Canonical features of human antibodies recognizing the influenza hemagglutinin trimer interface

SUMMARYBroadly reactive antibodies targeting the influenza A hemagglutinin (HA) head domain are thought to be rare and to require extensive somatic mutations or unusual structural features to achieve breadth against divergent HA subtypes. Here we describe common genetic and structural features of diverse human antibodies from several individuals recognizing the trimer interface (TI) of the influenza HA head, a recently identified site of vulnerability1–3. We examined the sequence of TI-reactive antibodies, determined crystal structures for TI antibody-antigen complexes, and analyzed the contact residues of the antibodies on HA to discover common genetic and structural features of TI antibodies. Our data reveal that many TI antibodies are encoded by a light chain variable gene segment incorporating a shared somatic mutation. In addition, these antibodies have a shared acidic residue in the heavy chain despite originating from diverse heavy chain variable gene segments. These studies show that the TI region of influenza HA is a major antigenic site with conserved structural features that are recognized by a common human B cell public clonotype. The canonical nature of this antibody-antigen interaction suggests that the TI epitope might serve as an important new target for structure-based vaccine design.

Download Full-text

The unmutated common ancestor of Gp41 conformational epitope targeting variable heavy chain 1-02 utilizing antibodies maintains antibody dependent cell cytotoxicity

10.1101/2021.09.23.21264029 ◽

2021 ◽

Author(s):

Brian Wrotniak ◽

Meghan E Garrett ◽

Sarah Baron ◽

Hakimuddin Sojar ◽

Alyssa Shon ◽

...

Keyword(s):

Heavy Chain ◽

Common Ancestor ◽

Vaccine Development ◽

Gene Segment ◽

Conformational Epitope ◽

Heptad Repeat ◽

Clade B ◽

Variable Heavy ◽

Dependent Cell ◽

Variable Gene

In studies on monoclonal Abs (mAbs) from long-term non-progressors (LTNPs), our laboratory has previously described highly mutated Abs against a complex conformational epitope with contributions from both gp41 heptad repeat regions. Despite using the VH1-02 gene segment, known to contribute to some of the broadest neutralizing Abs against HIV, members of these Abs, termed group 76C Abs, did not exhibit broad neutralization.<br />Because of the excessive mutations and use of VH1-02, our goal was to characterize the non-neutralizing functions of Abs of group 76C, to assess targeting of the epitope in various clinical presentations, and to assess the development of these Abs by comparison to their predicted common ancestor. Serum competition assays showed group 76C Abs were enriched in LTNPs, in comparison to VRC-01. Specific group 76C clones 6F5 and 6F11, expressed as recombinant Abs, both have robust ADCC activity, despite their sequence disparity. Sequence analysis predicted the common ancestor of this clonal group would utilize the germline non-mutated variable gene. We produced a recombinant ancestor Ab (76Canc) with a heavy chain utilizing the germline variable gene sequence paired to the 6F5 light chain. Competition with group 76C recombinant Ab 6F5 confirms 76Canc binds HIV envelope constructs near the original group C epitope. 76Canc demonstrates comparable ADCC to 6F5 and 6F11 when targeting both clade B and C HIV constructs. The functional capability of Abs utilizing germline VH1-02 has implications for disease control and vaccine development.

Download Full-text

Recombination between an expressed immunoglobulin heavy-chain gene and a germline variable gene segment in a Ly 1+ B-cell lymphoma

Nature ◽

10.1038/322843a0 ◽

1986 ◽

Vol 322 (6082) ◽

pp. 843-846 ◽

Cited By ~ 182

Author(s):

Robert Kleinfield ◽

Richard R. Hardy ◽

David Tarlinton ◽

Jeffery Dangl ◽

Leonard A. Herzenberg ◽

...

Keyword(s):

B Cell ◽

Heavy Chain ◽

Cell Lymphoma ◽

Gene Segment ◽

B Cell Lymphoma ◽

Chain Gene ◽

Heavy Chain Gene ◽

Immunoglobulin Heavy Chain Gene ◽

Variable Gene ◽

Variable Gene Segment

Download Full-text

The immunoglobulin heavy chain variable gene segment 4-31, IGHV 4-31, is differentially expressed in the brain and lymph nodes of patients with metastatic breast cancer.

