Systems Biology - Projects

Project Principal Investigator
Interdomain Lateral Gene Transfer Julie Dunning Hotopp PhD
NIAID-funded Genome Center for Infectious Diseases Integrated Genomics Research in Parasitic Tropical Diseases — Lymphatic Filariasis Subproject Julie Dunning Hotopp PhD
NIAID-funded Genome Center for Infectious Diseases Core Leader – Tech Core Julie Dunning Hotopp PhD
Immunological and functional consequences triggered by the gut microbiota regulate alloimmunity and cardiac transplant outcome
Predicting Protein Function and Mechanisms Andrew Neuwald PhD
A Systems Biology/Multi-Omics Approach to Elucidate the Causes of Vaginal Symptoms Jacques Ravel PhD
Genital Microbiome-Pathogen Interactions in a Sexual Transmission Network Jacques Ravel PhD
Omics-based Identification of Novel Vaccine Targets Against Neisseria gonorrhoeae Herve S.G. Tettelin PhD
Cardiac Micro-lesion Formation During Invasive Pneumococcal Disease Herve S.G. Tettelin PhD
Fitness Profiling of Streptococcus gordonii in Oral Microenvironments Herve S.G. Tettelin PhD

Interdomain Lateral Gene Transfer

Lateral gene transfer (LGT) is a widely recognized mechanism for acquiring novel gene functions in bacteria. Its role in eukaryotes is unclear, and the role of bacterial DNA in the process even less clear. Until recently only a few instances of LGT to multicellular eukaryotes were described. Yet our studies indicate that >70% of sequenced organisms infected with Wolbachia bacteria have LGT from the bacterial endosymbiont genome to the animal host genome. Once transferred, some DNA is transcribed possibly facilitating acquisition of novel gene functions.

Since Wolbachia reside in the host's eggs and sperm, the high frequency of inherited LGT is not surprising. However, is this limited to just Wolbachia? A careful examination of a variety of endosymbiont-infected arthropod genome sequencing projects should shed light on any correlation between endosymbiont niche and LGT frequency. Is non-inherited LGT equally important? The bacteria Agrobacterium tumefaciens causes crown gall disease in infected plants through LGT of a pathogenic plasmid. We hypothesize that human symbionts or pathogens could cause similar diseases through non-inherited LGT. However, in order to detect such events, large eukaryotic genome projects must be extensively and carefully searched with large numbers of bacterial genomes.


NIAID-funded Genome Center for Infectious Diseases Integrated Genomics Research in Parasitic Tropical Diseases — Lymphatic Filariasis Subproject

Parasitic diseases impose a tremendous toll on the global public health. Malaria causes up to 1.24 million deaths every year, while human filariasis is a neglected tropical disease that remains a major cause of disability in the developing world. This subproject focuses on the filarial nematode Brugia malayi, which causes lymphatic filariasis. Population genomics, multi-species transcriptomics, and whole genome sequencing are used to improve our understanding of the organisms responsible for this important neglected tropical disease.


NIAID-funded Genome Center for Infectious Diseases Core Leader – Tech Core

Genomics has revolutionized research into infectious diseases and is poised to revolutionize the clinic. Through the activities in this technology core, we provide high-throughput genome sequencing and analysis focused on understanding host, pathogen, and microbiome interactions as determinants of disease outcome. We provide state-of-the-art, large-scale, high-throughput sequencing data for analysis of genomes, transcriptomes, metagenomes, metatranscriptomes, and microRNAs using the best methodologies and technologies available.


Immunological and functional consequences triggered by the gut microbiota regulate alloimmunity and cardiac transplant outcome

The most important goal in transplantation is to achieve prolonged allograft survival, and eventually alloantigen specific tolerance. Yet, the occurrence of allograft vascular inflammation and fibrosis has not changed in over two decades. In preliminary studies we characterized gut microbiotas and identified single bacterial species that influence myeloid cell responses, lymph node structure, and the outcomes of murine cardiac allografts. The proposed work will use this murine model of cardiac allografting to further identify the functional mechanisms by which proinflammatory and anti-inflammatory microbiota alter adaptive immunity and ultimately allograft survival.

Many aspects of the innate and adaptive immunity are critically regulated by the microbiota. Microbial cells, their metabolites and nucleic acids engage various immune cells, resulting in pro- or anti-inflammatory signals that differ based on chemical structures, cellular receptors, and physiological context. The microbiota not only influences local immunity, but also has distant effects on systemic immunity. Local microbiota stimulation of innate and adaptive immune cells results in those cells or their products to migrate or traffic through lymphatics or blood, and influence diseases. However, the precise causal pathways linking microbiota components to immune cells and downstream effectors in most cases remain to be defined.

Solid organ transplantation has made significant progress over the past 35 years and has become a routine procedure. Cardiac transplantation is a common and successful transplant, with graft survival after one year exceeding 80-90%. Despite advances in all aspects of allografting, the rate of decline of cardiac and other graft function beyond the first year after transplant has not changed in over 20 years. All allografts eventually succumb to chronic vascular, interstitial or epithelial changes. Despite critical improvements in immunosuppressive regimens, immunologic monitoring, and molecular classification of organ pathology, chronic rejection still persists and its primary cause is not understood. Prior work has focused on distal events of fibrosis and inflammation, but not on proximal causes of inflammation and immunity.

