204 research outputs found
Recommended from our members
Clonify: unseeded antibody lineage assignment from next-generation sequencing data
No full textDefining the dynamics and maturation processes of antibody clonal lineages is crucial to understanding the humoral response to infection and immunization. Although individual antibody lineages have been previously analyzed in isolation, these studies provide only a narrow view of the total antibody response. Comprehensive study of antibody lineages has been limited by the lack of an accurate clonal lineage assignment algorithm capable of operating on next-generation sequencing datasets. To address this shortcoming, we developed Clonify, which is able to perform unseeded lineage assignment on very large sets of antibody sequences. Application of Clonify to IgG+ memory repertoires from healthy individuals revealed a surprising lack of influence of large extended lineages on the overall repertoire composition, indicating that this composition is driven less by the order and frequency of pathogen encounters than previously thought. Clonify is freely available at www.github.com/briney/clonify-python.Version of Recor
AntiRef92
No full textAntiRef92 is one of several AntiRef cluster datasets. AntiRef92 was created by clustering AntiRef94 at 92% sequence identity
The development and genetic origin of broadly neutralizing HIV antibodies
No full textSeveral of the most broadly neutralizing HIV antibodies (bnAbs) contain unique genetic or structural elements, including long heavy chain complementarity determining region 3 (HCDR3) loops and extensive somatic hypermutation. Two exceptionally broad, potently neutralizing HIV-specific antibodies, PG9 and PG16, encode HCDR3 loops that are among the longest of any antigen-specific antibody described to date. Passive immunization with two other bnAbs that encode long HCDR3s, 4E10 and 2F5, is able to protect against HIV infection. Induction of such long HCDR3 antibodies may be critical to the design of an effective vaccine strategy for HIV, however it is unclear at present how to induce such antibodies.
There has been speculation that antibodies with long HCDR3s are generated primarily through the accumulation of somatic hypermutation-associated insertions. These short insertion events are rare, and design of an immunogen that efficiently induces many such insertions in a single antibody sequence is likely to be extremely difficult. Through the use of high-throughput antibody sequencing, I have identified genetic evidence that these long HCDR3 antibodies are typically formed at the original recombination event, not through accumulation of somatic hypermutation-induced insertions. Antibodies with long HCDR3s were found in all tested individuals, and long HCDR3 antibodies typically use a restricted subset of D and J gene segments, resulting in the incorporation of highly conserved genetic elements in the majority of such antibody sequences. This work provides an important first step toward the realization of a vaccine that efficiently induces broadly neutralizing HIV antibodies with long HCDR3s by identifying a conserved genetic target through which B cells encoding antibodies with long HCDR3s may be induced selectively through vaccination
Improving antibody language models with native pairing
No full textMotivation. Existing large language models designed to predict antibody structure and function have been trained exclusively with unpaired antibody sequences. This is a substantial drawback, as each antibody represents a unique pairing of heavy and light chains that both contribute to antigen recognition. The cost of generating large datasets of natively paired antibody sequences is orders of magnitude higher than the cost of unpaired sequences, and the paucity of available paired antibody sequence datasets precludes training a state-of-the-art language model using only paired training data. Here, we sought to determine whether and to what extent natively paired training data improves model performance.
Results. Using a unique and recently reported dataset of approximately 1.6 x 106 natively paired human antibody sequences, we trained two baseline antibody language model (BALM) variants: BALM-paired and BALM-unpaired. We quantify the superiority of BALM-paired over BALM-unpaired, and we show that BALM-paired's improved performance can be attributed at least in part to its ability to learn cross-chain features that span natively paired heavy and light chains. Additionally, we fine-tuned the general protein language model ESM-2 using these paired antibody sequences and report that the fine-tuned model, but not base ESM-2, demonstrates a similar understanding of cross-chain features.
Files. The following files are included in this repository:
BALM-paired.tar.gz: Model weights for the BALM-paired model.
BALM-unpaired.tar.gz: Model weights for the BALM-unpaired model.
ESM2-650M_paired-fine-tuned.tar.gz: Model weights for the 650M-parameter ESM-2 model after fine-tuning with natively paired antibody sequences.
jaffe-paired-dataset_airr-annotation.tar.gz: All natively paired antibody sequences from the Jaffe dataset were annotated with abstar and subsequently filtered to remove duplicates or unproductive sequences. The annotated sequences are provided in an AIRR-compliant format.
train-test-eval_paired.tar.gz: Datasets used to train, test, and evaluate the BALM-paired model. Compressed folder containing three files: train.txt, test.txt, and eval.txt. Each file has one input sequence per line. This dataset was also used to fine-tune the 650M-parameter ESM-2 variant.
train-test-eval_unpaired.tar.gz: Datasets used to train, test, and evaluate the BALM-unpaired model. Compressed folder containing three files: train.txt, test.txt, and eval.txt. Each file has one input sequence per line.
Code: All code used for model training, testing, and figure generation is available under the MIT license on GitHub
Human peripheral blood antibodies with long HCDR3s are established primarily at original recombination using a limited subset of germline genes.
