Immunology, Phenotype First: How Mutations Have Established New Principles and Pathways in Immunology

233 Pages·2008·1.32 MB·English

by  B. Beutler

Current Topics in Microbiology and Immunology
Volume 321
Series Editors
Richard W. Compans
Emory University School of Medicine, Department of Microbiology and
Immunology, 3001 Rollins Research Center, Atlanta, GA 30322, USA
Max D. Cooper
Department of Pathology and Laboratory Medicine, Georgia Research Alliance,
Emory University, 1462 Clifton Road, Atlanta, GA 30322, USA
Tasuku Honjo
Department of Medical Chemistry, Kyoto University, Faculty of Medicine,
Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
Hilary Koprowski
Thomas Jefferson University, Department of Cancer Biology, Biotechnology
Foundation Laboratories, 1020 Locust Street, Suite M85 JAH, Philadelphia,
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Fritz Melchers
Biozentrum, Department of Cell Biology, University of Basel, Klingelbergstr.
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Michael B.A. Oldstone
Department of Neuropharmacology, Division of Virology, The Scripps Research
Institute, 10550 N. Torrey Pines, La Jolla, CA 92037, USA
Sjur Olsnes
Department of Biochemistry, Institute for Cancer Research, The Norwegian
Radium Hospital, Montebello 0310 Oslo, Norway
Peter K. Vogt
The Scripps Research Institute, Dept. of Molecular & Exp. Medicine, Division of
Oncovirology, 10550 N. Torrey Pines. BCC-239, La Jolla, CA 92037, USA
Bruce Beutler
Editor
Immunology, Phenotype First:
How Mutations Have
Established New Principles
and Pathways in Immunology
Editor
Bruce Beutler
Scripps Research Institute
Department of Immunology
10550 N. Torrey Pines Rd.
La Jolla CA 92037
USA
[email protected]
ISBN 978-3-540-75202-8 e-ISBN 978-3-540-75203-5
DOI 10.1007/978-3-540-75203-5
Current Topics in Microbiology and Immunology ISSN 0070-217x
Library of Congress Catalog Number: 2008926501
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Preface
This monograph deals with the impact of classical genetics in immunology, provid-
ing examples of how large immunological questions were solved, and new fields
opened to analysis through the study of phenotypes, either spontaneous or induced.
As broad as biology has become, there are those who do not fully understand what
the genetic approach is, and how it differs fundamentally from most of the methods
available to natural scientists. They may hold the opinion that genetics has run its
course since Mendel read his paper on peas in 1865. “Why bother with classical
genetics,” they may ask. “Won’t all genes be knocked out soon anyway?” Or they
are intimidated by genetics, with its heavy reliance on model organisms that seem
so alien. “What has C. elegans to do with me?” the questioning might go. “It
doesn’t even have lymphocytes.” Such skeptics may be unaware that the mouse is
fast becoming as tractable a model organism as the fly, and that humans may not be
too far behind. So I would like to introduce the topic with a few words about the
power of genetics, and why it has contributed so much to immunology, and to biol-
ogy in general.
Genetics, as the word is used here, is not merely the science of heredity, but
much more than that. It is the science of exceptions: the science that takes note of
heritable variation and seeks to explain it at the most fundamental level. It is the
science that splits phenomena into phenotypes; then assigns them to individual
genes and even portions of genes. Through genetics, unambiguous conclusions can
be drawn about the function of every protein we have. Although all science seeks
to explain phenomena, “phenotype” is available only to biologists. Only in biology
is an organism’s life-plan written in its genes, and subject to alteration by changing
a letter here or a word there.
Geneticists do not shrink from applying the scientific method, but it is not their
primary tool. They have something special, something that solves problems that are
ineluctable through hypothesis and experimentation. Why is genetics so powerful?
Several reasons might be cited.
First, genetic analysis is unbiased, while hypothesis-driven research is not. In
principle, hypotheses are merely tools and there is nothing personal about them,
and no reason to attach a bias to them. But people like to be right about things, even
when being wrong might better serve the advancement of human understanding.
