mumps, and rubella (MMR) vaccination, resulting in a population of cells that were activated in response to this specific immune challenge. Single-cell, full-length transcriptome sequencing of these B cells resulted in whole transcriptome characterization of each cell, as well as highly-accurate consensus sequences for the somatically rearranged and hypermutated light and heavy chain IG transcripts. A subset of antibodies synthesized based on their consensus heavy and light chain transcript sequences demonstrated binding to measles antigens and neutralization of measles live virus.
Collapse
|
19
|
Lee H, Shin K, Lee Y, Lee S, Lee S, Lee E, Kim SW, Shin HY, Kim JH, Chung J, Kwon S. Identification of B cell subsets based on antigen receptor sequences using deep learning. Front Immunol 2024; 15:1342285. [PMID: 38576618 PMCID: PMC10991714 DOI: 10.3389/fimmu.2024.1342285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
B cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispensable to identify both attributes. However, this approach accompanies high costs and inevitable information loss, hindering high-throughput investigation of B cell populations. Here, we present BCR-SORT, a deep learning model that predicts cell subsets from their corresponding BCR sequences by leveraging B cell activation and maturation signatures encoded within BCR sequences. Subsequently, BCR-SORT is demonstrated to improve reconstruction of BCR phylogenetic trees, and reproduce results consistent with those verified using physical isolation-based methods or prior knowledge. Notably, when applied to BCR sequences from COVID-19 vaccine recipients, it revealed inter-individual heterogeneity of evolutionary trajectories towards Omicron-binding memory B cells. Overall, BCR-SORT offers great potential to improve our understanding of B cell responses.
Collapse
Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yongju Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Soobin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Seungyoun Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Woo Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ha Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hoon Kim
- Department of Dermatology and Cutaneous Biology Research Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
20
|
Shingai M, Iida S, Kawai N, Kawahara M, Sekiya T, Ohno M, Nomura N, Handabile C, Kawakita T, Omori R, Yamagishi J, Sano K, Ainai A, Suzuki T, Ohnishi K, Ito K, Kida H. Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire. J Virol 2024; 98:e0199523. [PMID: 38323813 PMCID: PMC10949447 DOI: 10.1128/jvi.01995-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/14/2024] [Indexed: 02/08/2024] Open
Abstract
Historically, antibody reactivity to pathogens and vaccine antigens has been evaluated using serological measurements of antigen-specific antibodies. However, it is difficult to evaluate all antibodies that contribute to various functions in a single assay, such as the measurement of the neutralizing antibody titer. Bulk antibody repertoire analysis using next-generation sequencing is a comprehensive method for analyzing the overall antibody response; however, it is unreliable for estimating antigen-specific antibodies due to individual variation. To address this issue, we propose a method to subtract the background signal from the repertoire of data of interest. In this study, we analyzed changes in antibody diversity and inferred the heavy-chain complementarity-determining region 3 (CDRH3) sequences of antibody clones that were selected upon influenza virus infection in a mouse model using bulk repertoire analysis. A decrease in the diversity of the antibody repertoire was observed upon viral infection, along with an increase in neutralizing antibody titers. Using kernel density estimation of sequences in a high-dimensional sequence space with background signal subtraction, we identified several clusters of CDRH3 sequences induced upon influenza virus infection. Most of these repertoires were detected more frequently in infected mice than in uninfected control mice, suggesting that infection-specific antibody sequences can be extracted using this method. Such an accurate extraction of antigen- or infection-specific repertoire information will be a useful tool for vaccine evaluation in the future. IMPORTANCE As specific interactions between antigens and cell-surface antibodies trigger the proliferation of B-cell clones, the frequency of each antibody sequence in the samples reflects the size of each clonal population. Nevertheless, it is extremely difficult to extract antigen-specific antibody sequences from the comprehensive bulk antibody sequences obtained from blood samples due to repertoire bias influenced by exposure to dietary antigens and other infectious agents. This issue can be addressed by subtracting the background noise from the post-immunization or post-infection repertoire data. In the present study, we propose a method to quantify repertoire data from comprehensive repertoire data. This method allowed subtraction of the background repertoire, resulting in more accurate extraction of expanded antibody repertoires upon influenza virus infection. This accurate extraction of antigen- or infection-specific repertoire information is a useful tool for vaccine evaluation.
Collapse
Affiliation(s)
- Masashi Shingai
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sayaka Iida
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoko Kawai
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mamiko Kawahara
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Toshiki Sekiya
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Marumi Ohno
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Naoki Nomura
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Chimuka Handabile
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Tomomi Kawakita
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryosuke Omori
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Junya Yamagishi
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kaori Sano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuo Ohnishi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kimihito Ito
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroshi Kida
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| |
Collapse
|
21
|
Yang Y, Li J, Li D, Zhou W, Yan F, Wang W. Humanized mouse models: A valuable platform for preclinical evaluation of human cancer. Biotechnol Bioeng 2024; 121:835-852. [PMID: 38151887 DOI: 10.1002/bit.28618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/26/2023] [Indexed: 12/29/2023]
Abstract
Animal models are routinely employed to assess the treatments for human cancer. However, due to significant differences in genetic backgrounds, traditional animal models are unable to meet bioresearch needs. To overcome this restriction, researchers have generated and optimized immunodeficient mice, and then engrafted human genes, cells, tissues, or organs in mice so that the responses in the model mice could provide a more reliable reference for treatments. As a bridge connecting clinical application and basic research, humanized mice are increasingly used in the preclinical evaluation of cancer treatments, particularly after gene interleukin 2 receptor gamma mutant mice were generated. Human cancer models established in humanized mice support exploration of the mechanism of cancer occurrence and provide an efficient platform for drug screening. However, it is undeniable that the further application of humanized mice still faces multiple challenges. This review summarizes the construction approaches for humanized mice and their existing limitations. We also report the latest applications of humanized mice in preclinical evaluation for the treatment of cancer and point out directions for future optimization of these models.
Collapse
Affiliation(s)
- Yuening Yang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaqian Li
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Li
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Weilin Zhou
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Feiyang Yan
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Wang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
22
|
Balla B, Tripon F, Lazar E, Bănescu C. Analysis of Mutational Status of IGHV, and Cytokine Polymorphisms as Prognostic Factors in Chronic Lymphocytic Leukemia: The Romanian Experience. Int J Mol Sci 2024; 25:1799. [PMID: 38339076 PMCID: PMC10855205 DOI: 10.3390/ijms25031799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
The aim of the current study was to assess the associations between genetic risk factors (such as the mutational status of the IGHV gene and polymorphisms of the IL-10 and TNF-α genes) and CLL risk, prognosis, and overall survival. Another goal of this study was to evaluate the multivariate effect of the combination of multiple genetic risk factors (mutational status of the IGHV gene, somatic mutations, DNA CNVs, and cytokine SNPs) on the clinical characteristics and survival of patients. A total of 125 CLL patients and 239 healthy controls were included for comparative SNP analysis. IL-10 (rs1800896 and rs1800872) and TNF-α (rs361525 and rs1800750) SNPs and haplotypes were not associated with CLL risk. The absence of hypermutation in the IGHV gene was shown to be of important prognostic value, being associated with short OS. Further individual risk factors for short OS were an age above 65 years at diagnosis and the presence of somatic mutations and/or CNVs. In our multivariable analysis, the presence of somatic mutations and the IL-10 rs1800872 variant allele, and the association of CNVs with the IL-10 rs1800896 variant allele, were identified as risk factors for short OS. Moreover, the OS in unmutated IGHV patients was additionally affected (decreased) by the presence of CNVs and/or somatic mutations. Similarly, IL-10 rs1800896 modulated the OS in unmutated IGHV patients with CNVs.
Collapse
Affiliation(s)
- Beata Balla
- Department of Medical Genetics, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540139 Targu Mures, Romania; (B.B.); (C.B.)