10.31219/osf.io/y4hnq ◽

2020 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Metastatic Breast Cancer ◽

Brain Metastases ◽

Heavy Chain ◽

Light Chain ◽

Gene Segment ◽

Metastatic Breast ◽

Variable Gene ◽

The Brain ◽

Variable Gene Segment

One study reported the incidence of central nervous system metastases in breast cancer patients treated with trastuzumab as 34% (1). We mined published microarray data (2-4) to discover genes associated with brain metastasis in breast cancer. We identified significant differential expression of the immunoglobulin heavy chain variable gene segment IGHV 4-31 in the metastases of patients with metastatic breast cancer, both in the lymph nodes and in the brain. We recently described the differential expression of the immunoglobulin light chain kappa constant locus in the brain metastases of patients with metastatic breast cancer (5). These data suggest both heavy and light chain gene segments may potentially be among the loci whose expression is most significantly altered transcriptome-wide when comparing primary tumors of the breast and brain metastases in patients with metastatic breast cancer. IGHV 4-31 may be relevant to the biology underlying colonization of the brain with metastatic breast cancer clones.

Download Full-text

Cold agglutinin activity is common among human monoclonal IgM Rh system antibodies using the V4-34 heavy chain variable gene segment

Transfusion ◽

10.1046/j.1537-2995.1997.37111298088038.x ◽

1997 ◽

Vol 37 (11-12) ◽

pp. 1111-1116 ◽

Cited By ~ 21

Author(s):

SJ Thorpe ◽

CE Boult ◽

FK Stevenson ◽

ML Scott ◽

J Sutherland ◽

...

Keyword(s):

Heavy Chain ◽

Gene Segment ◽

Cold Agglutinin ◽

Variable Gene ◽

Variable Gene Segment

Download Full-text

Faculty Opinions recommendation of Allele-specific regulation of TCR beta variable gene segment chromatin structure.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1028441.337206 ◽

2005 ◽

Author(s):

Pierre Ferrier

Keyword(s):

Chromatin Structure ◽

Gene Segment ◽

Allele Specific ◽

Variable Gene ◽

Beta Variable ◽

Specific Regulation ◽

Variable Gene Segment

Download Full-text

Faculty Opinions recommendation of Regulation of interleukin 7-dependent immunoglobulin heavy-chain variable gene rearrangements by transcription factor STAT5.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1027010.326545 ◽

2005 ◽

Author(s):

Pierre Ferrier

Keyword(s):

Transcription Factor ◽

Heavy Chain ◽

Immunoglobulin Heavy Chain ◽

Gene Rearrangements ◽

Interleukin 7 ◽

Variable Gene

Download Full-text

Next generation methodology for updating HA vaccines against emerging human seasonal influenza A(H3N2) viruses

Scientific Reports ◽

10.1038/s41598-020-79590-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

James D. Allen ◽

Ted M. Ross

Keyword(s):

Influenza Virus ◽

Immune Responses ◽

Influenza A ◽

Seasonal Influenza ◽

Influenza Viruses ◽

Next Generation ◽

Virus Infections ◽

Wild Type ◽

Influenza Hemagglutinin ◽

H3n2 Influenza

AbstractWhile vaccines remain the best tool for preventing influenza virus infections, they have demonstrated low to moderate effectiveness in recent years. Seasonal influenza vaccines typically consist of wild-type influenza A and B viruses that are limited in their ability to elicit protective immune responses against co-circulating influenza virus variant strains. Improved influenza virus vaccines need to elicit protective immune responses against multiple influenza virus drift variants within each season. Broadly reactive vaccine candidates potentially provide a solution to this problem, but their efficacy may begin to wane as influenza viruses naturally mutate through processes that mediates drift. Thus, it is necessary to develop a method that commercial vaccine manufacturers can use to update broadly reactive vaccine antigens to better protect against future and currently circulating viral variants. Building upon the COBRA technology, nine next-generation H3N2 influenza hemagglutinin (HA) vaccines were designed using a next generation algorithm and design methodology. These next-generation broadly reactive COBRA H3 HA vaccines were superior to wild-type HA vaccines at eliciting antibodies with high HAI activity against a panel of historical and co-circulating H3N2 influenza viruses isolated over the last 15 years, as well as the ability to neutralize future emerging H3N2 isolates.