We previously showed in renal transplantation, large and persistent shifts in the composition and complexity of the gut microbiota as a result of immunosuppression and antibiotics. Such shifts in the microbiota are indicative of all organ transplants, including cardiac transplants. We therefore hypothesized that these changes could critically affect graft outcome. Our current studies dissected the interactions between the enteric microbiota and innate and adaptive immunity, in clinically-relevant cardiac transplantation models of acute and chronic rejection. Our results show that both pro-inflammatory and anti-inflammatory microbiota populations, as well as single bacteria, can be defined by their effects on the long-term outcome of the grafts. Mechanistic explorations suggest a differential stimulation of myeloid cells (i.e. macrophages and DC), resulting in changes in LN structure that influence allogeneic immunity. Thus, we hypothesize that the microbiota directly regulates innate immunity, which in turn regulates systemic inflammation and adaptive immunity, thereby determining the occurrence and progression of graft fibrosis, inflammation and graft survival. To investigate this hypothesis, we will take advantage of our expertise in microbiota analysis and in molecular and cellular transplant immunology. The definition of pro-inflammatory and anti-inflammatory microbiota and strains may provide a precise platform to define the most important upstream influences that initiate organ inflammation and scarring and could serve as potent diagnostic markers for allograft management.

The project was funded by the National Institutes of Health (NIH) - National Heart, Lung and Blood Institute (NHLBI): Project information can be found here.


Predicting Protein Function and Mechanisms

Finding out how proteins work - and what roles they play - is essential to understanding disease mechanisms. That information, in turn, can guide the development of new approaches to treating human diseases.

Over the last decade, scientists around the world have generated a treasure trove of data by sequencing the genomes of humans and other organisms. Exploiting that data, IGS scientists are developing and applying sophisticated statistical methods to understand how proteins work on the molecular level.

By using Bayesian statistical approaches that cast a broad net and allow genomic sequence data to speak for itself, IGS scientists are deciphering--in the light of available biochemical, structural and genetic information--life's own blueprints for encoding biological mechanisms. For example, this approach has shed new light on the mechanism of Ras-like GTPases - protein signaling pathway on-off switches that are associated with cancer and other human diseases.

More than a century ago, Gregor Mendel and other pioneer geneticists used statistical analysis of patterns of inherited traits to identify genetic mechanisms long before it was possible to characterize genes at the cellular and molecular levels. Similarly, IGS scientists and others are now breaking ground by using the statistical analysis of sequence patterns to characterize components of the cell's molecular machinery - in many cases well before those components can be characterized more directly.

More Information:

  • Andrew Neuwald PhD
  • The CHAIN Program - A tool for characterizing protein functional divergence in atomic detail.
  • MAPGAPs - A tool for identification, classification and accurate alignment of up to a million or more protein sequences.

Principal Investigator:

Genital Microbiome-Pathogen Interactions in a Sexual Transmission Network

Abundant lactobacilli in the human vagina are thought to protect against invasion by non-indigenous bacteria, including sexually transmitted infections caused by Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC). The means by which this happens are not well understood. It could be that these exclusionary mechanisms are properties of the vaginal microbiome, features of the host immune system and physiology, or some combination of both. The goal of this project is to employ a systems biology approach to identify biomarkers of the vaginal and penile microbiome, the host and the pathogens that are associated with increased or decreased risks of infection by CT, GC or both. Project 3 of this research program will rely on samples collected by the Clinical Core C from STING networks of sex partners who have been exposed to and possibly infected by CT, GC, or both. In these networks we expect that about 20-40% of the participants will have been exposed to, but not infected by these pathogens. This will give us the unique opportunity to assess the role of the microbiome in preventing or facilitating infections by CT and GC. Our overarching hypothesis is that when pathogen transmission does not occur the genetic traits of the infecting pathogen(s) may be insufficient to overcome the host response or the exclusionary mechanisms of the microbiome environment; or that features of the microbiome are protective or induce a protective mucosal environment. In this project, we will build on these findings and use modern ‘omic technologies to identify specific functional features of the vaginal and penile microbiota associated with susceptibility and resistance to infection and co-infection and the importance of host and pathogen genetic variation in this infection process, which will be done in collaboration with Projects 1 & 2. We will achieve these goals by addressing three integrated specific aims: Aim 1. Characterize the genomic variations in CT/GC in participants of the STING networks of sex partners; Aim 2. Use ‘omic approaches and system biology analysis characterize the molecular interactions between the host, the pathogens and the genital microbiota in discordant and concordant couples for CT/GC infections; Aim 3. Validate and explore mechanistic explanations for how the microbiota prevent or facilitate infection by CT/GC using an in vitro three-dimensional model of endocervical epithelial cells. Our long-term goal is to leverage the information generated in this project to develop improved diagnostic methods, identify novel targets for new drug development and develop targeted and effective curative or preventive therapies, and ultimately, promote health, reduce risk to unintended adverse sequelae of STI and improve the quality of life for men and women who are at risk of STIs.