- Center for Advanced Medical and Pharmaceutical Research, Genetics Laboratory, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540139 Targu Mures, Romania
- Medical Genetics Laboratory, Emergency County Hospital of Targu Mures, 540136 Targu Mures, Romania
| | - Florin Tripon
- Department of Medical Genetics, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540139 Targu Mures, Romania; (B.B.); (C.B.)
- Center for Advanced Medical and Pharmaceutical Research, Genetics Laboratory, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540139 Targu Mures, Romania
- Medical Genetics Laboratory, Emergency County Hospital of Targu Mures, 540136 Targu Mures, Romania
| | - Erzsebet Lazar
- Department of Internal Medicine, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540139 Targu Mures, Romania;
| | - Claudia Bănescu
- Department of Medical Genetics, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540139 Targu Mures, Romania; (B.B.); (C.B.)
- Center for Advanced Medical and Pharmaceutical Research, Genetics Laboratory, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures, 540139 Targu Mures, Romania
- Medical Genetics Laboratory, Emergency County Hospital of Targu Mures, 540136 Targu Mures, Romania
| |
Collapse
|
23
|
Arata K, Yamaguchi T, Takamune K, Yasumoto S, Kondo M, Kato SI, Yoshikuni M, Ohno K, Kato-Unoki Y, Okada G, Fujii T. Pattern recognition receptors involved in the immune system of hagfish (Eptatretus burgeri). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 151:105065. [PMID: 37741564 DOI: 10.1016/j.dci.2023.105065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
The initial defense against invading pathogenic microbes is the activation of innate immunity by binding of pattern recognition receptors (PRRs) to pathogen associated molecular patterns (PAMPs). To explain the action of PRRs from hagfish, one of the extant jawless vertebrates, we purified the GlcNAc recognition complex (GRC) from serum using GlcNAc-agarose. The GRC comprises four proteins of varying molecular masses: 19 kDa, 26 kDa, 27 kDa, and 31 kDa. Exposure of Escherichia coli to the GRC led to the phagocytic activation of macrophages, revealing the opsonic function of the GRC. The GRC in serum formed a large complex with a molecular mass of approximately 1200 kDa. The GRC bound to Escherichia coli but not to rabbit red blood cells, despite both having GlcNAc on their surface. These structural and binding properties are similar to those of mannose-binding lectin (MBL). The amino acid sequence of a portion of the 31 kDa protein in the GRC matched the amino acid sequence of variable lymphocyte receptor (VLR)-B in some place. According to the Western blot analysis, the 31 kDa protein was recognized by the anti-hagfish VLR-B antiserum. Based on the results, it appears that the GRC functions as a PRR like MBL and that its 31 kDa protein has a structure similar to that of VLR-B.
Collapse
Affiliation(s)
- Kenya Arata
- Department of Biological Science, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto, 860-8555, Japan
| | - Tomokazu Yamaguchi
- Department of Biological Science, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto, 860-8555, Japan
| | - Kazufumi Takamune
- Division of Natural Science, Faculty of Advanced Science and Technology, Kumamoto University(4), 2-39-1 Kurokami, Kumamoto, 860-8555, Japan.
| | - Shinya Yasumoto
- Department of Applied Aquabiology, National Fisheries University, Japan Fisheries Research and Education Agency, Shimonoseki, Yamaguchi, 759-6595, Japan
| | - Masakazu Kondo
- Department of Applied Aquabiology, National Fisheries University, Japan Fisheries Research and Education Agency, Shimonoseki, Yamaguchi, 759-6595, Japan
| | - Shin-Ichi Kato
- Fishery Research Laboratory, Kyushu University, Fukutsu, 811-3304, Japan
| | | | - Kaoru Ohno
- Interdisciplinary Research Unit, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, 444-8585, Aichi, Japan
| | - Yoko Kato-Unoki
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 812-8581, Japan
| | - Genya Okada
- Department of Health Sciences, Faculty of Human Culture and Science, Prefectural University of Hiroshima, Ujina-Higashi, Minami-ku, Hiroshima, 734-8558, Japan
| | - Tamotsu Fujii
- Department of Health Sciences, Faculty of Human Culture and Science, Prefectural University of Hiroshima, Ujina-Higashi, Minami-ku, Hiroshima, 734-8558, Japan
| |
Collapse
|
24
|
Wei J, Li J, Zong F, Xiao ZX, Cao Y. Computational Analysis of B-Cell Receptor (BCR) Immune Repertoires with Abalign. Curr Protoc 2024; 4:e1002. [PMID: 38406972 DOI: 10.1002/cpz1.1002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The widespread application of high-throughput sequencing technology has generated massive sequences of B-cell receptor (BCR) immune repertoires. Computational analysis of these data has gained significant attention due to the increasing importance of immunotherapy and precision medicine. It not only reveals the diversity and dynamic changes in immune responses, contributing to the study of associated diseases, but also provides valuable information for immunodiagnostics and drug development. Recently, we introduced a BCR-specific multiple sequence alignment (MSA) method along with a comprehensive platform software called Abalign, which stands out as an excellent choice for analyzing BCR immune repertoires due to its unique high-throughput processing capability. It offers ultra-fast MSA functionality and a wide range of analytical features, including BCR/antibody extraction, clonal grouping, lineage tree construction, mutation profiling, diversity statistics, VJ gene assignment, antibody humanization, and more. Importantly, users can perform these analyses using the graphical user interface without any programming skills or scripts. In this article, we present a series of protocols that integrate Abalign's analysis modules into a cohesive workflow. This step-by-step workflow provides detailed instructions for software installation, data preparation, and comprehensive analysis of BCR immune repertoires. This workflow facilitates the efficient acquisition of comprehensive results in profiling BCR immune repertoires, offering insights into the impacts of infectious diseases, allergies, autoimmune disorders, tumor immunology, and antibody drugs. Abalign is freely available at http://cao.labshare.cn/abalign/. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Resource preparation Basic Protocol 2: Analyzing BCR immune repertoires Support Protocol 1: Aiding antibody humanization Support Protocol 2: Constructing B-cell lineage trees Alternate Protocol: Running with Linux command line Basic Protocol 3: Comparing BCR immune repertoires.
Collapse
Affiliation(s)
- Jiachen Wei
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Junxian Li
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fanjie Zong
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| |
Collapse
|
25
|
Lapuente D, Winkler TH, Tenbusch M. B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity. Cell Mol Immunol 2024; 21:144-158. [PMID: 37945737 PMCID: PMC10805925 DOI: 10.1038/s41423-023-01095-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.
Collapse
Affiliation(s)
- Dennis Lapuente
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany.
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany
| |
Collapse
|
26
|
Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee NY, Jensen C, Ladd D, Hanssen F, Heumos S, Yaari G, Kowarik MC, Nahnsen S, Kleinstein SH. nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576147. [PMID: 38293151 PMCID: PMC10827190 DOI: 10.1101/2024.01.18.576147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets. nf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core/airrflow). Detailed documentation and example results are available on the nf-core website at (https://nf-co.re/airrflow).
Collapse
|
27
|
Durrant MG, Perry NT, Pai JJ, Jangid AR, Athukoralage JS, Hiraizumi M, McSpedon JP, Pawluk A, Nishimasu H, Konermann S, Hsu PD. Bridge RNAs direct modular and programmable recombination of target and donor DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577089. [PMID: 38328150 PMCID: PMC10849738 DOI: 10.1101/2024.01.24.577089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions, or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes involved in fundamental DNA repair processes such as homologous recombination or in the transposition of foreign genetic material by viruses and mobile genetic elements (MGEs). We report that IS110 insertion sequences, a family of minimal and autonomous MGEs, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables DNA insertion into genomic target sites as well as programmable DNA excision and inversion. The IS110 bridge system expands the diversity of nucleic acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements required for genome design.
