Research projects within the Gunilla Karlsson Hedestam group

On this page we have listed the research projects within the group.

Studies of adaptive immune receptor germline gene variation

Recent results using Next Generation sequencing have revealed significant allelic diversity in the genes encoding the human B and T cell receptors (BCRs/antibodies and TCRs). The production of individualized genetic profiles of adaptive immune receptor genes is therefore of interest, both to aid future personalized vaccination strategies and for diagnostic purposes. While standard deep sequencing approaches do not achieve necessary coverage to create full profiles of these genes, the use of IgDiscover and related technologies, can achieve this.

In this project, we characterize human genetic diversity in adaptive immune receptor genes, focusing initially on BCR and TCR V, D and J genes. These efforts will allow the production of improved genetic databases and an improved understanding of the frequency of different alleles present in different population.

In parallel, we apply similar approaches to characterize adaptive immune receptor genes in several non-human primate species for which genetic databases today are largely lacking.

References

Archaic humans have contributed to large-scale variation in modern human T cell receptor genes.
Corcoran M, Chernyshev M, Mandolesi M, Narang S, Kaduk M, Ye K, Sundling C, Färnert A, Kreslavsky T, Bernhardsson C, Larena M, Jakobsson M, Karlsson Hedestam GB
Immunity 2023 Mar;56(3):635-652.e6

Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies.
Pushparaj P, Nicoletto A, Sheward DJ, Das H, Castro Dopico X, Perez Vidakovics L, Hanke L, Chernyshev M, Narang S, Kim S, Fischbach J, Ekström S, McInerney G, Hällberg BM, Murrell B, Corcoran M, Karlsson Hedestam GB
Immunity 2023 Jan;56(1):193-206.e7

Analysis of IGH allele content in a sample group of rheumatoid arthritis patients demonstrates unrevealed population heterogeneity.
Hardt U, Corcoran MM, Narang S, Malmström V, Padyukov L, Karlsson Hedestam GB
Front Immunol 2023 ;14():1073414

Addressing IGHV Gene Structural Diversity Enhances Immunoglobulin Repertoire Analysis: Lessons From Rhesus Macaque.
Kaduk M, Corcoran M, Karlsson Hedestam GB
Front Immunol 2022 ;13():818440

Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.
Corcoran MM, Phad GE, Vázquez Bernat , Stahl-Hennig C, Sumida N, Persson MA, Martin M, Karlsson Hedestam GB
Nat Commun 2016 12;7():13642

Rhesus and cynomolgus macaque immunoglobulin heavy-chain genotyping yields comprehensive databases of germline VDJ alleles.
Vázquez Bernat N, Corcoran M, Nowak I, Kaduk M, Castro Dopico X, Narang S, Maisonasse P, Dereuddre-Bosquet N, Murrell B, Karlsson Hedestam GB
Immunity 2021 02;54(2):355-366.e4

High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis.
Vázquez Bernat N, Corcoran M, Hardt U, Kaduk M, Phad GE, Martin M, Karlsson Hedestam GB
Front Immunol 2019 ;10():660

Studies of expressed B cell receptor repertoires

B cell responses are the basis by which most effective anti-viral vaccines provide protection against infection and disease. Vaccines are still lacking for many human pathogens and in other cases they exist, but do not provide sufficiently broad or long-lasting responses.

A robust understanding of B cell biology is needed to develop broadly protective and durable antibody responses.

Comprehensive analyses of B cell clones engaged by a specific antigen during infection or immunization, and analysis of how such responses develop over time, are topics of specific interest. We focus particularly on neutralizing anti-viral antibodies and their targets. Characterization of vaccine-induced monoclonal antibodies combined with analysis of unfractionated polyclonal plasma samples and deep sequencing of antibody repertoires expressed by different B cell populations provide a rich source of information. With improved methods to sort antigen-specific B cell populations by flow cytometry and sequence large numbers of paired heavy and light chains, we can now make rapid progress to identify interesting antibody specificities against a range of targets. Questions we are particularly interested in are how antibody responses mature over time, clonal dynamics of the response, qualitative differences between the peripheral memory B cell compartment and the bone marrow plasma cell repertoire against a given antigen, and if specific germline immunoglobulin alleles are required for certain types of antibody specificities.

