Complete Genetically Engineered Mice Handbook 1st Edition John P. Sundberg PDF For All Chapters
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Genetically
Engineered
Mice
Handbook
Research Methods for Mutant Mice Series
Series Editor
John P. Sundberg
edited by
John P. Sundberg
Tsutomu Ichiki
A CRC title, part of the Taylor & Francis imprint, a member of the
Taylor & Francis Group, the academic division of T&F Informa plc.
Published in 2006 by
CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
Genetically engineered mice handbook / edited by John P. Sundberg and Tsutomu Ichiki.
p. cm. -- (Research methods for mutant mice series)
Includes bibliographical references and index.
ISBN 0-8493-2220-0 (alk. paper)
1. Transgenic mice--Handbooks, manuals, etc. I. Sundberg, John P. II. Ichiki, Tsutomu. III. Series.
QH470.M52G463 2005
616'.027333--dc22 2005041899
Index .................................................................................................................303
1 Genetically Engineered
Mice: Past, Present,
and Future
John P. Sundberg, Tsutomu Ichiki,
Jerrold M. Ward, and Björn Rozell
TABLE OF CONTENTS
Mutant mice have changed from curiosities in the nineteenth century, being pri-
marily of concern to mouse fanciers,1 to become the premier animal model for
human diseases, mammalian genetics, and biomedical research in the twenty-first
century. Archives of spontaneously occurring mutations, a valued resource for over
fifty years, are being supplemented and supplanted by genetically engineered mice
(GEMs) created by transgenesis, targeted mutagenesis, inducible mutagenesis,
gene trap, and chemical mutagenesis methods at an overwhelming rate. Evaluation
of these mice to determine clinical and physiological deviations from normal for
a particular inbred strain (i.e., phenotyping) has become a major undertaking in
the evaluation of these new strains. Current methods to create, archive, distribute,
and phenotype mice were the focus of a meeting, “Pathology of Genetically
Engineered Mice: Large Scale Phenotyping of Mutant Mice,” held in October
2003 in Kumamoto, Japan. Leaders in the field presented the current strategies,
which are summarized in this book. An overview of the field is given here.
1
2 Genetically Engineered Mice Handbook
since the first successes in the early 1980s.2 Another important development, the
blastocyst-derived embryonic stem cells,3,4 later led to the technique of targeted
mutagenesis, whereby known genes could be inactivated using homologous
recombination of genes containing molecular tags (LacZ or neomycin cassettes) to
interfere with transcription of specific exons producing so-called gene “knock-outs”
or “hypomorphs” for those genes not totally inactivated.5,6 Many of these targeted
mutations resulted in phenotypes similar to human diseases, but equal numbers
had no phenotype or were embryonic or neonatal lethals. Stressing the system
under investigation sometimes revealed differences from the background strains.7
Inasmuch as embryonic or perinatal lethality are fairly common consequences of
targeted mutagenesis, alternate gene constructs were developed to study these
genes in adult animals.
Conditional mutagenesis or the so-called “gene switch” approaches were
subsequently developed using Cre-recombinase together with LoxP or Frt sites.
Furthermore, inducible systems, based on tetracycline (tet-on/off), or progester-
one antagonists, led to even greater refinements whereby genes could be activated
or inactivated by adding exogenous systems.8,9 In this manner, effects of gene
inactivation could be studied either throughout the organism in selected organs,
or even in part of an organ. The neomycin (Neo) gene often leads to a suppression
of the mutant allele, resulting in a phenotype not different from normal. Thus,
making a construct where the Neo cassette is flanked by LoxP sequences enables
local and restricted excision of the Neo gene in skin, thereby activating the
targeted allele, thus enabling the creation of mouse models of a selected number
of human genetic diseases.10–13
As a complement to the technique of targeted mutagenesis, gene trap methods
provide another tool to approach the problem of identifying novel genes within
the genome. Genetic constructs with marker sequences are used to immediately
map mutant gene loci once an interesting phenotype is produced.14,15 Different
modalities of the gene trap technique are available.16 Because many more genes
are coded for in the human and mouse genome than are currently known
(www.celera.com), other approaches were needed to augment the mutations
derived by targeted mutagenesis or that occurred spontaneously. Spontaneous
mutations occur at a frequency 1/100000 offspring, however, this is not enough
to achieve a saturation of mutations throughout the genome. To increase the
frequency of mutations, chemical mutagenesis, specifically using ethylnitrosourea
(ENU), randomly produces single base pair changes, and increases the mutation
rate 100-fold. These old protocols are now used in large-scale mutagenesis
projects, potentially providing a wealth of novel mutant mice that can subse-
quently have the mutant locus mapped and defined.17–24 A new version of this
technique uses ethylmethanesulfonate on embryonic stem cells25 with similar
results. Back-crossing the chimeric mice to C57BL/6 immediately provides a
rapid tool to map the mutant gene locus.