Collapse
Affiliation(s)
- Matthew G. Durrant
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T. Perry
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley - University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - James J. Pai
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
| | - Aditya R. Jangid
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Masahiro Hiraizumi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | | - April Pawluk
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
| | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Inamori Research Institute for Science, 620 Suiginya-cho, Shimogyo-ku, Kyoto 600-8411, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Silvana Konermann
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick D. Hsu
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| |
Collapse
|
28
|
Zhu Y, Tang H, Xie W, Chen S, Zeng H, Lan C, Guan J, Ma C, Yang X, Wang Q, Wei L, Zhang Z, Yu X. The multilevel extensive diversity across the cynomolgus macaque captured by ultra-deep adaptive immune receptor repertoire sequencing. SCIENCE ADVANCES 2024; 10:eadj5640. [PMID: 38266093 PMCID: PMC10807814 DOI: 10.1126/sciadv.adj5640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The extent to which AIRRs differ among and within individuals remains elusive. Via ultra-deep repertoire sequencing of 22 and 25 tissues in three cynomolgus macaques, respectively, we identified 84 and 114 novel IGHV and TRBV alleles, confirming 72 (85.71%) and 100 (87.72%) of them. The heterogeneous V gene usage patterns were influenced, in turn, by genetics, isotype (for BCRs only), tissue group, and tissue. A higher proportion of intragroup shared clones in the intestinal tissues than those in other tissues suggests a close intra-intestinal adaptive immunity network. Significantly higher mutation burdens in the public clones and the inter-tissue shared IgM and IgD clones indicate that they might target the shared antigens. This study reveals the extensive heterogeneity of the AIRRs at various levels and has broad fundamental and clinical implications. The data generated here will serve as an invaluable resource for future studies on adaptive immunity in health and diseases.
Collapse
Affiliation(s)
- Yan Zhu
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Haipei Tang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Wenxi Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Sen Chen
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huikun Zeng
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Division of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Chunhong Lan
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Junjie Guan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Cuiyu Ma
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiujia Yang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Qilong Wang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhenhai Zhang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
| | - Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Division of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| |
Collapse
|
29
|
Bailey SM, Cross EM, Kinner-Bibeau L, Sebesta HC, Bedford JS, Tompkins CJ. Monitoring Genomic Structural Rearrangements Resulting from Gene Editing. J Pers Med 2024; 14:110. [PMID: 38276232 PMCID: PMC10817574 DOI: 10.3390/jpm14010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
The cytogenomics-based methodology of directional genomic hybridization (dGH) enables the detection and quantification of a more comprehensive spectrum of genomic structural variants than any other approach currently available, and importantly, does so on a single-cell basis. Thus, dGH is well-suited for testing and/or validating new advancements in CRISPR-Cas9 gene editing systems. In addition to aberrations detected by traditional cytogenetic approaches, the strand specificity of dGH facilitates detection of otherwise cryptic intra-chromosomal rearrangements, specifically small inversions. As such, dGH represents a powerful, high-resolution approach for the quantitative monitoring of potentially detrimental genomic structural rearrangements resulting from exposure to agents that induce DNA double-strand breaks (DSBs), including restriction endonucleases and ionizing radiations. For intentional genome editing strategies, it is critical that any undesired effects of DSBs induced either by the editing system itself or by mis-repair with other endogenous DSBs are recognized and minimized. In this paper, we discuss the application of dGH for assessing gene editing-associated structural variants and the potential heterogeneity of such rearrangements among cells within an edited population, highlighting its relevance to personalized medicine strategies.
Collapse
Affiliation(s)
- Susan M. Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Erin M. Cross
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | | | - Henry C. Sebesta
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Joel S. Bedford
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | | |
Collapse
|
30
|
Wang P, Fredj Z, Zhang H, Rong G, Bian S, Sawan M. Blocking Superantigen-Mediated Diseases: Challenges and Future Trends. J Immunol Res 2024; 2024:2313062. [PMID: 38268531 PMCID: PMC10807946 DOI: 10.1155/2024/2313062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/15/2023] [Accepted: 12/30/2023] [Indexed: 01/26/2024] Open
Abstract
Superantigens are virulence factors secreted by microorganisms that can cause various immune diseases, such as overactivating the immune system, resulting in cytokine storms, rheumatoid arthritis, and multiple sclerosis. Some studies have demonstrated that superantigens do not require intracellular processing and instated bind as intact proteins to the antigen-binding groove of major histocompatibility complex II on antigen-presenting cells, resulting in the activation of T cells with different T-cell receptor Vβ and subsequent overstimulation. To combat superantigen-mediated diseases, researchers have employed different approaches, such as antibodies and simulated peptides. However, due to the complex nature of superantigens, these approaches have not been entirely successful in achieving optimal therapeutic outcomes. CD28 interacts with members of the B7 molecule family to activate T cells. Its mimicking peptide has been suggested as a potential candidate to block superantigens, but it can lead to reduced T-cell activity while increasing the host's infection risk. Thus, this review focuses on the use of drug delivery methods to accurately target and block superantigens, while reducing the adverse effects associated with CD28 mimic peptides. We believe that this method has the potential to provide an effective and safe therapeutic strategy for superantigen-mediated diseases.
Collapse
Affiliation(s)
- Pengbo Wang
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
| | - Zina Fredj
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
| | - Hongyong Zhang
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
| | - Guoguang Rong
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
| | - Sumin Bian
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
| | - Mohamad Sawan
- CenBRAIN Neurotech, School of Engineering, Westlake University, Hangzhou 310030, China
| |
Collapse
|
31
|
Dragoi G. The generative grammar of the brain: a critique of internally generated representations. Nat Rev Neurosci 2024; 25:60-75. [PMID: 38036709 DOI: 10.1038/s41583-023-00763-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
The past decade of progress in neurobiology has uncovered important organizational principles for network preconfiguration and neuronal selection that suggest a generative grammar exists in the brain. In this Perspective, I discuss the competence of the hippocampal neural network to generically express temporally compressed sequences of neuronal firing that represent novel experiences, which is envisioned as a form of generative neural syntax supporting a neurobiological perspective on brain function. I compare this neural competence with the hippocampal network performance that represents specific experiences with higher fidelity after new learning during replay, which is envisioned as a form of neural semantic that supports a complementary neuropsychological perspective. I also demonstrate how the syntax of network competence emerges a priori during early postnatal life and is followed by the later development of network performance that enables rapid encoding and memory consolidation. Thus, I propose that this generative grammar of the brain is essential for internally generated representations, which are crucial for the cognitive processes underlying learning and memory, prospection, and inference, which ultimately underlie our reason and representation of the world.
Collapse
Affiliation(s)
- George Dragoi
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.
- Wu Tsai Institute, Yale University, New Haven, CT, USA.
| |
Collapse
|
32
|
Mehryar MM, Shi X, Li J, Wu Q. DNA polymerases in precise and predictable CRISPR/Cas9-mediated chromosomal rearrangements. BMC Biol 2023; 21:288. [PMID: 38066536 PMCID: PMC10709867 DOI: 10.1186/s12915-023-01784-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Recent studies have shown that, owning to its cohesive cleavage, Cas9-mediated CRISPR gene editing outcomes at junctions of chromosomal rearrangements or DNA-fragment editing are precise and predictable; however, the underlying mechanisms are poorly understood due to lack of suitable assay system and analysis tool. RESULTS Here we developed a customized computer program to take account of staggered or cohesive Cas9 cleavage and to rapidly process large volumes of junctional sequencing reads from chromosomal rearrangements or DNA-fragment editing, including DNA-fragment inversions, duplications, and deletions. We also established a sensitive assay system using HPRT1 and DCK as reporters for cell growth during DNA-fragment editing by Cas9 with dual sgRNAs and found prominent large resections or long deletions at junctions of chromosomal rearrangements. In addition, we found that knockdown of PolQ (encoding Polθ polymerase), which has a prominent role in theta-mediated end joining (TMEJ) or microhomology-mediated end joining (MMEJ), results in increased large resections but decreased small deletions. We also found that the mechanisms for generating small deletions of 1bp and >1bp during DNA-fragment editing are different with regard to their opposite dependencies on Polθ and Polλ (encoded by the PolL gene). Specifically, Polθ suppresses 1bp deletions but promotes >1bp deletions, whereas Polλ promotes 1bp deletions but suppresses >1bp deletions. Finally, we found that Polλ is the main DNA polymerase responsible for fill-in of the 5' overhangs of staggered Cas9 cleavage ends. CONCLUSIONS These findings contribute to our understanding of the molecular mechanisms of CRISPR/Cas9-mediated DNA-fragment editing and have important implications for controllable, precise, and predictable gene editing.