References

Vaccination induces HIV broadly neutralizing antibody precursors in humans.
Leggat DJ, Cohen KW, Willis JR, Fulp WJ, deCamp AC, Kalyuzhniy O, Cottrell CA, Menis S, Finak G, Ballweber-Fleming L, Srikanth A, Plyler JR, Schiffner T, Liguori A, Rahaman F, Lombardo A, Philiponis V, Whaley RE, Seese A, Brand J, Ruppel AM, Hoyland W, Yates NL, Williams LD, Greene K, Gao H, Mahoney CR, Corcoran MM, Cagigi A, Taylor A, Brown DM, Ambrozak DR, Sincomb T, Hu X, Tingle R, Georgeson E, Eskandarzadeh S, Alavi N, Lu D, Mullen TM, Kubitz M, Groschel B, Maenza J, Kolokythas O, Khati N, Bethony J, Crotty S, Roederer M, Karlsson Hedestam GB, Tomaras GD, Montefiori D, Diemert D, Koup RA, Laufer DS, McElrath MJ, McDermott AB, Schief WR
Science 2022 Dec;378(6623):eadd6502

VDJ Gene Usage in IgM Repertoires of Rhesus and Cynomolgus Macaques.
Chernyshev M, Kaduk M, Corcoran M, Karlsson Hedestam GB
Front Immunol 2021 ;12():815680

Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization.
Aljedani SS, Liban TJ, Tran K, Phad G, Singh S, Dubrovskaya V, Pushparaj P, Martinez-Murillo P, Rodarte J, Mileant A, Mangala Prasad V, Kinzelman R, O'Dell S, Mascola JR, Lee KK, Karlsson Hedestam GB, Wyatt RT, Pancera M
PLoS Pathog 2021 Sep;17(9):e1009543

Single-cell and deep sequencing of IgG-switched macaque B cells reveal a diverse Ig repertoire following immunization.
Sundling C, Zhang Z, Phad GE, Sheng Z, Wang Y, Mascola JR, Li Y, Wyatt RT, Shapiro L, Karlsson Hedestam GB
J Immunol 2014 Apr;192(8):3637-44

High-resolution definition of vaccine-elicited B cell responses against the HIV primary receptor binding site.
Sundling C, Li Y, Huynh N, Poulsen C, Wilson R, O'Dell S, Feng Y, Mascola JR, Wyatt RT, Karlsson Hedestam GB
Sci Transl Med 2012 Jul;4(142):142ra96

Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign.
Tran K, Poulsen C, Guenaga J, de Val N, de Val Alda N, Wilson R, Sundling C, Li Y, Stanfield RL, Wilson IA, Ward AB, Karlsson Hedestam GB, Wyatt RT
Proc Natl Acad Sci U S A 2014 Feb;111(7):E738-47

Particulate Array of Well-Ordered HIV Clade C Env Trimers Elicits Neutralizing Antibodies that Display a Unique V2 Cap Approach.
Martinez-Murillo P, Tran K, Guenaga J, Lindgren G, Àdori M, Feng Y, Phad GE, Vázquez Bernat N, Bale S, Ingale J, Dubrovskaya V, O'Dell S, Pramanik L, Spångberg M, Corcoran M, Loré K, Mascola JR, Wyatt RT, Karlsson Hedestam GB
Immunity 2017 05;46(5):804-817.e7

Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses.
Phad GE, Pushparaj P, Tran K, Dubrovskaya V, Àdori M, Martinez-Murillo P, Vázquez Bernat N, Singh S, Dionne G, O'Dell S, Bhullar K, Narang S, Sorini C, Villablanca EJ, Sundling C, Murrell B, Mascola JR, Shapiro L, Pancera M, Martin M, Corcoran M, Wyatt RT, Karlsson Hedestam GB
J Exp Med 2020 02;217(2):

SARS-CoV-2-directed B cell responses and isolation of spike-specific monoclonal antibodies

Antibody responses to SARS-CoV-2 are central for individual and population-level immunity. However, with recently emerged virus variants, responses from prior exposures or vaccination are not fully protective. Seroprevalence studies and detailed antibody mapping studies are key to our understanding of protective immunity.

