The overall focus of the Pipkin lab is to elucidate how chromatin structure and transcription controls the gene expression programs that establish and maintain the differentiated states of T cells. The lab specifically studies how naïve CD8 T cells differentiate into effector and memory cytotoxic T lymphocytes (CTL). CTL are killer lymphocytes that hold outstanding promise for controlling viral infections and cancer therapeutically, as they can be employed in adoptive immunotherapy and are the target of successful vaccination. The Pipkin lab has developed novel approaches to map the fundamental repeating structures of chromatin (nucleosomes) at unprecedented resolution, novel reporter genes to track cells in vivo that induce expression of Prf1, an essential gene that is required for the anti-tumor killing activity of CTL, and the only systems to conduct genome-scale pooled RNAi screens in T cells, in vivo, during the course of actual viral infections. Using these tools and approaches, the Pipkin lab is clarifying how transcription factors govern the specific organization of nucleosomes that enforces CTL differentiation, identifying the chromatin regulatory factors that maintain the differentiated state epigenetically, and demonstrating how these processes mediate durable immunity.

Our laboratory focuses on entry processes of enveloped viruses and the various ways that the innate and adaptive immune responses inhibit these processes. We also apply our insights toward developing therapeutic strategies that enhance or supplement these immune responses. Our work can be divided into three categories: (1) biochemical studies of the HIV-1 entry process and its inhibition, (2) identification and characterization of obligate factors, including receptors, necessary for the entry of other enveloped viruses, and (3) identification and characterization of host restriction factors that inhibit early steps in the viral life cycle, in particular those of the IFITM family.

In addition to these scientific goals, we are developing a means of providing sustained, universal protection from HIV-1. Our most effective strategy uses adeno-associated virus (AAV) to express, eCD4-Ig, an exceptionally broad and potent HIV-1 entry inhibitor. We have shown that this strategy protects rhesus macaques from virus challenges greater than any human is likely to encounter, and thus it provides more effective protection than any conventional vaccine approach. To improve the safety of this approach, we are also developing regulatory switches that can dose or inactivate an AAV transgene.

Viruses enter cells through common underlying mechanisms. Parallel studies of the entry processes of various viruses can therefore highlight differences among them, as well as their similarities. The Choe laboratory studies a wide range of viruses to better understand their entry pathways and the mechanisms of pathogenesis of viral diseases. In doing so, we identified a number of viral receptor and host factors critical for viral infection and pathogenesis. These include: the HIV-1 coreceptor CCR5, and its post-translational modification tyrosine sulfation critical HIV-1 infection; the SARS-CoV receptor angiotensin-converting enzyme 2 (ACE2) and the lysosomal enzyme cathepsin L as an essential target-cell factors for SARS-CoV infection; transferrin receptor 1 (TfR1) as the receptor for New World hemorrhagic fever arenaviruses, and an antibody that inhibits the infection of all five pathogenic New World arenaviruses. We also study how the TIM family of phosphatidylserine receptors promote infections of a wide range of enveloped viruses including filoviruses and flaviviruses such as West Nile, dengue and Zika viruses. More recently, we included adeno-associated virus (AAV), the preferred gene therapy vector, in our study with the goal of improving its transduction efficiency in specific target cells.

The underlying theme of the research performed in the Solt laboratory is to understand the biologically relevant roles of nuclear receptors, a superfamily of ligand regulated transcription factors, in the immune system. Our lab uses a combination of molecular biology, genetic, and chemical biology approaches coupled with mouse models of autoimmunity and chronic inflammation to study how different nuclear receptors’ expression, function, and activity affects disease. As ligand-regulated transcription factors, nuclear receptors are excellent therapeutic targets for the treatment of a variety of diseases. Therefore, we also work in collaboration with medicinal chemists to develop small molecule ligands to these receptors to further probe their function in vitro and in vivo. Each receptor is unique and can have ligand- and/or tissue-specific effects. Thus, we aim to gain a better understanding of nuclear receptor activity in tissue and disease-specific contexts to determine their therapeutic potential and for more rational drug design.