Time and again, scientists try to “prove the hypothesis” (and occasionally even
v
vi Preface
write that they have done so) though they have been taught from their earliest days
that the goal is to “test the hypothesis.”
Genetic inquiry is different. Either the phenotype exists or it does not; either the
phenotype is strong enough to map or it is not; either the mutation is found or it is
not. Finding a mutation may be disappointing insofar as it may reside in a gene with
well-known functions, in which case little progress may have been made. But there
is no question of bending the rules. The geneticist is an explorer. His or her prior
conceptions about how a biological system works will help in forming a decision
as to whether a particular phenomenon is worth investigating, and may also help in
deciding how to construct a screen. But preconceptions will not mislead.
Second, genetics is calculated to produce surprise. In foreswearing hypotheses,
there is a certain humility, an admission that biological complexity outstrips our
ability to guess at how a given process works. Instead, we surrender to the possibil-
ity of surprise, and even trust in surprise. Of course, it may be argued that hypothe-
sis-driven research also produces surprise. One devises experiments to test
hypotheses, and the outcome may run contrary to expectation. All the same, the
genetic approach does not even ask a question. It merely seeks exceptions to the
status quo. And some of those exceptions may be bizarre, or even undreamed of.
Third, genetics asks why things go wrong. It is a deconstructive process, rather
than one of invention. It must be granted that looking at the effects of damage is not
unique to genetics, but all the same, it is fundamental to genetics, and is a powerful
approach whenever it is applied in biology. By studying the effects of strokes,
tumors, and traumatic injuries, clinical neurologists and pathologists were able to
deduce the function of many parts of the human brain. For example, they inferred
that a “homunculus” must exist in the posterior frontal cortex (and close by it, a
second homunculus in the anterior parietal cortex), wherein each part of the body
is spatially reflected, so that a lesion might affect adjacent areas of the body: the
face, neck, arm, and trunk, for example, or the trunk and the legs and feet; but never
the face and feet without involvement of intermediate structures. Geneticists follow
much the same practice as neurologists, focusing intently on the effects of sponta-
neous mutations or those induced at random by mutagens, brought to their attention
because something has gone wrong. They are able to decipher the function of each
part of the genome, which contains its own “homunculus” just as the brain does,
but one that is enormously more fractured and complex. The proteins that are
required for limb development (or innate immune sensing, or any complex func-
tion) each have their physical representation in the genome, and though the corre-
sponding genes may be widely scattered, they can all be found through mutagenesis
and careful phenotypic screening.
Fourth, genetic conclusions are comparatively solid. The reliability of
genetic conclusions is derived from the reliability of the technology upon which
genetic research is based (the unbiased mapping of phenotypes to critical
regions, and ultimately, DNA sequencing). This is not to say that geneticists are
never wrong, or that there was never a case in which a phenotype was incor-
rectly attributed to a particular mutation. But such mistakes are rare. When
genetic data conflict with biochemical data, or data developed from immunological
Preface vii
assays, or data from cell transfection studies, or any combination thereof, the
genetic data are usually correct.
The stories told in this book are some of the most important in immunology.
Each begins with a phenotype and comes to a profound conclusion about cause. In
some cases autoimmunity was at issue; in others cancer; in others a failure to detect
or respond to infection. But in all instances, the biological function of a given pro-
tein or protein family was discovered. Finding the mechanism through which that
protein functions presents the next challenge, and in all cases, the challenge has yet
to be met in full. Ultimately, the geneticist must usually make hypotheses after all.
Usually he or she is not alone: the field has been opened to many other workers
once the key genetic advance has been made.