In this project, we follow antibody levels in the population and assess neutralizing antibody responses against SARS-CoV-2 variants of concern. We also study memory B cell responses in defined cohorts of exposed individuals by using single B cell sorting, isolation of virus-specific monoclonal antibodies and NGS-based bulk BCR repertoire sequencing to of antibody affinity maturation and persistence in the memory B cell compartment.

In collaboration with the Murrell group, we recently characterized a set of highly potent monoclonal antibodies that neutralize Omicron and related variants. In other projects, we investigate the role of VDJ germline gene variation for neutralizing antibody responses against this virus to understand inter-individual variation in the response against SARS-CoV-2.

References

Vaccination of SARS-CoV-2-infected individuals expands a broad range of clonally diverse affinity-matured B cell lineages.
Chernyshev M, Sakharkar M, Connor RI, Dugan HL, Sheward DJ, Rappazzo CG, Stålmarck A, Forsell MNE, Wright PF, Corcoran M, Murrell B, Walker LM, Karlsson Hedestam GB
Nat Commun 2023 Apr;14(1):2249

Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses.
Pushparaj P, Nicoletto A, Dopico XC, Sheward DJ, Kim S, Ekström S, Murrell B, Corcoran M, Karlsson Hedestam GB
Front Virol 2023 Mar;3():1128253

Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies.
Sheward DJ, Kim C, Fischbach J, Sato K, Muschiol S, Ehling RA, Björkström NK, Karlsson Hedestam GB, Reddy ST, Albert J, Peacock TP, Murrell B
Lancet Infect Dis 2022 Nov;22(11):1538-1540

Evasion of neutralising antibodies by omicron sublineage BA.2.75.
Sheward DJ, Kim C, Fischbach J, Muschiol S, Ehling RA, Björkström NK, Karlsson Hedestam GB, Reddy ST, Albert J, Peacock TP, Murrell B
Lancet Infect Dis 2022 Oct;22(10):1421-1422

Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study.
Sheward DJ, Kim C, Ehling RA, Pankow A, Castro Dopico X, Dyrdak R, Martin DP, Reddy ST, Dillner J, Karlsson Hedestam GB, Albert J, Murrell B
Lancet Infect Dis 2022 Jun;22(6):813-820

Probabilistic classification of anti-SARS-CoV-2 antibody responses improves seroprevalence estimates.
Castro Dopico X, Muschiol S, Grinberg NF, Aleman S, Sheward DJ, Hanke L, et al.
Clin Transl Immunology. 2022 Mar 2;11(3):e1379

Beta RBD boost broadens antibody-mediated protection against SARS-CoV-2 variants in animal models.
Sheward DJ, Mandolesi M, Urgard E, Kim C, Hanke L, Perez Vidakovics L, Pankow A, Smith NL, Castro Dopico X, McInerney GM, Coquet JM, Karlsson Hedestam GB, Murrell B
Cell Rep Med 2021 11;2(11):100450

Seropositivity in blood donors and pregnant women during the first year of SARS-CoV-2 transmission in Stockholm, Sweden.
Castro Dopico X, Muschiol S, Christian M, Hanke L, Sheward DJ, Grinberg NF, Rorbach J, Bogdanovic G, Mcinerney GM, Allander T, Wallace C, Murrell B, Albert J, Karlsson Hedestam GB
J Intern Med 2021 09;290(3):666-676

SARS-CoV-2 protein subunit vaccination of mice and rhesus macaques elicits potent and durable neutralizing antibody responses.
Mandolesi M, Sheward DJ, Hanke L, Ma J, Pushparaj P, Perez Vidakovics L, Kim C, Àdori M, Lenart K, Loré K, Castro Dopico X, Coquet JM, McInerney GM, Karlsson Hedestam GB, Murrell B
Cell Rep Med 2021 04;2(4):100252