Collapse
Affiliation(s)
- Mohammadreza M Mehryar
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Xin Shi
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- WLA Laboratories, Shanghai, 201203, China.
| |
Collapse
|
33
|
Janes ME, Kinlein A, Flajnik MF, Du Pasquier L, Ohta Y. Genomic view of the origins of cell-mediated immunity. Immunogenetics 2023; 75:479-493. [PMID: 37735270 PMCID: PMC11019866 DOI: 10.1007/s00251-023-01319-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/10/2023] [Indexed: 09/23/2023]
Abstract
NKp30 is an activating natural killer cell receptor (NKR) with a single-exon variable (VJ)-type immunoglobulin superfamily (IgSF) domain. Such VJ-IgSF domains predate the emergence of the antigen receptors (immunoglobulin and T cell receptor), which possess the same domain but undergo gene rearrangement. NCR3, the gene encoding NKp30, is present in jawed vertebrates from sharks to mammals; thus, unlike most NKR that are highly divergent among vertebrate taxa, NKp30 is uniquely conserved. We previously hypothesized that an ancestral NCR3 gene was encoded in the proto-major histocompatibility complex (MHC), the region where many immune-related genes have accumulated. Herein, we searched in silico databases to identify NCR3 paralogues and examined their genomic locations. We found a paralogue, NCR3H, in many vertebrates but was lost in mammals. Additionally, we identified a set of voltage-gated sodium channel beta (SCNB) genes as NCR3-distantly-related genes. Like NCR3, both NCR3H and SCNB proteins contain a single VJ-IgSF domain followed by a transmembrane region. These genes map to MHC paralogous regions, originally described in an invertebrate, along with genes encoding cell adhesion molecules involved in NK cell recognition networks. Other genes having no obvious relationship to immunity also map to these paralogous regions. These gene complexes were traced to several invertebrates, suggesting that the foundation of these cellular networks emerged before the genome-wide duplications in early gnathostome history. Here, we propose that this ancestral region was involved in cell-mediated immunity prior to the emergence of adaptive immunity and that NCR3 piggybacked onto this primordial complex, heralding the emergence of vertebrate NK cell/T cells.
Collapse
Affiliation(s)
- Morgan E Janes
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA
| | - Allison Kinlein
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA
| | - Louis Du Pasquier
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA.
| |
Collapse
|
34
|
Weber LL, Reiman D, Roddur MS, Qi Y, El-Kebir M, Khan AA. TRIBAL: Tree Inference of B cell Clonal Lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568874. [PMID: 38076836 PMCID: PMC10705245 DOI: 10.1101/2023.11.27.568874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
B cells are a critical component of the adaptive immune system, responsible for producing antibodies that help protect the body from infections and foreign substances. Single cell RNA-sequencing (scRNA-seq) has allowed for both profiling of B cell receptor (BCR) sequences and gene expression. However, understanding the adaptive and evolutionary mechanisms of B cells in response to specific stimuli remains a significant challenge in the field of immunology. We introduce a new method, TRIBAL, which aims to infer the evolutionary history of clonally related B cells from scRNA-seq data. The key insight of TRIBAL is that inclusion of isotype data into the B cell lineage inference problem is valuable for reducing phylogenetic uncertainty that arises when only considering the receptor sequences. Consequently, the TRIBAL inferred B cell lineage trees jointly capture the somatic mutations introduced to the B cell receptor during affinity maturation and isotype transitions during class switch recombination. In addition, TRIBAL infers isotype transition probabilities that are valuable for gaining insight into the dynamics of class switching. Via in silico experiments, we demonstrate that TRIBAL infers isotype transition probabilities with the ability to distinguish between direct versus sequential switching in a B cell population. This results in more accurate B cell lineage trees and corresponding ancestral sequence and class switch reconstruction compared to competing methods. Using real-world scRNA-seq datasets, we show that TRIBAL recapitulates expected biological trends in a model affinity maturation system. Furthermore, the B cell lineage trees inferred by TRIBAL were equally plausible for the BCR sequences as those inferred by competing methods but yielded lower entropic partitions for the isotypes of the sequenced B cell. Thus, our method holds the potential to further advance our understanding of vaccine responses, disease progression, and the identification of therapeutic antibodies.
Collapse
Affiliation(s)
- Leah L. Weber
- Department of Computer Science, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Derek Reiman
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Mrinmoy S. Roddur
- Department of Computer Science, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Yuanyuan Qi
- Department of Computer Science, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Mohammed El-Kebir
- Department of Computer Science, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Aly A. Khan
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
35
|
Weill JC, Weller S, Reynaud CA. B cell diversification in gut-associated lymphoid tissues: From birds to humans. J Exp Med 2023; 220:e20231501. [PMID: 37824081 PMCID: PMC10568490 DOI: 10.1084/jem.20231501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
Several species generate their preimmune repertoire in gut-associated lymphoid tissues (GALT), compensating a reduced germline V gene repertoire by post-rearrangement diversification mechanisms (gene conversion and/or somatic hypermutation) in these environments that act as primary lymphoid organs. We summarize here these processes for three different species (chickens, sheep, and rabbits) and further discuss the analogous process that T-independent B cell responses in humans represent: we indeed recently showed that response against bacterial polysaccharides mobilize marginal zone B cells that prediversified against gut antigens. While the initial diversification strategy differs in these two cases, i.e., repertoire formation driven by gut-derived mitotic signals vs. response against gut antigens, the common feature of these two processes is the mobilization of a B cell compartment prediversified in GALT for immune responses against distinct systemic antigens.
Collapse
Affiliation(s)
- Jean-Claude Weill
- Université Paris Cité, Institut national de la santé et de la recherche médicale U1151, Centre national de la recherche scientifique UMR-8253, Institut Necker Enfants Malades , Paris, France
| | - Sandra Weller
- Université Paris Cité, Institut national de la santé et de la recherche médicale U1151, Centre national de la recherche scientifique UMR-8253, Institut Necker Enfants Malades , Paris, France
| | - Claude-Agnès Reynaud
- Université Paris Cité, Institut national de la santé et de la recherche médicale U1151, Centre national de la recherche scientifique UMR-8253, Institut Necker Enfants Malades , Paris, France
| |
Collapse
|
36
|
Pelissier A, Stratigopoulou M, Donner N, Dimitriadis E, Bende RJ, Guikema JE, Rodriguez Martinez M, van Noesel CJ. Convergent evolution and B-cell recirculation in germinal centers in a human lymph node. Life Sci Alliance 2023; 6:e202301959. [PMID: 37640448 PMCID: PMC10462906 DOI: 10.26508/lsa.202301959] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023] Open
Abstract
Germinal centers (GCs) play a central role in generating an effective immune response against infectious pathogens, and failures in their regulating mechanisms can lead to the development of autoimmune diseases and cancer. Although previous works study experimental systems of the immune response with mouse models that are immunized with specific antigens, our study focused on a real-life situation, with an ongoing GC response in a human lymph node (LN) involving multiple asynchronized GCs reacting simultaneously to unknown antigens. We combined laser capture microdissection of individual GCs from human LN with next-generation repertoire sequencing to characterize individual GCs as distinct evolutionary spaces. In line with well-characterized GC responses in mice, elicited by immunization with model antigens, we observe a heterogeneous clonal diversity across individual GCs from the same human LN. Still, we identify shared clones in several individual GCs, and phylogenetic tree analysis combined with paratope modeling suggest the re-engagement and rediversification of B-cell clones across GCs and expanded clones exhibiting shared antigen responses across distinct GCs, indicating convergent evolution of the GCs.
