Research Cores

Updates are coming!  In July 2016 we received new funding from NIH.  Check back soon for details on our new research cores!

Mullins Tree
Flow Cytometry

    Core A: Nonhuman Primate Core

    Leader: Shiu-Lok Hu, PhD, University of Washington · Seattle, Washington

    With the advent of highly active anti-retroviral therapy (HAART), significant progress has been achieved in the control of viral replication and prolongation of AIDS-free survival in HIV infected individuals.  However, current therapeutic modalities do not effectively target or eliminate latent viral reservoirs.  As a result, virus often rebounds after cessation of therapy.  Significant side effects and drug resistance are common due to the necessity for long-term multidrug therapy.  An ultimate goal for anti-HIV therapy should therefore be virological eradication, i.e., to cure HIV infection.  To date, the feasibility of virologic eradication has only been demonstrated in one HIV-infected patient (the “Berlin Patient”) given an allogeneic hematopoietic cell transplant (HCT) from a CCR5Δ32 homozygous donor.  Although this is an important proof-of-concept study, the likelihood of using HLA-matched and CCR5Δ32 homozygous donor as a general therapeutic approach is remote.

    The overall objective of this Collaboratory is to explore strategies to introduce specific modifications in host and proviral DNA to target and eliminate the latent HIV reservoir.  The goal of this Core is to provide comprehensive support for the preclinical, proof-of-concept studies in non-human primates.  These studies will allow us to address fundamental questions regarding the mechanisms that brought about eradication of latent HIV reservoirs in the “Berlin Patient”, and will permit the optimization of potentially curative approaches that may be applied to the vast majority of HIV infected individuals.


    Core B: Transplantation Core

    Leader: Hans-Peter Kiem, MD, Fred Hutchinson Cancer Research Center · Seattle, Washington

    Preclinical nonhuman primate SHIV models have played a crucial role in the development of anti-HIV treatment strategies.  Studies with a number of pathogenic SHIV viruses have been performed in this model, exhibiting distinct disease patterns, which directly parallel the spectrum of disease seen in HIV-infected patients.  SIV- and SHIV-infected nonhuman primates have similar clinical and surrogate markers of infection such as antiviral antibodies, hematopoietic abnormalities, and virus load in the peripheral circulation and lymphoid tissues as HIV-infected patients.  The importance of the SIV- and SHIV-infected model lies in the fact that, unlike the human population, the timing of infection can be controlled and findings can be quantified and directly correlated with disease under controlled conditions. Infected macaques develop CD4+ T-cell loss usually in a few weeks and develop AIDS at intervals ranging from a few weeks to two years.  Histological changes in the lymphoid and other tissues closely resemble those seen in human AIDS.  Furthermore, organ-specific disease, including encephalitis, can also be studied.  Thus, the SHIV/macaque model is an appropriate model to study AIDS gene therapy strategies.

    We have published extensively on improving gene transfer to hematopoietic stem cells.  The core leader, Dr. Kiem, has more than 15 years experience with preclinical model transplantation and cellular modification studies.


    Core C: Sequencing Core

    Leader: Roger Bumgarner, PhD, University of Washington · Seattle, Washington

    In this Core, Dr. Bumgarner’s group will be responsible for performing sequencing analysis of viral populations isolated from a nonhuman primate model of hematopoietic cell transplant (HCT) aimed at a targeted cure for HIV.  The underlying hypothesis being tested is that conditioning and HCT regimens that do not eliminate the latent reservoir will bias the remaining virus toward more ancestral sequences, and sequences representing anatomic sites (for example, GALT or CNS) containing the most persistent reservoir.  We will perform genetic analysis on viral sequences obtained from blood, cerebral spinal fluid, and the intestinal tract, before and at intervals during the year after HCT to test this hypothesis.


    Core D: Immunology Core

    Leader: Stephen C. De Rosa, MD, Fred Hutchinson Cancer Research Center · Seattle, Washington

    The Immunology Core primarily provides support for Project 1 and Project 3. The Core will longitudinally measure the SHIV-specific CD4+ and CD8+ T cells in the blood of nonhuman primate models at different stages in the treatment regimens.  These measurements will be made using a flow cytometric intracellular cytokine staining (ICS) assay.  For this assay, peripheral blood mononuclear cells (PBMC) are stimulated ex vivo for 6 hours with pools of overlapping 15-mer peptides that match the sequence of the HIV/SIV proteins encoded by the virus used to infect the nonhuman primate models.  Depending on the amount of PBMC available at each time point, responses to all SHIV-encoded proteins or only selected proteins will be examined.  This is a multi-parametric assay that measures multiple cytokines as well as memory markers:  therefore, we can measure both the magnitude and the character or quality of the response. Many groups have published reports proposing associations between effective or non-effective T-cell responses and particular functional or phenotypic profiles.  Thus, a detailed characterization of the T-cell responses that are gained or lost subsequent to the treatment interventions in these projects will be informative for correlating with treatment outcome.


    Core E: Administrative Core

    Leader: Keith Jerome, MD, PhD, Fred Hutchinson Cancer Research Center · Seattle, Washington

    This is a complex and highly interactive program bringing together experts in multiple fields.  Thus, a strong administrative structure is critical to the successful performance of our work.  The Administrative Core coordinates the administrative, fiscal and organizational aspects of our Collaboratory, facilitates scientific communication, and provides fixed support services to each of the Projects and Cores. Our integrated research program includes leading scientists based at the FHCRC, UW, Seattle Children’s, City of Hope, and Sangamo Biosciences.  Administrative staff members in the Core provide a bridge between these institutions.  All are experienced in coordination of the administrative complexities that a combined program creates.