Contrary to the techniques employing homologous recombination (gene-driven
approach), the discovery of the chemically induced mutations are phenotype
driven (vide infra). This requires a setup whereby mutations affecting different
Genetically Engineered Mice 3
GENE MAPPING
Finding abnormal mice, at least those with dominant mutations, is often relatively
simple. Figuring out what the defects are and whether the lesions resemble those
found in human or domestic animal diseases is described below. Mapping the
mutant gene locus is relatively easy for single gene mutations. A variety of
methods and approaches is available. In mice, unlike humans, it is possible to
set up breedings between inbred strains carrying the mutated gene and different
strains carrying two copies of the wild-type gene. Recessive mutations will be
expressed in the second, F2 generation, from such an intercross. The mouse
genome can then be rapidly screened using simple sequence length polymorphism
(SSLP) and single nucleotide polymorphism (SNP) technologies with molecular
markers at regular intervals (15–20 cM).36,37 A shift in genes from 50 percent of
both inbred strains to the strain that originally carried the mutated gene indicates
linkage. The gene can be localized by refining this approach with additional
markers (saturation mapping) within the suspected interval. The gene can be
identified by sequencing through known genes in that interval, or positional
cloning of the gene, then creating targeted mutations of the gene or rescuing it
by transgenesis with the known gene or BAC clones containing the interval.36,38
The availability of anchored full-length mouse cDNA clones and other genetic
tools is of great help in determining candidate genes for positional cloning.
PHENOTYPING APPROACHES
Classic approaches to phenotyping utilize basic medical techniques, and these are
discussed in detail in several chapters in this book. Physical examination of the
normal and mutated mice may reveal obvious changes. Collection of blood, serum,
plasma, urine, and other body fluids can be analyzed using equipment modified
from human clinical pathology laboratories.47 Blood values for commonly used
strains are published.48,49 The Mouse Phenome Project (www.jax.org/phenome)
was created to actively obtain a wide variety of data on individual mouse strains
from researchers around the world and put them online.50 This is a major effort
to make these types of data on major inbred strains of mice freely available to the
biomedical research community.
Careful, systematic, and detailed necropsies of mutant and control mice at
defined ages with histopathology remain a standard for defining lesions. Com-
parative pathology between human and domestic animals provides insight into
whether the mutant mice are potential models for specific diseases or unique tools
to dissect the function of a gene or organ. Numerous textbooks were published
recently providing overviews on these methods and the types of lesions commonly
found in aging and mutant mice.51–54 Many Web sites are online and are constantly
Genetically Engineered Mice 5
being updated with similar information. How to access and use these are described
in detail in other chapters in this book. Approaches to setting up such phenotyping
programs are also now available.55
Very specialized equipment was developed for each organ system. Much
effort is being put into tools to better define neurological abnormalities in mice.52
The SHIRPA protocol was developed to provide a panel of clinical evaluations
and analytical tests to determine if mice had neurological abnormalities.56 These
are being adapted by many of the ENU programs worldwide as well as by startup
companies providing phenotyping services. Specialty books on various organ
systems are also being published.57–59
Because anatomic and clinical pathologists with mouse expertise are relatively
few and far between, there has been downscaling of traditional diagnostic equip-
ment with intense development of very sophisticated equipment to provide rapid,
high-throughput, low-labor information. X-ray machines, originally designed for
scanning electronic boards, work extremely well with mammography film to
provide flat-plate images of mice (www.faxitron.com).60 CAT scans, Pet scans,
MRIs, and other methods are now available to provide real-time, three-dimensional
images of mouse organs or to test physiologic parameters (www.scanco.ch,
www.imtekinc.com, www.optiscan.com, www.colinst.com). New technologies are
constantly under development.61–65
SUMMARY
The laboratory mouse is a domestic animal. Veterinarians, physicians, and bio-
medical researchers can now use both traditional technology and microanalytical
tools to evaluate mutant or experimentally manipulated mice to answer fundamental
medical and biological questions. The area is reviewed here to provide key refer-
ences and Web sites from which specific information and resources can be found.