Collapse
Affiliation(s)
- Aurelien Pelissier
- https://ror.org/02js37d36 IBM Research Europe, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Maria Stratigopoulou
- Department of Pathology, Amsterdam University Medical Centers, Location AMC, Lymphoma and Myeloma Center Amsterdam, Amsterdam, Netherlands
| | - Naomi Donner
- Department of Pathology, Amsterdam University Medical Centers, Location AMC, Lymphoma and Myeloma Center Amsterdam, Amsterdam, Netherlands
| | | | - Richard J Bende
- Department of Pathology, Amsterdam University Medical Centers, Location AMC, Lymphoma and Myeloma Center Amsterdam, Amsterdam, Netherlands
| | - Jeroen E Guikema
- Department of Pathology, Amsterdam University Medical Centers, Location AMC, Lymphoma and Myeloma Center Amsterdam, Amsterdam, Netherlands
| | | | - Carel Jm van Noesel
- Department of Pathology, Amsterdam University Medical Centers, Location AMC, Lymphoma and Myeloma Center Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
37
|
Fernández-Quintero ML, Pomarici ND, Fischer ALM, Hoerschinger VJ, Kroell KB, Riccabona JR, Kamenik AS, Loeffler JR, Ferguson JA, Perrett HR, Liedl KR, Han J, Ward AB. Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines. Antibodies (Basel) 2023; 12:67. [PMID: 37873864 PMCID: PMC10594513 DOI: 10.3390/antib12040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Antibodies and other new antibody-like formats have emerged as one of the most rapidly growing classes of biotherapeutic proteins. Understanding the structural features that drive antibody function and, consequently, their molecular recognition is critical for engineering antibodies. Here, we present the structural architecture of conventional IgG antibodies alongside other formats. We emphasize the importance of considering antibodies as conformational ensembles in solution instead of focusing on single-static structures because their functions and properties are strongly governed by their dynamic nature. Thus, in this review, we provide an overview of the unique structural and dynamic characteristics of antibodies with respect to their antigen recognition, biophysical properties, and effector functions. We highlight the numerous technical advances in antibody structure prediction and design, enabled by the vast number of experimentally determined high-quality structures recorded with cryo-EM, NMR, and X-ray crystallography. Lastly, we assess antibody and vaccine design strategies in the context of structure and dynamics.
Collapse
Affiliation(s)
- Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nancy D. Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna-Lena M. Fischer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Katharina B. Kroell
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna S. Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James A. Ferguson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailee R. Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
38
|
Murray JS. Dichotomy in TCR V-domain dynamics binding the opposed inclined planes of pMHC-II and pMHC-I α-helices. Mol Immunol 2023; 162:111-124. [PMID: 37677988 DOI: 10.1016/j.molimm.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/24/2023] [Accepted: 07/09/2023] [Indexed: 09/09/2023]
Abstract
Ligand recognition by the human α/β T-cell antigen receptor (TCR) heterodimer protein, unlike the surface immunoglobulin (sIg) B-cell receptor, is not governed by relative binding affinity. Its interaction with the peptide (p) plus major histocompatibility complex (MHC) protein (abbrev. pMHC) likely involves some different molecular mechanism linking pMHC binding to T-cell functions. Recent analytical geometry of TCR:pMHC-II solved crystallographic structures (n = 40) revealed that each variable (V)-domain is bound in similar, yet mathematically unique orientations to its target pMHC groove. The relative position of the central cysteine of each V-domain was examined by multivariable calculus in spherical coordinates, where a simple volume element (dV) was found to describe clonotypic geometry with pMHC-II. Here, the study was expanded to include TCR:pMHC-I structures, and to model a physical mechanism, specifically involving the two directionally opposed inclined planes (IP) manifest by the two major α-helices prominent in both MHC-I and MHC-II proteins. Calculations for rotational torque of each V-domain, together with acceleration up and down the slopes of both MHC α-helices were used to estimate the time a given V-domain spends sliding down its cognate MHC IP. This V-domain rotation/sliding mechanism appears to be quantitatively unique for each TCR:pMHC V-domain (n = 40). However, there is an apparent and common dichotomy between the mobility of each V-domain with respect to the two classes of MHC proteins. Evolutionary motifs in the MHC helices support that the V-domains negotiate the opposed inclined planes of pMHC ligands in clonotypic fashion. Thus, this model is useful in understanding how mechanical forces are linked to TCR function.
Collapse
|
39
|
Arons E, Henry K, Haas C, Gould M, Tsintolas J, Mauter J, Zhou H, Burbelo PD, Cohen JI, Kreitman RJ. Characterization of B-cell receptor clonality and immunoglobulin gene usage at multiple time points during active SARS-CoV-2 infection. J Med Virol 2023; 95:e29179. [PMID: 37877800 DOI: 10.1002/jmv.29179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
Although monoclonal antibodies to the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are known, B-cell receptor repertoire and its change in patients during coronavirus disease-2019 (COVID-19) progression is underreported. We aimed to study this molecularly. We used immunoglobulin heavy chain (IGH) variable region (IGHV) spectratyping and next-generation sequencing of peripheral blood B-cell genomic DNA collected at multiple time points during disease evolution to study B-cell response to SARS-CoV-2 infection in 14 individuals with acute COVID-19. We found a broad distribution of responding B-cell clones. The IGH gene usage was not significantly skewed but frequencies of individual IGH genes changed repeatedly. We found predominant usage of unmutated and low mutation-loaded IGHV rearrangements characterizing naïve and extrafollicular B cells among the majority of expanded peripheral B-cell clonal lineages at most tested time points in most patients. IGH rearrangement usage showed no apparent relation to anti-SARS-CoV-2 antibody titers. Some patients demonstrated mono/oligoclonal populations carrying highly mutated IGHV rearrangements indicating antigen experience at some of the time points tested, including even before anti-SARS-CoV-2 antibodies were detected. We present evidence demonstrating that the B-cell response to SARS-CoV-2 is individual and includes different lineages of B cells at various time points during COVID-19 progression.
Collapse
Affiliation(s)
- Evgeny Arons
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | | | - Christopher Haas
- Medstar Franklin Square Medical Center, Baltimore, Maryland, USA
| | - Mory Gould
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Jack Tsintolas
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Jack Mauter
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Hong Zhou
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Robert J Kreitman
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| |
Collapse
|
40
|
Zhu H, Zhao Z, Xu J, Chen Y, Cai J, Shi C, Zhou L, Zhu Q, Ji L. Comprehensive landscape of the T and B-cell repertoires of newly diagnosed gestational diabetes mellitus. Genomics 2023; 115:110681. [PMID: 37453476 DOI: 10.1016/j.ygeno.2023.110681] [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: 02/10/2023] [Revised: 06/03/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
This study conducted a high-throughput sequencing analysis of the T- and B- repertoires in the newly diagnosed GDM patients and evaluated the association between abnormal adaptive immunity and GDM. The unique TCR CDR3 clonotypes were mildly decreased in GDM patients, and the similarity of TCR V-J distributions was higher in the GDM group. Moreover, the usages of the V gene and V-J pair and the frequency distributions of some CDR3 amino acids (AAs) both in BCR and TCR were significantly different between groups. Moreover, the cytokines including IL-4, IL-6, IFN-γ and IL-17A were synchronously elevated in the GDM cases. Our findings provide a comprehensive view of BCR and TCR repertoires at newly diagnosed GDM patients, revealing the mild reduction in unique TCRB CDR3 sequences and slight alteration of the V gene, V-J combination and CDR3 (AA) usages of BCR and TCR. This work provides deep insight into the mechanism of maternal adaptive immunity in GDM and provides novel diagnostic biomarkers and potential immunotherapy targets for GDM.