Reverse genetic methods are among the most powerful tools to be used in testing
these hypotheses. Again, the situation might be compared to that of the neuroscien-
tist, who creates brain lesions in experimental animals in order to test the function
of distinct parts of the brain, alone or in conjunction with one another. Reverse
geneticists, who deliberately target genes for destruction, attempt to test the func-
tion of particular parts of the genome. In both cases, nothing may be found, either
because of functional redundancy, or because the investigator simply does not know
what to look for. But at times, concrete and specific understanding is gained.
The interpretation of phenotypes is facilitated when there is a strong conceptual
framework within which to operate. This is certainly the case in immunology, a
relatively sophisticated science that has taught us quite a lot, though enormously
less than it has left to teach. We know of innate immunity and adaptive immunity;
we know of humoral immunity and cellular immunity. We know of antibody and
complement. And we know of T cells, B cells, T-regulatory cells, antigen-presenting
cells, natural killer cells, macrophages, and granulocytes. Each has a distinct role
to play in protecting us from infection, or conversely, in causing inflammatory dis-
ease. Mutations can make things go very wrong where every cell and protein just
mentioned is concerned. Yet we still lack a fully coherent understanding of exactly
why we reject cells from unrelated individuals yet tolerate the placental allograft.
We do not know why some among us develop autoimmunity while the majority
does not. We do not understand why all microbes are recognized (for some, recog-
nition receptors have yet to be found), and why some defy the immune response so
effectively even when they are detected. This is the perfect playground for a geneti-
cist: a desirable mixture of ignorance and understanding. And it is likely to remain
this way for a very long time.
Yes, all genes will soon be knocked out. But many knockout mutations will be
embryonic lethal, or will have other effects that mask the essential immunological
function of the proteins concerned. Others will present no obvious phenotype, not
because the gene in question has no function, but because we simply do not know
what to look for. There is no escape from starting with phenotype. Biologists will
always return to the phenotype-first approach.
We live at the dawn of a golden age of genetics, in which a phenovariant may be
seen in the morning and the causal mutation known by noon. Stories formally similar
to the ones presented here may soon be increasingly common, and we must all hope
viii Preface
that they will be. But it should not be forgotten that these particular discoveries—
whether in mice or in humans, most of them pursued before the respective genomes
were sequenced and some of them at a time when sequencing was performed
mostly manually—were heroic in their own time and have laid the foundation for
some of the most important concepts in immunology.
La Jolla, USA Bruce Beutler
Contents
Part I Immunodeficiency
The Forward Genetic Dissection of Afferent Innate Immunity.................. 3
B. Beutler, E.M.Y. Moresco
Genetic Analysis of Resistance to Infections in Mice:
A/J meets C57BL/6J ....................................................................................... 27
J.-F. Marquis, P. Gros
Host Defenses Against Human Papillomaviruses:
Lessons from Epidermodysplasia Verruciformis ......................................... 59
G. Orth
Innate Resistance to Flavivirus Infections and the Functions
of 2´-5´ Oligoadenylate Synthetases .............................................................. 85
T. Mashimo, D. Simon-Chazottes, J.-L. Guénet
Cmv1and Natural Killer Cell Responses to Murine
Cytomegalovirus Infection ............................................................................. 101
A.A. Scalzo, W.M. Yokoyama
Genetic Dissection of Host Resistance to Mycobacterium
tuberculosis: The sst1 Locus and the Ipr1 Gene ........................................... 123
I. Kramnik
Part II Self-Reactivity
Scurfy, the Foxp3 Locus, and the Molecular Basis
of Peripheral Tolerance .................................................................................. 151
M.W. Appleby, F. Ramsdell
Fevers, Genes, and Innate Immunity ............................................................ 169
J.G. Ryan, D.L. Kastner
ix
x Contents
Itchy Mice: The Identifi cation of a New Pathway
for the Development of Autoimmunity .......................................................... 185
L.E. Matesic, N.G. Copeland, N.A. Jenkins
TIM Gene Family and Their Role in Atopic Diseases ................................. 201
D.T. Umetsu, S.E. Umetsu, G.J. Freemen, R.H. DeKruyff
Index ................................................................................................................. 217