Biology Reference
In-Depth Information
inferred network reflects in vivo regulation remains an open
question. Further, non-combinatorial perturbations may not
accurately reflect overall functionality
[8]
, as partial
redundancy is abundant in many biological processes.
As technologies able to perform multiple single cell
measurements increase in scale (currently an upper limit of
100 proteins can be simultaneously profiled by mass
cytometry, and 96 genes can be assayed by microfluidics)
they could serve an important role in whole network
reconstruction based on cell-to-cell variance
[7,34,35]
.
However, recent work showing large functional cell-to-cell
variation in an individual sample between what were
previously considered the same cell types, complicates the
interpretation of inferred networks for any single cell
[1,32]
. Hence a prime challenge is to understand the origin
of the newly unmasked variation, its function, and how it
relates ultimately to variation in immune response.
Human Immune Monitoring
Vaccination marks one of the greatest achievements of
science and is by far the medical intervention that has saved
the most lives. However, infectious disease and immune-
related diseases contribute to over 25% of deaths in
developed countries and more than 50% of deaths in
developing countries. Our understanding of the immuno-
logical mechanisms by which vaccines work is limited, and
we do not yet know why vaccines fail to protect a certain
percentage of people in specific subpopulations. For
example, roughly only 40% of adults over the age of 65
mount an effective response to the standard yearly influ-
enza vaccine
[42]
, and only 50% of children in developing
countries exhibit neutralizing antibodies to oral polio
vaccination, vs. 90% in the developed world
[43]
. Studies
in cancer research have shown that disease-specific signa-
tures can be detected in gene expression, often earlier than
a definite diagnosis can be made clinically, and that
subgroups of patients may be identified with specific gene
expression signatures that are prognostic of treatment
outcome
[44,45]
. Phenotypically, it has long been noted
that there is considerable variation in the immune responses
of individuals. Thus, it is tempting to speculate that there
are specific immune states, even among those considered
healthy, and that these states affect vaccine responses as
well as disease susceptibility and outcome.
Vaccination presents a safe and controlled perturbation
in which to study immune system response. Vaccine effi-
cacy varies as a function of many variables, including the
type of vaccine (e.g., killed or attenuated virus), the adju-
vant introduced with the vaccine to stimulate innate
response, and, as mentioned above, it is affected by
demographic and geographic attributes. Recent studies are
combining multiple high-bandwidth measurements of the
immune system in humans and animal models measured
pre and post vaccination. The outcome variable in these
studies is the degree of protection elicited by a given
vaccine in a subject. For most vaccines, this is currently
measured by the magnitude of the antigen (vaccine)-
specific antibody titers in blood after vaccination. However,
it is well known that in some cases this correlate does not
actually correspond to protection, or at least corresponds to
only a part of the requirements for protection. This exem-
plifies our limited understanding of the biological mecha-
nisms involved in the response to a given vaccine. Thus,
one goal is to identify improved correlates of protection
(biomarkers) that can be used to identify individuals who
respond suboptimally to vaccination, and the mechanism of
immunity involved in eliciting response, whose study may
help devise improved vaccines and vaccination protocols
[37,38]
.
Two independent studies employing a systems approach
to vaccination were performed on the yellow fever YF-17D
SYSTEM-FOCUSED SYSTEMS
IMMUNOLOGY
Protective immunity is not the end outcome of any single
cell, but rather relies on processes that span multiple cells
or cell populations and which are greatly affected by the
microenvironment. In contrast to the above cell-focused
approach, a growing number of medical researchers and
immunologists are embracing high-bandwidth technologies
to assay the entire immune system. A strong driving
force for these efforts is clinical, as no good metrics of
immunological health currently exist
[36]
. Early efforts
used gene expression microarrays to profile immune
system state; more recently other multiplex immunoassays
technologies probing different layers of the immune system
have been introduced: soluble proteins by bead and elec-
trochemiluminesce based assays from blood-derived serum
or plasma; multicolor flow and mass-based cytometry for
enumerating protein markers for different cell types; and
the abundance of intracellular phosphoproteins, to name
a few. These pan-cell system-wide analyses are not only
yielding blood-based biomarkers, but also provide para-
digm-shifting new insights into immunology. In the first
part of this section, we examine the insights from recent
efforts to comprehensively profile human subjects to
understand the immunological mechanisms of vaccination
[37
39]
(the approach is sometimes referred to as 'systems
vaccinology'). We note that these represent only a subset of
efforts that are applied to 'system-level' profiling of
immune-related diseases,
e
infections and inflammation
[39
41]
. We will highlight common themes and challenges
that have arisen in the first part of this section. In the second
part, we will focus on the application of next-generation
DNA sequencing to the analysis of the B-cell antibody
repertoire and TCR sequences.
e