Collapse
Affiliation(s)
- Hui Zhu
- Department of Internal Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Zhijia Zhao
- School of Public Health, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Jin Xu
- School of Public Health, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, PR China; Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Yanming Chen
- School of Public Health, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Jie Cai
- Center for Reproductive Medicine, Ningbo Women and Children's Hospital, Ningbo, Zhejiang 315211, PR China
| | - Chaoyi Shi
- Center for Reproductive Medicine, Ningbo Women and Children's Hospital, Ningbo, Zhejiang 315211, PR China
| | - Liming Zhou
- Center for Reproductive Medicine, Ningbo Women and Children's Hospital, Ningbo, Zhejiang 315211, PR China
| | - Qiong Zhu
- Department of Pediatrics, Affiliated People's Hospital of Ningbo University, Ningbo, Zhejiang 315040, PR China
| | - Lindan Ji
- Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, PR China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, School of Medicine, Ningbo, Zhejiang 315211, PR China.
| |
Collapse
|
41
|
Ott JA, Mitchell C, Sheppard M, Deiss TC, Horton JMC, Haakenson JK, Huang R, Kelley AR, Davis BW, Derr JN, Smider VV, Criscitiello MF. Evolution of immunogenetic components encoding ultralong CDR H3. Immunogenetics 2023; 75:323-339. [PMID: 37084012 PMCID: PMC10119515 DOI: 10.1007/s00251-023-01305-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/03/2023] [Indexed: 04/22/2023]
Abstract
The genomes of most vertebrates contain many V, D, and J gene segments within their Ig loci to construct highly variable CDR3 sequences through combinatorial diversity. This nucleotide variability translates into an antibody population containing extensive paratope diversity. Cattle have relatively few functional VDJ gene segments, requiring innovative approaches for generating diversity like the use of ultralong-encoding IGHV and IGHD gene segments that yield dramatically elongated CDR H3. Unique knob and stalk microdomains create protracted paratopes, where the antigen-binding knob sits atop a long stalk, allowing the antibody to bind both surface and recessed antigen epitopes. We examined genomes of twelve species of Bovidae to determine when ultralong-encoding IGHV and IGHD gene segments evolved. We located the 8-bp duplication encoding the unique TTVHQ motif in ultralong IGHV segments in six Bovid species (cattle, zebu, wild yak, domestic yak, American bison, and domestic gayal), but we did not find evidence of the duplication in species beyond the Bos and Bison genera. Additionally, we analyzed mRNA from bison spleen and identified a rich repertoire of expressed ultralong CDR H3 antibody mRNA, suggesting that bison use ultralong IGHV transcripts in their host defense. We found ultralong-encoding IGHD gene segments in all the same species except domestic yak, but again not beyond the Bos and Bison clade. Thus, the duplication event leading to this ultralong-encoding IGHV gene segment and the emergence of the ultralong-encoding IGHD gene segment appears to have evolved in a common ancestor of the Bos and Bison genera 5-10 million years ago.
Collapse
Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Christian Mitchell
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Morgan Sheppard
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Thad C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - J M Cody Horton
- Department of Veterinary Integrative Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Jeremy K Haakenson
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ruiqi Huang
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | | | - Brian W Davis
- Department of Veterinary Integrative Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - James N Derr
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Vaughn V Smider
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Bryan, TX, 77807, USA.
| |
Collapse
|
42
|
Westhrin M, Blazevski J, Textor A, Abdollahi P, Gopalakrishnan RP, Ngo LT, Hofgaard PO, Heinzelbecker J, Bobic S, Fossum E, Spång HCL, Braathen R, Bogen B. Id-neoantigen vaccine induces therapeutic CD8 + T cells against multiple myeloma: H chain-loss escapees cause FLC MM. J Immunother Cancer 2023; 11:e006944. [PMID: 37607769 PMCID: PMC10445383 DOI: 10.1136/jitc-2023-006944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Multiple myeloma (MM) cancers originate from plasma cells that have passed through the germinal center reaction where somatic hypermutation of Ig V regions takes place. Myeloma protein V regions often express many mutations and are thus a rich source of neoantigens (traditionally called idiotopes (Id)). Therefore, these are highly tumor-specific and excellent targets for immunotherapy. METHODS We have developed a DNA Id vaccine which as translated protein targets conventional dendritic cells (cDC) for CCL3-mediated delivery of myeloma protein V regions in a single-chain fragment variable (scFv) format. Vaccine efficacy was studied in the mouse MM model, mineral oil-induced plasmacytoma 315.BM. RESULTS The Id vaccine protected mice against a challenge with MM cells. Moreover, the vaccine had a therapeutic effect. However, in some of the vaccinated mice, MM cells not producing H chains escaped rejection, resulting in free light chain (FLC) MM. Depletion of CD8+ T cells abrogated vaccine efficacy, and protection was observed to be dependent on cDC1s, using Batf3-/- mice. Modifications of scFv in the vaccine demonstrated that CD8+ T cells were specific for two mutated VH sequences. CONCLUSIONS VH neoantigen-specific CD8+ T cells elicited by CCL3-containing Id vaccines had a therapeutic effect against MM in a mouse model. MM cells could escape rejection by losing expression of the H chain, thus giving rise to FLC MM.
Collapse
Affiliation(s)
- Marita Westhrin
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jana Blazevski
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ana Textor
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Pegah Abdollahi
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | | | - Linda Thuy Ngo
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Peter Olaf Hofgaard
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Julia Heinzelbecker
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sonja Bobic
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Even Fossum
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | | | - Ranveig Braathen
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Bjarne Bogen
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
43
|
Suresh J, Wu Y, Sabaratnam R, Brijlall S, Kyle B, Torlakovic EE. Dual Expression of Immunoglobulin Light Chains in Plasma Cell Myeloma: A Case Report and Literature Review. Appl Immunohistochem Mol Morphol 2023; 31:447-451. [PMID: 36314594 DOI: 10.1097/pai.0000000000001069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 08/19/2022] [Indexed: 11/25/2022]
Abstract
Typically, myeloma cells express a monoclonal immunoglobulin (Ig), either heavy or light chain. Here, we present a case of multiple myeloma with clonal dual expression of kappa and lambda light chain in a 74-year-old woman. Awareness of rare biphenotypic myeloma is important for proper diagnostic workup. A 74-year-old woman underwent hip replacement with an incidental finding of 20% plasma cells in the femoral head. Subsequent bone marrow biopsy also showed about 30% of plasma cells negative for CD20, CD56, and CD117. Immunohistochemistry (IHC) and in situ hybridization studies showed a mixture of kappa and lambda plasma cells. Flow cytometry showed ambiguous results for cytoplasmic Ig light chains kappa and lambda. However, cyclin D1 was highly expressed by plasma cells, and increased free kappa light chains were identified in serum. Further investigation by double IHC demonstrated co-expression of kappa and lambda light chains in the same cells. Fluoresces in situ hybridization studies were positive for t(11;14)(q13;q32) and the deletion 13q. Since its first description by Taylor and Burns in 1974, the demonstration of restricted cytoplasmic Ig light chain expression by immunohistochemistry is 1 of the basic tools for corroborating clonality of the plasma cells in tissue biopsy. IHC results in myeloma with dual expression of Ig light chains may suggest polyclonal plasma cell population, especially when plasma cells do not form sheets in the bone marrow. In an appropriate clinical setting, other investigations are needed to exclude plasma cell neoplasm, even with seemingly "polytypic" results by IHC.