Download Full-text

Subnuclear cyclin D3 compartments and the coordinated regulation of proliferation and immunoglobulin variable gene repression

Journal of Experimental Medicine ◽

10.1084/jem.20120800 ◽

2012 ◽

Vol 209 (12) ◽

pp. 2199-2213 ◽

Cited By ~ 25

Author(s):

Sarah E. Powers ◽

Malay Mandal ◽

Satoshi Matsuda ◽

Ana V. Miletic ◽

Matthew H. Cato ◽

...

Keyword(s):

Cell Cycle Progression ◽

Gene Segment ◽

Cyclin D3 ◽

Cyclin D2 ◽

Cycle Progression ◽

Nuclear Compartment ◽

Regulation Of Proliferation ◽

Variable Gene ◽

V Gene ◽

Phosphoinositide 3 Kinase

Ubiquitously expressed D-type cyclins are required for hematopoiesis but are dispensable in other cell lineages. Furthermore, within different hematopoietic progenitor populations the D-type cyclins play nonredundant roles. The basis of this lineage and developmental specificity is unknown. In pro–B cells we demonstrate four distinct nuclear D-type cyclin compartments, including one cyclin D3 fraction associated with CDK4 and another phosphoinositide 3-kinase–regulated fraction not required for proliferation. A third fraction of cyclin D3 was associated with the nuclear matrix and repression of >200 genes including the variable (V) gene segments Igkv1-117, Iglv1, and Igh-VJ558. Consistent with different subnuclear compartments and functions, distinct domains of cyclin D3 mediated proliferation and Igk V gene segment repression. None of the cyclin D3 nuclear compartments overlapped with cyclin D2, which was distributed, unbound to CDK4, throughout the nucleus. Furthermore, compartmentalization of the cyclins appeared to be lineage restricted because in fibroblasts, cyclin D2 and cyclin D3 occupied a single nuclear compartment and neither bound CDK4 efficiently. These data suggest that subnuclear compartmentalization enables cyclin D3 to drive cell cycle progression and repress V gene accessibility, thereby ensuring coordination of proliferation with immunoglobulin recombination.

Download Full-text

Characterization of an enhanced antigenic change in the pandemic 2009 H1N1 influenza virus haemagglutinin

Journal of General Virology ◽

10.1099/vir.0.061598-0 ◽

2014 ◽

Vol 95 (5) ◽

pp. 1033-1042 ◽

Cited By ~ 5

Author(s):

Blanca García-Barreno ◽

Teresa Delgado ◽

Sonia Benito ◽

Inmaculada Casas ◽

Francisco Pozo ◽

...

Keyword(s):

Influenza Virus ◽

Amino Acid ◽

Influenza A ◽

Point Mutations ◽

Antigenic Site ◽

Single Amino Acid ◽

Antigenic Structure ◽

Human Antibody ◽

2009 H1n1

Murine hybridomas producing neutralizing mAbs specific to the pandemic influenza virus A/California/07/2009 haemagglutinin (HA) were isolated. These antibodies recognized at least two different but overlapping new epitopes that were conserved in the HA of most Spanish pandemic isolates. However, one of these isolates (A/Extremadura/RR6530/2010) lacked reactivity with the mAbs and carried two unique mutations in the HA head (S88Y and K136N) that were required simultaneously to eliminate reactivity with the murine antibodies. This unusual requirement directly illustrates the phenomenon of enhanced antigenic change proposed previously for the accumulation of simultaneous amino acid substitutions at antigenic sites of the influenza A virus HA during virus evolution (Shih et al., Proc Natl Acad Sci USA, 104 , 6283–6288, 2007). The changes found in the A/Extremadura/RR6530/2010 HA were not found in escape mutants selected in vitro with one of the mAbs, which contained instead nearby single amino acid changes in the HA head. Thus, either single or double point mutations may similarly alter epitopes of the new antigenic site identified in this work in the 2009 H1N1 pandemic virus HA. Moreover, this site is relevant for the human antibody response, as shown by competition of mAbs and human post-infection sera for virus binding. The results are discussed in the context of the HA antigenic structure and challenges posed for identification of sequence changes with possible antigenic impact during virus surveillance.

Download Full-text