Research

Antibody Sequencing Technologies

Antibodies are a critical feature of our adaptive immune system, and each antibody is comprised of a unique heavy and a light chain peptide sequence that is encoded by a single B cell.  Our lab uses a technique first invented by our PI to characterize the repertoire of paired antibody heavy and light chain sequences from over one million single B cells at a time.  This suite of technologies comprises RT-PCR-based DNA molecular engineering, massively parallel emulsion droplet reactions, Next Generation DNA sequencing, and high-throughput computational analysis.   We are applying this unique workflow to characterize the response to vaccines and diseases, both in human patients and in animal models.

 

Left Overview of our unique workflow for paired antibody heavy and light chain analysis. From DeKosky et al., Nature Medicine 2015.  Right Diagram of a custom-built flow-focusing device for single cell emulsification. From McDaniel & DeKosky et al., Nature Protocols 2016.

 

References:

 

DeKosky & Lungu et al., PNAS, 2016. PMID: 27114511, PMCID: PMC4868480, DOI: 10.1073/pnas.1525510113

McDaniel DeKosky et al., Nature Protocols, 2016. PMID: 26844430, DOI: 10.1038/nprot.2016.024

DeKosky BJ et al., Nature Medicine, 2015. PMID: 25501908, DOI: 10.1038/nm.3743

DeKosky BJ et al., Nature Biotechnology, 2013. PMID: 23334449, PMCID: PMC3910347, DOI: 10.1038/nbt.2492

HIV Broadly Neutralizing Antibodies

An effective HIV vaccine is desperately needed to combat the HIV pandemic.  While the high genetic diversity and immunoevasion strategies of HIV-1 have frustrated vaccine efforts to date, recent work has demonstrated that HIV broadly neutralizing antibodies (bNAbs) can provide protection against new infections, and that bNAbs can also be induced via vaccination in some animal models.  Our work analyzes the comprehensive antibody response to HIV infection and vaccination to gain insights regarding the design of effective vaccines that will protect against HIV transmission.  

 

(a) Developmental phylogeny of the CAP256-VRC26 antibody lineage. Several VRC26 antibody variants were discovered using the high-throughput B cell sequencing technologies described here. From Doria-Rose et al., Nature 2014. (b) Paired heavy and light chain quantification of increased prevalence of VRC01-class precursor sequences in immunized transgenic mice. From Tian et al, Cell 2016.

 

References:

 

Doria-Rose et al., Nature, 2014. PMID: 24590074, PMCID: PMC4395007, DOI: 10.1038/nature13036

Gorman et al., Nature Structural & Molecular Biology, 2016. PMID: 26689967, PMCID: PMC4833398, DOI: 10.1038/nsmb.314

Tian M et al.,  Cell, 2016. PMID: 27610571, PMCID: PMC5103708 [Available on 2017-09-08], DOI: 10.1016/j.cell.2016.07.029

 

Epstein-Barr Virus and Infectious Mononucleosis

Epstein-Barr Virus (EBV) is highly prevalent pathogen that infects the majority of the world's population, and initial infections can lead to lifelong latent infection with periodic reactivation over the course of an individual's lifetime.  Primary infection often leads to infectious mononucleosis, which has a wide range of disease severities and can comprise a devastating illness that leads to long-term fatigue in some patients, however others may be completely asymptomatic when exposed to EBV.  Our research aims to understand the molecular features of antibody-based immunity that are correlated with different EBV disease severities.  We hope that this work will accelerate the development of more effective EBV vaccine and therapeutic strategies.

Rapid Antibody Discovery

Our single-cell antibody sequencing platform allows us to collect the full antibody sequences (i.e., both the paired heavy and light chains of the antibody variable region) from a repertoire of B cells in an immunized or exposed human patient.  We are applying this technology to rapidly discover antibodies that neutralize viral pathogens, both to understand the immune response to viruses and to develop new treatment and prevention options.  Our unique technology enables the rapid and cost-effective isolation of antibody molecules from large repertoires of human antibodies.

 

References:

 

Kwong PD, et al., “Antibodyomics: Bioinformatics Technologies for Understanding B Cell Immunity to HIV-1” Immunological Reviews, Accepted, 2016

Wang B et al., Scientific Reports, 2015. PMID: 26355042, PMCID: PMC4564727, DOI: 10.1038/srep13926

Facilities

Lab Infrastructure

Our lab is fully-equipped to conduct advanced research in molecular immunology.  We have multiple custom-built instruments for single-cell isolation via flow focusing and magnetic-bead based single-cell emulsion RT-PCR.  We also have a full molecular biology suite and tissue culture area, including incubators, shakers, protein purification (e.g. Akta FPLC), and general molecular biology lab equipment such as liquid nitrogen cryopreservation and ultra-low temperature freezers, Innova incubator/shakers, gel electrophoresis and documentation platforms, and small- and standard-volume spectrophotometers.  

 

The recently installed Immunology Core Facility contains advanced equipment for biological research.  Highlights include a brand-new BD-Fusion flow cytometer, an MSD Quick-Plex, and a CTL Ultimate Elispot machine.  We also have access to the KU Genome Sequencing Facility for Illumina MiSeq and HiSeq NextGeneration Sequencing.

 

High-throughput computational data analysis is conducted using the KU Advanced Computing Facility (recently renovated by a $4.6 million NIH grant led by collaborator Luke Huan), which boasts over 6,000 computational cores for distributed parallel processing of large-scale biological data.  

Research Environment

The Immune Engineering Lab is located in the Simons Biosciences Research Building and is centrally situated in a major biological research center on KU’s main campus in Lawrence, KS.  We are adjacent to the Higuchi Biosciences Center, the McCollum Pharmaceutical Research labs, the Multidisciplinary Research Building (MRB), and the KU School of Pharmacy. 

 

MRB houses the Center for Computational Bioinformatics, the Macromolecule & Vaccine Stabilization Center, the Kansas Vaccine Institute, and the Immunology Core Facility.  Several collaborator research labs are located in the biological research nexus around our building and in the Department of Molecular Biosciences.  We also work with researchers in the Department of Electrical Engineering and Computer Science for developing new computational algorithms to process biological data.