Molecular Virology & Immune System Genomics

Immune System Genomics

New technologies and advances in next-generation sequencing have allowed for comprehensive studies of the human immune system. Understanding immune system dynamics in response to infection and vaccines will revolutionize how we predict outcomes and identify new therapeutic targets to improve vaccines and therapeutic interventions for infectious diseases. Research in Dr. Bradley’s lab focuses on harnessing these technologies to understand molecular mechanisms of immune cell responses, identify genetic influences on the immune response, and determine the dynamics of the antibody repertoire and viral evolution over time.

1. Genome and transcriptome sequencing of humans and animal models infected with HIV-1 or vaccinated with HIV immunogens

Developing an efficacious HIV-1 vaccine remains a top global priority. A key attribute of a successful vaccine will be elicitation of broadly neutralizing antibodies. Our laboratory is interested in identifying gene expression and genetic changes in specific immune cells that result in a permissive cellular environment for the development of HIV neutralizing antibodies. We also utilize these genomics approaches to evaluate and monitor the immune response to vaccine candidates with the goal of identifying important molecular mechanisms of vaccine-mediate protection.

2. High-throughput determination of the antibody repertoire

A key component of the adaptive immune system is the generation of a diverse repertoire of B-lymphocyte antigen receptors (BCRs). BCRs are anchored onto the surface of the B cells and secreted by B cells in the forms of antibodies. Current mechanism for BCR diversity can yield a repertoire with a theoretical 1013 number of possible BCRs. The B cell repertoire changes in response to infections and vaccination but also is perturbed by aging, autoimmunity and allergy. Our lab uses high-throughput sequencing to sequence the entire population of BCRs in samples (from 100s to 1,000,000s of sequences) to understand how the antibody repertoire develops after infection or vaccination. We can use this information to track the development of broadly neutralizing HIV antibodies and identify key roadblocks in their elicitation by a vaccine.

3. Study of HIV-1 genetic variation

The sequencing of the HIV virus from infected humans or simian-human immunodefiecency virus (SHIV) from monkeys are utilized as vaccine antigens, in neutralization assays and understanding viral escape from the host immune response. The Bradley lab performs single-genome amplification of HIV and SHIV from infected humans and monkeys, respectively. We use this sequence data to identify sites of immune pressure on the virus over the course of infection that can be targeted by future vaccines.

Characterization of virus stocks

As part of the EQAPOL Viral Diversity Panel, the Bradley lab is involved in the characterization of HIV viral stocks. The goal of the EQAPOL program is to establish a set of fully characterized viruses from early acute HIV infections that are consistent with the degree of viral evolution present globally. Samples that are gathered from newly-identified HIV-infected individuals with rare, unique or difficult to identify isolates, and propagated to high titer in culture are evaluated, characterized, and fully sequenced by the Bradley lab before adding them to a central repository where they will be available to the NIAID-approved laboratories. The current EQAPOL Viral Diversity panel includes over 300 viral isolates representing 6 subtypes (A, B, C, D, F, G), 2 sub-subtypes (F1, F2), 10 circulating recombinant forms (CRFs) (01, 02, 04, 11, 14, 22, 24, 47, 59, 70), 67 unique recombinant forms (URFs), 3 HIV-2, 1 group P, and 5 group O viruses from 35 countries.

Viral genetic analysis (VGA) core

The Bradley lab is also the home to the VGA core facility that provides sequencing (NGS and Sanger) and genomic technologies to serve the needs of the Duke Human Vaccine Institute, Duke Center for AIDS Research, Duke University and also external Collaborators. The facility offers state-of-the-art instrumentation for Sanger sequencing and high Throughput RNA/ DNA sequencing, library preparation and quantification, NGS runs and data analysis. The core is also integrated with the Chromium Single Cell 3’ Solution that provides high-throughput, single cell expression measurements that enable discovery of gene expression dynamics and molecular profiling of individual cell types. In addition, isolation and analysis of sequences for single nucleotide polymorphisms within the HIV-1 genome (Single Genome Amplification), PCR Purification, Site Directed Mutagenesis and characterization of virus tocks can be done using VGA core facilities and expertise.