A Systems Biology/Multi-Omics Approach to Elucidate the Causes of Vaginal Symptoms

Vaginal discharge, burning, itching, and malodor are the most common vaginal symptoms reported by reproductive-age women resulting in millions of health care visits annually in the United States alone. These symptoms create substantial discomfort, are often recurrent, and negatively impact women’s self- esteem and quality of life. Often, women resort to ill-advised alternative treatments in an attempt to ameliorate their symptoms that only provide a short-lived relief, and in many cases increase symptom severity. These symptoms are associated with numerous serious gynecological and obstetric outcomes, including an increased risk for sexually transmitted infections. The long-term goal of the proposed work is to develop a more complete understanding of the underlying causes of vaginal symptoms so that targeted and effective strategies can be developed to effectively prevent or treat vaginal discharge, discomfort, and malodor. The multi-omics datasets we propose to gather and analyze will allow us to test the central hypothesis that symptoms are emergent properties of the vaginal microbiome that result from the interplay of specific functions, and not simply microbial composition of vaginal microbiomes and host responses elicit these signs and symptoms. To achieve this, we will leverage a unique set of vaginal swabs samples and extensive metadata that were prospectively collected daily by 135 women for 10 weeks. During this study, women experienced either 1) clear episodes of vaginal symptoms, 2) chronic and persistent symptoms or 3) no symptoms. The study design affords a unique opportunity to use ‘omics technologies on samples collected before, during and after episode of vaginal symptoms and compare these to women with chronic or no symptoms, and identify specific predictive biomarkers that will translate to more personalized management of women’s health. The project addresses two specific aims: (1) Determine the composition and function of the vaginal microbiome by characterizing bacterial metagenomes, the host and bacterial transcriptomes and metabolomes, and markers of innate immunity in vaginal samples collected prior to, during and after episodes of vaginal symptoms and compare these to comparable data from asymptomatic women. (2) Develop predictive and causal models of symptom onset using integrative systems biology approaches using a multi- prong modeling strategy that includes lasso regression, ridge regression and elastic net regression combined with robust and modern model selection techniques, and network analyses, we will achieve a predictive and causal model that is a balance of robustness, explanatory power, and size (in terms of the number of predictor variables). Armed with detailed knowledge of changes in genomic factor of the microbiota and the host during the onset and recovery from vaginal symptoms it will be possible to develop more accurate and sensitive diagnostic procedures, new therapeutic strategies, and effective means to ensure vaginal homeostasis.

This research reported is supported by the National Institute of Allergy and Infectious Diseases, of the National Institutes of Health.


Omics-based Identification of Novel Vaccine Targets Against Neisseria gonorrhoeae

The diplococcic bacterium Neisseria gonorrhoeae (Gc) is the causative agent of the sexually transmitted infection (STI) gonorrhea. The ability of major surface proteins to vary their expression significantly complicates the development of a vaccine against Gc. Our project focuses on Gc changes that occur under relevant physiological conditions that would be encountered in vivo. We hypothesize that specific differentially regulated Gc surface proteins are selected for during infection and these events enhance infectivity across multiple strains, thus providing targets for vaccine development. We will first characterize these profiles using Gc laboratory strains then extrapolate them to similarities in profiles observed between Gc clinical isolates that are readily transmitted and/or display enhanced infectivity. Targets identified from this innovative and integrative research strategy will constitute a novel foundation of Gc host interaction determinants relevant to enhanced infectivity that will be pursued in follow-up larger studies and clinical trials to determine their viability as vaccine candidates.

[PI: Hervé, Vonetta Edwards, postdoc]


Cardiac Micro-lesion Formation During Invasive Pneumococcal Disease

I have performed dual RNA-seq profiling of the host-pathogen interplay during disseminated Streptococcus pneumoniae infection in a mouse model. We were able to simultaneously profile bacterial and mouse gene responses using whole infected hearts, as well as infected blood. These studies led to the identification of novel anatomical site-specific expression of determinants of pneumococcal pathogenesis, gave insights into their mechanism of interaction with the host, and provided key information on currently considered and future protein candidates for vaccine development. We are now extending this project to study multiple anatomical sites in the mouse and combine transcriptomics with metabolomics studies. As a part of the GCID, we are also studying host-pneumococcus interactions and biofilms, with or without the influence of the influenza virus, using an ex-vivo primary cadaver lung cell culture system.

[PI: Carlos Orihuela, U. of Alabama at Birmingham]


Fitness Profiling of Streptococcus gordonii in Oral Microenvironments

Streptococcus gordonii is an initial colonizer of the biofilm that forms tooth surfaces. Identification of S. gordonii genes essential for species survival and proliferation under synergistic or antagonistic conditions will provide essential insights into community dynamics that favor or disfavor a state of oral health. We are using Tn-seq to identify and examine genes involved in S. gordonii fitness under selected in vitro model conditions relevant to those in the oral cavity.

[PI: Meg Virckerman, U. at Buffalo]