Collapse
Affiliation(s)
- Janarthanee Suresh
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
| | - Yue Wu
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
- Saskatchewan Health Authority, Saskatoon
| | | | - Shashi Brijlall
- Department of Pathology
- Department of Orthopedic, Victoria Hospital, Prince Albert Parkland Health Region, SK, Canada
| | - Barry Kyle
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
- Saskatchewan Health Authority, Saskatoon
| | - Emina E Torlakovic
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan
- Saskatchewan Health Authority, Saskatoon
| |
Collapse
|
44
|
Walker K, Baravalle R, Holyfield R, Kalms J, Wright H, Seewooruthun C, Muskett FW, Scott-Tucker A, Merritt A, Henry A, Lawson ADG, Hall G, Prosser C, Carr MD. Identification and characterisation of anti-IL-13 inhibitory single domain antibodies provides new insights into receptor selectivity and attractive opportunities for drug discovery. Front Immunol 2023; 14:1216967. [PMID: 37483614 PMCID: PMC10359924 DOI: 10.3389/fimmu.2023.1216967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
Interleukin-13 (IL-13) is a cytokine involved in T-cell immune responses and is a well validated therapeutic target for the treatment of asthma, along with other allergic and inflammatory diseases. IL-13 signals through a ternary signalling complex formed with the receptors IL-13Rα1 and IL-4Rα. This complex is assembled by IL-13 initially binding IL-13Rα1, followed by association of the binary IL-13:IL-13Rα1 complex with IL-4Rα. The receptors are shared with IL-4, but IL-4 initially binds IL-4Rα. Here we report the identification and characterisation of a diverse panel of single-domain antibodies (VHHs) that bind to IL-13 (KD 40 nM-5.5 μM) and inhibit downstream IL-13 signalling (IC50 0.2-53.8 μM). NMR mapping showed that the VHHs recognise a number of epitopes on IL-13, including previously unknown allosteric sites. Further NMR investigation of VHH204 bound to IL-13 revealed a novel allosteric mechanism of inhibition, with the antibody stabilising IL-13 in a conformation incompatible with receptor binding. This also led to the identification of a conformational equilibrium for free IL-13, providing insights into differing receptor signalling complex assembly seen for IL-13 compared to IL-4, with formation of the IL-13:IL-13Rα1 complex required to stabilise IL-13 in a conformation with high affinity for IL-4Rα. These findings highlight new opportunities for therapeutic targeting of IL-13 and we report a successful 19F fragment screen of the IL-13:VHH204 complex, including binding sites identified for several hits. To our knowledge, these 19F containing fragments represent the first small-molecules shown to bind to IL-13 and could provide starting points for a small-molecule drug discovery programme.
Collapse
Affiliation(s)
- Kayleigh Walker
- Leicester Institute of Structural and Chemical Biology, and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Roberta Baravalle
- Leicester Institute of Structural and Chemical Biology, and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Rachel Holyfield
- Leicester Institute of Structural and Chemical Biology, and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Jacqueline Kalms
- Leicester Institute of Structural and Chemical Biology, and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
- UCB Biopharma, UCB Pharma, Slough, United Kingdom
| | - Helena Wright
- Leicester Institute of Structural and Chemical Biology, and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Chitra Seewooruthun
- Leicester Institute of Structural and Chemical Biology, and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Frederick W. Muskett
- Leicester Institute of Structural and Chemical Biology, and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | | | - Andy Merritt
- LifeArc, Centre for Therapeutics Discovery, Stevenage Bioscience Catalyst, Stevenage, United Kingdom
| | | | | | - Gareth Hall
- Leicester Institute of Structural and Chemical Biology, and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Christine Prosser
- Leicester Institute of Structural and Chemical Biology, and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
- UCB Biopharma, UCB Pharma, Slough, United Kingdom
| | - Mark D. Carr
- Leicester Institute of Structural and Chemical Biology, and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| |
Collapse
|
45
|
Jeusset L, Abdollahi N, Verny T, Armand M, De Septenville A, Davi F, Bernardes JS. ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors. NAR Genom Bioinform 2023; 5:lqad064. [PMID: 37388820 PMCID: PMC10304752 DOI: 10.1093/nargab/lqad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/25/2023] [Accepted: 06/26/2023] [Indexed: 07/01/2023] Open
Abstract
High throughput sequencing of adaptive immune receptor repertoire (AIRR-seq) has provided numerous human immunoglobulin (IG) sequences allowing specific B cell receptor (BCR) studies such as the antigen-driven evolution of antibodies (soluble forms of the membrane-bound IG part of the BCR). AIRR-seq data allows researchers to examine intraclonal differences caused primarily by somatic hypermutations in IG genes and affinity maturation. Exploring this essential adaptive immunity process could help elucidate the generation of antibodies with high affinity or broadly neutralizing activities. Retracing their evolutionary history could also clarify how vaccines or pathogen exposition drive the humoral immune response, and unravel the clonal architecture of B cell tumors. Computational methods are necessary for large-scale analysis of AIRR-seq properties. However, there is no efficient and interactive tool for analyzing intraclonal diversity, permitting users to explore adaptive immune receptor repertoires in biological and clinical applications. Here we present ViCloD, a web server for large-scale visual analysis of repertoire clonality and intraclonal diversity. ViCloD uses preprocessed data in the format defined by the Adaptive Immune Receptor Repertoire (AIRR) Community. Then, it performs clonal grouping and evolutionary analyses, producing a collection of useful plots for clonal lineage inspection. The web server presents diverse functionalities, including repertoire navigation, clonal abundance analysis, and intraclonal evolutionary tree reconstruction. Users can download the analyzed data in different table formats and save the generated plots as images. ViCloD is a simple, versatile, and user-friendly tool that can help researchers and clinicians to analyze B cell intraclonal diversity. Moreover, its pipeline is optimized to process hundreds of thousands of sequences within a few minutes, allowing an efficient investigation of large and complex repertoires.
Collapse
Affiliation(s)
- Lucile Jeusset
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Paris, France
| | - Nika Abdollahi
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- IMGT, the international ImMunoGeneTics Information System, CNRS, Institute of Human Genetics, Montpellier University, France
| | - Thibaud Verny
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- Ecole des Mines ParisTech, Paris, France
| | - Marine Armand
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Paris, France
| | | | - Frédéric Davi
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Paris, France
| | - Juliana Silva Bernardes
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| |
Collapse
|
46
|
Xie S, Yan R, Zheng A, Shi M, Tang L, Li X, Liu J, Gan Y, Wang Y, Jiang D, Liu L, Wu H, Wang Z. T cell receptor and B cell receptor exhibit unique signatures in tumor and adjacent non-tumor tissues of hepatocellular carcinoma. Front Immunol 2023; 14:1161417. [PMID: 37313417 PMCID: PMC10258310 DOI: 10.3389/fimmu.2023.1161417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/16/2023] [Indexed: 06/15/2023] Open
Abstract
Background The tumor microenvironment in hepatocellular carcinoma (HCC) is complicated. Tumor-infiltrating T and B cells play a pivotal role in anti-tumor immunity. T cell receptor (TCR) and B cell receptor (BCR) features may reflect the disease-associated antigen response. Methods By combining bulk TCR/BCR-sequencing, RNA-sequencing, whole exome-sequencing, and human leukocyte antigen-sequencing, we examined the immune repertoire (IR) features of tumor and adjacent non-tumor tissues obtained from 64 HCC patients. Results High IR heterogeneity with weak similarity was discovered between tumor and non-tumor tissues. Higher BCR diversity, richness, and somatic hypermutation (SHM) were found in non-tumor tissues, while TCRα and TCRβ diversity and richness were comparable or higher in tumor. Additionally, lower immune infiltration was found in tumor than non-tumor tissues; the microenvironment in tumor appeared to keep stably inhibited and changed slightly with tumor progression. Moreover, BCR SHM was stronger, whereas TCR/BCR diversity declined with HCC progression. Importantly, we found that higher IR evenness in tumor and lower TCR richness in non-tumor tissues indicated better survival in HCC patients. Collectively, the results revealed that TCR and BCR exhibited distinct features in tumor and non-tumor tissues. Conclusions We demonstrated that IR features vary between different tissues of HCC. IR features may represent a biomarker for the diagnosis and treatment of HCC patients, providing references for subsequent immunotherapy research and strategy selection.
