Wednesday, September 18, 2013

NIAID-DVI: Systems Vaccinology -- Bali Pulendran

Blog Series: NIAID-DVI

So as I stated in an earlier blog...some things flew well above my head at this meeting so some of these blogs will be a re-print of the abstract and some general links and thoughts as well as a load of definitions and attempts to understand the components that made up said persons abstract with a healthy dose of trying to understand what they do. Also some of the presentations drove me to take lots of notes from which I could draw on while others, I'll admit my eyes glazed over...and the only note I wrote (several times on many talks was)
"Crash Course Immunology?"
It actually became a bit comic with how many presentations I wrote that on. I now have a new found appreciation for what immunologists do AND a new understanding of why I don't do it. So kudos to all vaccinologists and immunologists everywhere!

Systems Vaccinology: enabling rational design and systems biology
Bali Pulendran
Emory University

Abstract: Despite their great success, we understand little about how effective vaccines stimulate protective immune responses, and advance in systems biology. Two recent developments promise to yield such understanding: the appreciation of the crucial role of the innate immune system in sensing microorganisms and tuning immune responses, and advances in systems biology. In this presentation, I will discuss how these developments are yielding insights into the mechanism of some of the most successful vaccines ever developed. Furthermore, such developments promise to address a major challenge in vaccinology: that the efficacy of a vaccine can only be ascertained retrospectively, upon infection. The identification of molecular signature induced rapidly after vaccination, which correlate with and predict the later development of protective immune responses, would represent a strategy to prospectively determine vaccine efficacy. Such a strategy would be particularly useful when evaluating the efficacy or immunogenicity of untested vaccine, or in identifying individuals with sub-optimal responses amongst the high risk populations, such as infants or the elderly. We have recently used a systems biology approach to identify early gene signatures that correlate with, and predict the later immune response in humans vaccinated iwth the live attenuated yellow fever vaccine YF-17D, or with the influenza vaccines. I will review these studies and discuss their broader implications for vaccinology.

and...awesome.

So this is what I typically do when I get an abstract like this and happen to have the internet on my phone. I start looking shit up. Caveat: You miss a lot of the talk when you do this. Alternate suggestion...smile your way through the talk and look shit up later. I've highlighted the above words or things we'll dive into now that I have the abstract and internet at my disposal.

So here's the list: 
  • Systems Biology
  • innate immune response
  • 'tuning' immune response
  • vaccinology
  • vaccine efficacy
  • efficacy versus immunogenicity
  • 'early' gene signatures
  • molecular signature
  • yellow fever vaccine YF-17D
Systems Biology:
  • Wikipedia: "Systems biology is an emerging approach applied to biomedical and biological scientific research. Systems biology is a biology-based inter-disciplinary field of study that focuses on complex interactions within biological systems, using a more holistic perspective approach to biological and biomedical research. Particularly from year 2000 onwards, the concept has been used widely in the biosciences in a variety of contexts. One of the outreaching aims of systems biology is to model and discover emergent properties, properties of cells, tissues and organisms functioning as a system whose theoretical description is only possible using techniques which fall under the remit of systems biology. These typically involve metabolic networks or cell signaling networks. --Thank you wikipedia
  • Harvard School of Medicine: "Systems biology is the study of systems of biological components, which may be molecules, cells, organisms or entire species. Living systems are dynamic and complex, and their behavior may be hard to predict from the properties of individual parts. To study them, we use quantitative measurements of the behavior of groups of interacting components, systematic measurement technologies such as genomics, bioinformatics and proteomics, and mathematical and computational models to describe and predict dynamical behavior. Systems problems are emerging as central to all areas of biology and medicine."
  • Coursera offers a course in basic Systems Biology where they define it as "An introduction to current concepts of how cellular molecules come together to form systems, how these systems exhibit emergent properties, and how these properties are used to make cellular decisions"
  • If you look at the Institute of Systems Biology Faculty Page you'll see that systems biology spans several disciplines: complex molecular machine, genetics, influenza, immunology, organism-environmental interactions, gene regulatory networks, molecular/cell biology, cancer, proteomics, protein chemistry, biochemical reaction networks, transcriptional regulation, and signal/image processing.
  • For a sampling of articles that fall under 'Systems Biology' see Nature's site.
  • For jobs, trainings, conferences and papers that fall under systems biology check out the Systems Biology Portal
  • The NIH even has a Systems Biology Center.
  • Pacific Northwest National Laboratories (PNNL) has a Systems Biology section and they group the following under it's umbrella: Multi-cellular networks, cell signalling, network biology, biomarkers, oxidative stress and radiation, environmental science, and biofilms.
Seems like systems biology is more of a catch-all for 'pulling out and looking at bigger pictures'. So lets drill down and see what Bali was talking about in using Systems Biology and it's applications as well as implications for Vaccinology...

oh...quick definition Vaccinology: basically, the development of vaccines. Easy enough right?
"I pictured myself as a virus or a cancer cell and tried to sense what it would be like." ~Jonas Salk
Can't mention vaccines/vaccinology without mentioning Jonas Salk right? I especially like his response to patenting of vaccines and 'who' owns vaccines: 
 "Well, the people, I would say. There is no patent. Could you patent the sun?" (source)
But I digress...if you read this blog a lot you'll notice I do that quite a bit.