No full textA number of antibodies that efficiently neutralize microbial targets contain long heavy chain complementarity determining region 3 (HCDR3) loops. For HIV, several of the most broad and potently neutralizing antibodies have exceptionally long HCDR3s. Two broad potently neutralizing HIV-specific antibodies, PG9 and PG16, exhibit secondary structure. Two other long HCDR3 antibodies, 2F5 and 4E10, protect against mucosal challenge with SHIV. Induction of such long HCDR3 antibodies may be critical to the design of an effective vaccine strategy for HIV and other pathogens, however it is unclear at present how to induce such antibodies. Here, we present genetic evidence that human peripheral blood antibodies containing long HCDR3s are not primarily generated by insertions introduced during the somatic hypermutation process. Instead, they are typically formed by processes occurring as part of the original recombination event. Thus, the response of B cells encoding antibodies with long HCDR3s results from selection of unusual clones from the naïve repertoire rather than through accumulation of insertions. These antibodies typically use a small subset of D and J gene segments that are particularly suited to encoding long HCDR3s, resulting in the incorporation of highly conserved genetic elements in the majority of antibody sequences encoding long HCDR3s
Commonality despite exceptional diversity in the baseline human antibody repertoire
No full textIn principle, humans can produce an antibody response to any non-self-antigen molecule in the appropriate context. This flexibility is achieved by the presence of a large repertoire of naive antibodies, the diversity of which is expanded by somatic hypermutation following antigen exposure. The diversity of the naive antibody repertoire in humans is estimated to be at least 10 unique antibodies. Because the number of peripheral blood B cells in a healthy adult human is on the order of 5 × 10, the circulating B cell population samples only a small fraction of this diversity. Full-scale analyses of human antibody repertoires have been prohibitively difficult, primarily owing to their massive size. The amount of information encoded by all of the rearranged antibody and T cell receptor genes in one person-the 'genome' of the adaptive immune system-exceeds the size of the human genome by more than four orders of magnitude. Furthermore, because much of the B lymphocyte population is localized in organs or tissues that cannot be comprehensively sampled from living subjects, human repertoire studies have focused on circulating B cells. Here we examine the circulating B cell populations of ten human subjects and present what is, to our knowledge, the largest single collection of adaptive immune receptor sequences described to date, comprising almost 3 billion antibody heavy-chain sequences. This dataset enables genetic study of the baseline human antibody repertoire at an unprecedented depth and granularity, which reveals largely unique repertoires for each individual studied, a subpopulation of universally shared antibody clonotypes, and an exceptional overall diversity of the antibody repertoire
Secondary Mechanisms of Affinity Maturation in the Human Antibody Repertoire
No full textV(D)J recombination and somatic hypermutation (SHM) are the primary mechanisms for diversification of the human antibody repertoire. These mechanisms allow for rapid humoral immune responses to a wide range of pathogenic challenges. V(D)J recombination efficiently generate a virtually limitless diversity through random recombination of variable (V), diversity (D) and joining (J) genes with diverse nontemplated junctions between the selected gene segments. Following antigen stimulation, affinity maturation by SHM produces antibodies with refined specificity mediated by mutations typically focused in complementarity determining regions (CDRs), which form the bulk of the antigen recognition site. While V(D)J recombination and SHM are responsible for much of the diversity of the antibody repertoire, there are several secondary mechanisms that, while less frequent, make substantial contributions to antibody diversity including V(DD)J recombination (or D-D fusion), somatic-hypermutation-associated insertions and deletions, and affinity maturation and antigen contact by non-CDR regions of the antibody. In addition to enhanced diversity, these mechanisms allow the production of antibodies that are critical to response to a variety of viral and bacterial pathogens but that would be difficult to generate using only the primary mechanisms of diversification
Human Peripheral Blood Antibodies with Long HCDR3s Are Established Primarily at Original Recombination Using a Limited Subset of Germline Genes
No full textStructural conservation of Lassa virus glycoproteins and recognition by neutralizing antibodies
No full textLassa fever is an acute hemorrhagic fever caused by the zoonotic Lassa virus (LASV). The LASV glycoprotein complex (GPC) mediates viral entry and is the sole target for neutralizing antibodies. Immunogen design is complicated by the metastable nature of recombinant GPCs and the antigenic differences among phylogenetically distinct LASV lineages. Despite the sequence diversity of the GPC, structures of most lineages are lacking. We present the development and characterization of prefusion-stabilized, trimeric GPCs of LASV lineages II, V, and VII, revealing structural conservation despite sequence diversity. High-resolution structures and biophysical characterization of the GPC in complex with GP1-A-specific antibodies suggest their neutralization mechanisms. Finally, we present the isolation and characterization of a trimer-preferring neutralizing antibody belonging to the GPC-B competition group with an epitope that spans adjacent protomers and includes the fusion peptide. Our work provides molecular detail information on LASV antigenic diversity and will guide efforts to design pan-LASV vaccines
PHOTOISOMERIZATION DYNAMICS OF STILBENE AND AZOBENZENE DERIVATIVE OBSERVED BY FEMTOSECOND TRANSIENT ABSORPTION SPECTROSCOPY
No full textAuthor Institution: The University of Wisconsin-Madison, Department of Chemistry, 1101 University Avenue, Madison, WI 53706Ultrafast femtosecond pump and probe transient electronic absorption spectroscopy experiments were performed to gain insights into the photoisomerization dynamics in the condensed phase of two prototypical molecules, stilbene and a derivative of azobenzene. For example, in the stilbene case, a UV pump - continuum probe experiment measures the excited state dynamics, allowing us to compare the isomerization reaction starting from either the cis or the trans isomer. Information on how energy flows in the ground state molecule can also be obtained with an IR pump (either CH stretch overtone or stretch-bend combination) - UV probe setup. These data are critical in order to understand how vibrations could affect the isomerization process, as a vibrational mediation of this phenomena represents the ultimate goal of these experiments
- …