Collapse
Affiliation(s)
- Shi Xie
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong Yan
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Anqi Zheng
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mengfen Shi
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | | | - Xueying Li
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiabang Liu
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yifan Gan
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yu Wang
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Deke Jiang
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Li Liu
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - 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
| | - Zhanhui Wang
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
47
|
Marx A, Osváth M, Szikora B, Pipek O, Csabai I, Nagy Á, Bödör C, Matula Z, Nagy G, Bors A, Uher F, Mikala G, Vályi-Nagy I, Kacskovics I. Liquid biopsy-based monitoring of residual disease in multiple myeloma by analysis of the rearranged immunoglobulin genes-A feasibility study. PLoS One 2023; 18:e0285696. [PMID: 37235573 DOI: 10.1371/journal.pone.0285696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
The need for sensitive monitoring of minimal/measurable residual disease (MRD) in multiple myeloma emerged as novel therapies led to deeper responses. Moreover, the potential benefits of blood-based analyses, the so-called liquid biopsy is prompting more and more studies to assess its feasibility. Considering these recent demands, we aimed to optimize a highly sensitive molecular system based on the rearranged immunoglobulin (Ig) genes to monitor MRD from peripheral blood. We analyzed a small group of myeloma patients with the high-risk t(4;14) translocation, using next-generation sequencing of Ig genes and droplet digital PCR of patient-specific Ig heavy chain (IgH) sequences. Moreover, well established monitoring methods such as multiparametric flow cytometry and RT-qPCR of the fusion transcript IgH::MMSET (IgH and multiple myeloma SET domain-containing protein) were utilized to evaluate the feasibility of these novel molecular tools. Serum measurements of M-protein and free light chains together with the clinical assessment by the treating physician served as routine clinical data. We found significant correlation between our molecular data and clinical parameters, using Spearman correlations. While the comparisons of the Ig-based methods and the other monitoring methods (flow cytometry, qPCR) were not statistically evaluable, we found common trends in their target detection. Regarding longitudinal disease monitoring, the applied methods yielded complementary information thus increasing the reliability of MRD evaluation. We also detected indications of early relapse before clinical signs, although this implication needs further verification in a larger patient cohort.
Collapse
Affiliation(s)
- Anita Marx
- Department of Immunology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Doctoral School of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Magdolna Osváth
- Department of Immunology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Doctoral School of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Bence Szikora
- Department of Immunology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Orsolya Pipek
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ákos Nagy
- Department of Pathology and Experimental Cancer Research, HCEMM-SE Molecular Oncohematology Research Group, Semmelweis University, Budapest, Hungary
| | - Csaba Bödör
- Department of Pathology and Experimental Cancer Research, HCEMM-SE Molecular Oncohematology Research Group, Semmelweis University, Budapest, Hungary
| | - Zsolt Matula
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - Ginette Nagy
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - András Bors
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - Ferenc Uher
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - Gábor Mikala
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - István Vályi-Nagy
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - Imre Kacskovics
- Department of Immunology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| |
Collapse
|
48
|
Zong F, Long C, Hu W, Chen S, Dai W, Xiao ZX, Cao Y. Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires. Nucleic Acids Res 2023:7173809. [PMID: 37207341 DOI: 10.1093/nar/gkad400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/23/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
The utilization of high-throughput sequencing (HTS) for B-cell receptor (BCR) immune repertoire analysis has become widespread in the fields of adaptive immunity and antibody drug development. However, the sheer volume of sequences generated by these experiments presents a challenge in data processing. Specifically, multiple sequence alignment (MSA), a critical aspect of BCR analysis, remains inadequate for handling massive BCR sequencing data and lacks the ability to provide immunoglobulin-specific information. To address this gap, we introduce Abalign, a standalone program specifically designed for ultrafast MSA of BCR/antibody sequences. Benchmark tests demonstrate that Abalign achieves comparable or even better accuracy than state-of-the-art MSA tools, and shows remarkable advantages in terms of speed and memory consumption, reducing the time required for high-throughput analysis from weeks to hours. In addition to its alignment capabilities, Abalign offers a broad range of BCR analysis features, including extracting BCRs, constructing lineage trees, assigning VJ genes, analyzing clonotypes, profiling mutations, and comparing BCR immune repertoires. With its user-friendly graphic interface, Abalign can be easily run on personal computers instead of computing clusters. Overall, Abalign is an easy-to-use and effective tool that enables researchers to analyze massive BCR/antibody sequences, leading to new discoveries in the field of immunoinformatics. The software is freely available at http://cao.labshare.cn/abalign/.
Collapse
Affiliation(s)
- Fanjie Zong
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Chenyu Long
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Wanxin Hu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Shuang Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Wentao Dai
- NHC Key Laboratory of Reproduction Regulation & Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| |
Collapse
|
49
|
Nakamura Y, Moi ML, Shiina T, Shin-I T, Suzuki R. Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases. Viruses 2023; 15:v15051186. [PMID: 37243272 DOI: 10.3390/v15051186] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
T-cell recognition of antigen epitopes is a crucial step for the induction of adaptive immune responses, and the identification of such T-cell epitopes is, therefore, important for understanding diverse immune responses and controlling T-cell immunity. A number of bioinformatic tools exist that predict T-cell epitopes; however, many of these methods highly rely on evaluating conventional peptide presentation by major histocompatibility complex (MHC) molecules, but they ignore epitope sequences recognized by T-cell receptor (TCR). Immunogenic determinant idiotopes are present on the variable regions of immunoglobulin molecules expressed on and secreted by B-cells. In idiotope-driven T-cell/B-cell collaboration, B-cells present the idiotopes on MHC molecules for recognition by idiotope-specific T-cells. According to the idiotype network theory formulated by Niels Jerne, such idiotopes found on anti-idiotypic antibodies exhibit molecular mimicry of antigens. Here, by combining these concepts and defining the patterns of TCR-recognized epitope motifs (TREMs), we developed a T-cell epitope prediction method that identifies T-cell epitopes derived from antigen proteins by analyzing B-cell receptor (BCR) sequences. This method allowed us to identify T-cell epitopes that contain the same TREM patterns between BCR and viral antigen sequences in two different infectious diseases caused by dengue virus and SARS-CoV-2 infection. The identified epitopes were among the T-cell epitopes detected in previous studies, and T-cell stimulatory immunogenicity was confirmed. Thus, our data support this method as a powerful tool for the discovery of T-cell epitopes from BCR sequences.
Collapse
Affiliation(s)
| | - Meng Ling Moi
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan
| | | | - Ryuji Suzuki
- Repertoire Genesis Inc., Osaka 567-0085, Japan
- Department of Rheumatology and Clinical Immunology, Clinical Research Center for Rheumatology and Allergy, National Hospital Organization Sagamihara National Hospital, Kanagawa 252-0392, Japan
| |
Collapse
|
50
|
Cyr MG, Wilson HD, Spierling AL, Chang J, Peng H, Steinberger P, Rader C. Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution. J Mol Biol 2023; 435:168085. [PMID: 37019174 PMCID: PMC10148915 DOI: 10.1016/j.jmb.2023.168085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
Monoclonal antibody (mAb)-based biologics are well established treatments of cancer. Antibody discovery campaigns are typically directed at a single target of interest, which inherently limits the possibility of uncovering novel antibody specificities or functionalities. Here, we present a target-unbiased approach for antibody discovery that relies on generating mAbs against native target cell surfaces via phage display. This method combines a previously reported method for improved whole-cell phage display selections with next-generation sequencing analysis to efficiently identify mAbs with the desired target cell reactivity. Applying this method to multiple myeloma cells yielded a panel of >50 mAbs with unique sequences and diverse reactivities. To uncover the identities of the cognate antigens recognized by this panel, representative mAbs from each unique reactivity cluster were used in a multi-omic target deconvolution approach. From this, we identified and validated three cell surface antigens: PTPRG, ICAM1, and CADM1. PTPRG and CADM1 remain largely unstudied in the context of multiple myeloma, which could warrant further investigation into their potential as therapeutic targets. These results highlight the utility of optimized whole-cell phage display selection methods and could motivate further interest in target-unbiased antibody discovery workflows.
Collapse
Affiliation(s)
- Matthew G Cyr
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA; Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA. https://twitter.com/CyrialDilutions
| | - Henry D Wilson
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
| | - Anna-Lena Spierling
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Jing Chang
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Peter Steinberger
- Institute of Immunology, Medical University of Vienna, Vienna, Austria
| | - Christoph Rader
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA; Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA.
| |
Collapse
|