Back to Bali's abstract and systems biology applied to vaccinology:

     Bali's group had a nice article in Seminars in Immunology, "Systems biological approaches to measure and understand vaccine immunity in humans" where the approach is discussed at length. He contends that the development of vaccines in the past has been largely based on trial and error and to a certain degree that is how vaccine development still operates. The reference links in the below paragraph match up with the papers reference numbering and will take you to the links in the paper...
"Systems vaccinology (Fig. 1) is an effort to apply tools from systems biology to vaccine studies, and has started to bear fruits in the past few years [7], [8], [9] and [10]. The tools of systems biology consist of a number of high-throughput technologies (often dubbed as “omics”), including DNA microarrays, protein arrays, deep sequencing and mass spectrometry (please see Germain et al. [11] for a comprehensive review). They enable system-wide unbiased molecular measurements, which can then be used to reconstruct the events in an immune response...Thus, the combination of omics and conventional immunlological parameters, with the help of computational modeling, will advance vaccinology in several fronts"

  • The benefits of such an approach: 
    1. When things are evaluated within a 'system-wide' context than vaccine response mechanisms can be better understood which would assist in optimization of immunogenicity equating to more durable protection.
      • Immunogenicity: (since it was one of the 'the words' from above): The ability of an antigen to elicit immune responses is called immunogenicity, which can be humoral and/or cell-mediated immune responses --Thank you again wikipedia
    2. Identifying early predictors of vaccine efficacy will assist in vaccine development. Usually, the 'correlates of protection' are not well defined or not applicable to all populations. How do we find correlates of protection beyond what we already know? Molecular predictors should help with that.
      • Vaccine efficacy:  (Oh Wikipedia what would I do without you?) The reduction in the incidence of a disease among people who have received a vaccine compared to the incidence in unvaccinated people. It is usually measured in a randomised controlled trial (RCT) The efficacy of a new vaccine is measured in phase II or phase III clinical trials by giving one group of people a vaccine and comparing the incidence of disease in that group to another group of people who do not receive the vaccine.
      • The basic formula is written as:
        VE = (ARU - ARV)/ARU (x 100)
        where
        VE = vaccine efficacy;
        ARU = attack rate in the unvaccinated population
        and
        ARV = attack rate in the vaccinated population.
         
      • Vaccine efficacy versus vaccine effectiveness: vaccine efficacy shows how effective the vaccine could be given ideal circumstances and 100% vaccine uptake; vaccine effectiveness measures how well a vaccine performs when is used in routine circumstances in the community. (ala Wikipedia)
    3. Detection of molecular signatures, if found as early as possible will help guide clinical trail design.
      • Molecular signature: "Molecular signatures are sets of genes, mRNA transcripts, proteins, genetic variants or other variables that can be used as markers for a particular cell or tissue phenotype, such as a cancerous or diabetic state. Signatures have a two-fold purpose: they may be useful for disease diagnosis or risk assessment (prediction), but they may also implicate molecules not previously known to be involved in the underlying molecular pathology (discovery)." --I pulled this from Nilsson's really nice paper in BMC Bioinformatics. It's an older paper, but it provides a nice background with examples of what can be considered a molecular signature (see Figure below).

Bali also gives a nice example of how a systems approach informs vaccine developments using a gene module that was publically available that shows the linkage between CAMK4 activity and T cell activation explaining a CAMK phenotype. Also using antibody response and gene expression to link to the gene modules activity (see figure below).




Some other nice articles talking about, defining, characterizing and offering up examples of 'Systems Vaccinology' from Bali's group:
So now that we have hopefully a nicer understanding of systems biology and how it's being applied to vaccinology; Bali mentioned their work on the yellow fever vaccine using a systems biology approach. They identified "early gene signatures that correlate with and predict the later immune response in humans vaccinated with the live attenuated yellow fever vaccine, YF-17D".

For those unfamiliar with the timeline for Yellow Fever vaccine development, Bali's article in Nature Review in Immunology, Perspectives section has a nice summary in timeline format:


He mentions that it wasn't until Stokes, Bauer and Hudson showed that rhesus macaques were susceptible to the disease following inoculation with blood isolated from an infected human that the groundwork for development of the yellow fever vaccine YF-17D was laid. The article is a good read if you want to update yourself on the development and history behind YF-17D.

