Systems analysis of host-parasite interactions.

Parasitic diseases caused by protozoan pathogens lead to hundreds of thousands of deaths per year in addition to substantial suffering and socioeconomic decline for millions of people worldwide. The lack of effective vaccines coupled with the widespread emergence of drug-resistant parasites necessitates that the research community take an active role in understanding host-parasite infection biology in order to develop improved therapeutics. Recent advances in next-generation sequencing and the rapid development of publicly accessible genomic databases for many human pathogens have facilitated the application of systems biology to the study of host-parasite interactions. Over the past decade, these technologies have led to the discovery of many important biological processes governing parasitic disease. The integration and interpretation of high-throughput -omic data will undoubtedly generate extraordinary insight into host-parasite interaction networks essential to navigate the intricacies of these complex systems. As systems analysis continues to build the foundation for our understanding of host-parasite biology, this will provide the framework necessary to drive drug discovery research forward and accelerate the development of new antiparasitic therapies

Memory T cells in latent mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset

An understanding of the immunological footprint of Mycobacterium tuberculosis (MTB) CD4 T cell recognition is still incomplete. Here we report that human Th1 cells specific for MTB are largely contained in a CXCR3+CCR6+ memory subset and highly focused on three broadly immunodominant antigenic islands, all related to bacterial secretion systems. Our results refute the notion that secreted antigens act as a decoy, since both secreted proteins and proteins comprising the secretion system itself are targeted by a fully functional T cell response. In addition, several novel T cell antigens were identified which can be of potential diagnostic use, or as vaccine antigens. These results underline the power of a truly unbiased, genome-wide, analysis of CD4 MTB recognition based on the combined use of epitope predictions, high throughput ELISPOT, and T cell libraries using PBMCs from individuals latently infected with MTB

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Battling Drug Resistance: A Tale of Two Pathogens

HIV/AIDS, malaria, and tuberculosis are the world’s three deadliest infectious diseases of humans, often referred to as the ‘Big Three’. Together, they are responsible for more than 10% of all the deaths worldwide each year. What is perhaps most worrisome is the fact that the current therapies that treat these conditions are losing their efficacy due to the emergence of antimicrobial drug resistance. Accordingly, research is urgently needed to address the growing problem of drug resistance and to help drive the development of novel therapeutics. In the first chapter of this doctoral dissertation, three strategies to combat drug resistance are discussed: 1. Developing therapeutics that target host-derived factors, 2. Identifying new antimicrobial inhibitors, and 3. Investigating host-pathogen biology using systems analysis to drive the development of novel therapeutics. Examples of research utilizing these strategies are discussed in the following chapters, with a particular focus on two of the “Big Three” pathogens- HIV-1 and the malaria parasite, Plasmodium. The identification and characterization of a novel host factor that regulates HIV-1 reverse transcription is described in Chapter 2. In Chapter 3, the development of a high-throughput phenotypic assay to identify novel antimalarial drugs is discussed, and in Chapter 4, a broad review of systems biology-based research of host-parasite interactions (with an emphasis on Plasmodium) is included. The Appendix includes preliminary data and future aims for systems biology research aimed at understanding Plasmodium liver-stage development. Through the combination of these scientific efforts, we will surely strength our position in the ongoing battle against antimicrobial drug resistance

A high-­‐throughput luciferase-­‐based assay for the discovery of therapeutics that prevent malaria

In order to identify the most attractive starting points for drugs that can be used to prevent malaria, a diverse chemical space comprised of tens of thousands to millions of small molecules may need to be examined. Achieving this throughput necessitates the development of efficient ultra-­‐high throughput screening methods. Here, we report the development and evaluation of a luciferase-­‐based phenotypic screen optimized for a 1536 well format. This assay uses the rodent malaria parasite, Plasmodium berghei, and a human hepatoma cell line. We use this assay to evaluate several biased and unbiased compound libraries, including two small sets of molecules (400 and 89 compounds, respectively) with known activity against malaria parasite blood stage parasites and a set of 9,900 diversity oriented synthesis (DOS) derived compounds. Of the compounds screened we obtain hit rates of 12-­‐13% and 0.6% in preselected and naïve libraries, respectively, and identify 52 compounds with activity of less than 1 µM with minimal host cell toxicity. Our data demonstrate the utility of this method to identify scaffold families that are known to have causal prophylactic activity in both human and animal models of malaria, as well as novel compounds, including some with activity only against parasite exoerythrocytic stages

Systems analysis of host-parasite interactions.

Parasitic diseases caused by protozoan pathogens lead to hundreds of thousands of deaths per year in addition to substantial suffering and socioeconomic decline for millions of people worldwide. The lack of effective vaccines coupled with the widespread emergence of drug-resistant parasites necessitates that the research community take an active role in understanding host-parasite infection biology in order to develop improved therapeutics. Recent advances in next-generation sequencing and the rapid development of publicly accessible genomic databases for many human pathogens have facilitated the application of systems biology to the study of host-parasite interactions. Over the past decade, these technologies have led to the discovery of many important biological processes governing parasitic disease. The integration and interpretation of high-throughput -omic data will undoubtedly generate extraordinary insight into host-parasite interaction networks essential to navigate the intricacies of these complex systems. As systems analysis continues to build the foundation for our understanding of host-parasite biology, this will provide the framework necessary to drive drug discovery research forward and accelerate the development of new antiparasitic therapies

Additional file 1: Figure S1. of Cytosolic sulfotransferase 1A1 regulates HIV-1 minus-strand DNA elongation in primary human monocyte-derived macrophages

SULT1A1 is highly expressed in monocytes. The expression level for each cytosolic sulfotransferase in CD4+ T cells and CD14+ monocytes was derived from publically available expression data from BioGPS and normalized to the median expression of that sulfotransferase in all tissues tested. (PDF 26 kb