According to the latest statistics published by the UNAIDS/WHO in December 2007, 33.2 million people were living with the Human Immunodeficiency Virus (HIV). In 2007, 2.1 million people died as a result of the acquired Immunodeficiency Syndrome (AIDS). Although antiretroviral drugs have had a dramatically beneficial impact on HIV-infected individuals who have access to treatment, they have had a negligible impact on the global epidemic. Therapies for retroviral infections in humans now used in clinical practice have limitations in that they often only shorten the duration of disease symptoms or fail to completely eradicate the virus with viral replication and disease recurring after discontinuation of the drug therapy. Additionally, the emergence of HIV variants with drug-resistance is an ongoing clinical problem. Clearly having a larger repertoire of therapeutic agents would be beneficial for combating the HIV epidemic.

Retroviruses, due to their limited genome size and content, require the assistance of multiple host cellular proteins at each step in their elaborate replication cycle. Host cells, in response, have evolved many mechanisms for inhibiting viral replication. We have taken a general approach to identify the molecular interactions occurring within a cell that are critical for viral replication, or genes that have evolved in mammalian cells to block viral replication. The discovery of cellular factors involved in retroviral replication and an increased knowledge of their mode of action may lead to important antiviral approaches in clinical settings as one could block the modified use without affecting cell viability.

I am interested in developing practical immune interventions against globally relevant human pathogens. HIV is the current topic of my research. My group is using rhesus macaque models of HIV/AIDS to develop active and passive immunization strategies for preventing and treating HIV infection.

Neurodegenerative diseases

Our laboratory focuses on the study of neurodegenerative diseases, especially those linked to protein misfolding (protein misfolding neurodegenerative diseases, or PMNDs). These diseases comprise Alzheimer’s, Parkinson’s, Huntington’s, prion diseases, fronto-temporal dementia, and amyotrophic lateral sclerosis. None of them are curable. They are all due to host proteins loosing their natural, functional conformation and adopting a new shape that renders them neurotoxic and prone to aggregation.

Prion diseases constitute the prototypic PMND. These rapidly fatal neurodegenerative diseases affect humans and animals and are caused by infectious aggregates of the prion protein PrP, called prions. In humans, prions cause Creutzfeldt-Jakob disease. In animals, the recent epidemic of bovine spongiform encephalopathy in the United Kingdom has caused major turmoil throughout Europe, and later, in other countries such as Japan, Canada and the United States, because the bovine prion disease is transmissible to humans causing variant Creutzfeldt-Jakob disease. The transmissibility of the latter by blood transfusion created a novel public health issue.

Alzheimer’s and Parkinson’s diseases affect 5.8 and 1 Million people in the USA, respectively. Their incidence has steadily increased with an aging population, having a major impact on public health, society and the economy. Alzheimer’s disease is the 6th leading cause of death in developed countries. Amyotrophic lateral sclerosis (ALS or Lou Gehrig’s disease) is an orphan disease causing a progressive muscle weakness and paralysis, affecting an estimated 30,000 people in the USA.

In recent years, it has been discovered that aggregates of amyloidogenic proteins such as Ab, tau, a-synuclein or SOD-1 involved in Alzheimer’s, Parkinson diseases and amyotrophic lateral sclerosis, respectively, spread from cell to cell in culture and in the living organism similarly to PrP aggregates, showing “prion-like” behavior. There are other features common to these toxic proteins and the way they injure neurons (e.g. toxicity of low molecular weight aggregates, impairment of protein degradation mechanisms such as autophagy, mitochondrial distress).

Our aim is the development of novel, disease-modifying therapeutic approaches for protein misfolding neurodegenerative diseases. We think that this aim will be best achieved by intervention strategies based on targeting toxic protein aggregates, and blocking the neurodegenerative process to achieve neuroprotection. We are pursuing these goals by studying the underlying biology, defining therapeutic targets, identifying active molecules by high-throughput screening and developing lead compounds. The latter two tasks are performed in collaboration with our lead identification and chemist colleagues on campus.

Next-generation antibodies for cancer therapy