A quick aside for the following articles cited and text to come:
  • innate immune response: The innate immune system, also known as non-specific immune system and first line of defense, comprises the cells and mechanisms that defend the host from infection by other organisms in a non-specific manner. This means that the cells of the innate system recognize and respond to pathogens in a generic way, it does not confer long-lasting or protective immunity to the host. The innate immune system is an evolutionarily older defense strategy, and is the dominant immune system found in plants, fungi, insects, and in primitive multicellular organisms. 
    • The major functions of the vertebrate innate immune system include:
      • Recruiting immune cells to sites of infection, through the production of chemical factors, including specialized chemical mediators, called cytokines.
      • Activation of the complement cascade to identify bacteria, activate cells and to promote clearance of dead cells or antibody complexes.
      • The identification and removal of foreign substances present in organs, tissues, the blood and lymph, by specialized white blood cells.
      • Activation of the adaptive immune system through a process known as antigen presentation.
      • Acting as a physical and chemical barrier to infectious agents.
Wikipedia is doing a fine job of giving me a bit of a Immunology Crash Course I would say...
  • adaptive immune response: The adaptive immune system, also known as the acquired immune system or, more rarely, as the specific immune system, is composed of highly specialized, systemic cells and processes that eliminate or prevent pathogen growth. The adaptive immune systems is only found in vertebrates. Acquired immunity creates immunological memory after an initial response to a specific pathogen, leading to an enhanced response to subsequent encounters with that same pathogen. The acquired response is said to be "adaptive" because it prepares the body's immune system for future challenges.  
    • The system is highly adaptable because of somatic hypermutation (a process of accelerated somatic mutations), and V(D)J recombination (an irreversible genetic recombination of antigen receptor gene segments). This mechanism allows a small number of genes to generate a vast number of different antigen receptors, which are then uniquely expressed on each individual lymphocyte. Because the gene rearrangement leads to an irreversible change in the DNA of each cell, all of the progeny (offspring) of that cell will then inherit genes encoding the same receptor specificity, including the Memory B cells and Memory T cells that are the keys to long-lived specific immunity.
Wow...this post is starting to illustrate just how extensive my love-affair with Wikipedia is.

To put innate and adaptive immunity in context with virus response:
Back to Yellow Fever and Systems Vaccinology...

Here's the paper: Querec et al., 2008. Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nature Immunol 10: 116. --open access!

Again they were looking for 'early' gene signatures that would assist in predicting immune responses in individuals that were vaccinated with the yellow fever vaccine, YF-17D. A lot of this I am pulling nearly verbatim from the article as my background is insufficient to 'paraphrase'.
  • They studied the protein cytokine response after vaccination at various time points.
  • They evaluated the frequency and activation status of antigen-presenting cells, including DCs and monocytes, in the blood at various times after vaccination.
  • They performed transcriptional profiling of total peripheral blood mononuclear cells (PBMCs) from the 15 subjects (they used: Affymetrix Human Genome U133 Plus 2.0 Array).
  • They used the DAVID Bioinformatics Database to analyze gene ontology showing enrichment of genes related to immunological response, cell motility and biopolymer metabolism.
  • They analyzed those genes further using TOUCAN which does transcription factor binding site analysis.
  • Using these methods:
    • They found a closely interacting network of 50 interferon and antiviral genes, 
      • IRF7, OAS1, OAS2, OAS3 and OASL
      • Genes involved in viral recognition, including TLR7, DDX58 (RIG-I), IFIH1 (MDA-5), DHX58 (LGP2) and EIF2AK2 (PKR)
      • Genes mediating antiviral immunity, such as CXCL10 (IP-10), MX1 
      • Complement genes SERPING1 (C1IN) and C3AR1 
      • They also observed YF-17D signals through RIG-I and MDA-5 to induce NF-kappaB activation.

  • They provide data to support the use of HLA-DR and CD38 to measure the magnitude of the YF-17D–specific CD8+ T cell response
  • Neither the induction of IP-10 or IL1A (IL-1alpha) nor the upregulation of CD86 on antigen-presenting cells correlated with the magnitude of the CD8+ T cell response. 
  • There was no correlation between the expression of the genes identified in the gene expression analysis and the magnitude of the CD8+ T cell response
  • They identified 839 (via the methods above) genes that correlated with the magnitude of the CD8+ T cell response
  • Using principle component analysis they were able to identify a group of gene signatures that correlate with the magnitude of CD8+ T cell response (Figure 3 in the article and Table 1)
  • Of the 24 cytokines assayed, IP-10 and IL-1alpha were significantly induced after vaccination.
    • iP-10 and IL1A (IL-1alpha) are reliable markers of YF-17D vaccination, and they may play an integral role in responses to other flaviviruses
  • By way of Summary, it was a long article, very detailed and involved:
    • Vaccination induced genes that regulate virus innate sensing
    • Vaccination induced Type I interferon production
    • Analyses identified a gene signature, including complement protein C1qB and eukaryotic translation initiation factor 2 alpha kinase 4—an orchestrator of the integrated stress response—that correlated with and predicted YF-17D CD8+ T cell responses with up to 90% accuracy. 
    • A distinct signature, including B cell growth factor TNFRS17, predicted the neutralizing antibody response with up to 100% accuracy. 
    • They provided a "global picture of vaccine-induced innate immune responses" that can also be used to "predict the magnitude of the subsequent adaptive immune response and uncover new correlates of vaccine efficacy."
And there you have it...applications and implications of systems biology in the field of vaccinology.

Wow this blog was a long one...

Fie upon you oh systems vaccinology for being so interesting and unknown to me...as if I don't have enough on my plate as it is!

I shall end on a Yellow Fever (Dengue) video from the National Library of Medicine archives that I found from 1945 called: "It's up to you: dengue-yellow fever control" (I love finding this stuff)



Til next time!...