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2 Sharing Research Tools:
The Laboratory Mouse
David Einhorn
TABLE OF CONTENTS
1980.....................................................................................................................12
Cold Spring Harbor.............................................................................................13
The “Harvard Mouse”.........................................................................................14
Cre-Lox ...............................................................................................................14
NIH and the Memoranda of Understanding (MOU) .........................................15
NIH Policy ..........................................................................................................16
Issues Raised in NIH Sharing Policy .................................................................18
Definition of Research Tools ..................................................................18
Reach-Through Rights ............................................................................18
Patenting Mice ........................................................................................20
Sharing Mice within Academia ..........................................................................20
Jackson Mouse Repository .................................................................................21
The Research Exemption ....................................................................................22
References ...........................................................................................................24
This chapter examines the historic change in perception of the laboratory mouse
from that of a research tool, freely exchanged among scientists, to its being
considered intellectual property. This transformation was triggered by the con-
fluence of three milestones: (1) the U.S. Supreme Court decision allowing
patenting of genetically altered life; (2) passage of the Bayh–Dole Act; and
(3) development of technologies to genetically engineer mice. Three examples
are discussed that illuminate the tension between the scientific sharing ethic and
the demands of commercialization: (1) the P53 knock-out mouse, (2) the “Harvard
Mouse” Patent, and (3) the Cre-lox technology. We consider how the National
Institutes of Health (NIH) dealt with this tension and review its policy statement,
“Sharing Biomedical Research Resource: Principles and Guidelines for Recipi-
ents of NIH Research Grants and Contracts.” “Reach-through” and other prob-
lematic provisions in licenses and material transfer agreements are addressed. As
a model, The Jackson Laboratory’s approach to facilitating the availability and
distribution of mouse strains is considered. From the overall perspective on how
11
12 Genetically Engineered Mice Handbook
the patent system may inhibit research in academia, we also consider a recent
judicial decision regarding the “experimental use” exemption.
The remarkable advances in molecular biology over the past quarter century
have been a challenge to the traditional ethic in academia of encouraging the free
flow of ideas and information. Universities and nonprofit research institutions
(hereafter “Academia”) have always viewed themselves as fundamentally differ-
ent from for-profit companies (hereafter “For-Profits”), inasmuch as the raison
d’être of Academia is research and education and not the pursuit of lucre on
behalf of shareholders. However, the tremendous advances in biology, and the
commercial opportunities created in the new industry of biotechnology, have
presented a challenge to the tradition of openness and freedom of exchange in
Academia, because efforts to protect and exploit intellectual property developed
in Academia through patenting or licensing inevitably involve some secrecy and
restriction of availability.1
The Jackson Laboratory (hereafter “Jackson”) is a nonprofit research institu-
tion situated on an idyllic island in the state of Maine. As well as being a
preeminent mammalian genetics research and educational institution, Jackson has
been for many years and continues to be the most important source in the world
for strains of laboratory research mice. For 75 years, Jackson has been identifying
and characterizing spontaneous mutant mice in its colonies, importing spontane-
ous mutant mice from scientists worldwide, creating congenic strains carrying
these mutations, developing inbred and other mouse lines, and in the past decade
serving as an international repository of strains of genetically engineered mice
(also called induced mutant mice) developed by scientists from virtually every
major research institution in the world. The laboratory mouse, and more recently
the genetically altered mouse, is generally understood to be the single most
important research tool for studying human disease. It is therefore not surprising
that genetically altered mice have been the trigger points of public debate over
research access and commercialization, with Jackson a principal player in the
drama. To understand this debate we need to take a short historical journey.
1980
The year 1980 was significant in this story. First, it was the year the U.S. Supreme
Court decided Diamond v. Chakrabarty.2 Before that landmark decision, there
was a widely accepted legal assumption that living organisms were unpatentable,
because they were considered products of Mother Nature and not of man. In
Chakrabarty, the Supreme Court (in a sharply divided 5–4 decision) ruled that a
living genetically engineered microorganism was patentable subject matter, and
that the litmus test of patentability was not between living and nonliving matter,
but between products of Nature and “anything under the sun made by man.”
That same year of 1980, the U.S. Congress passed the Bayh–Dole Act.3 Prior
to Bayh–Dole, the federal government owned, but rarely patented or commer-
cialized, inventions that arose from federally funded research in Academia. Out
Sharing Research Tools 13
of realization that the federal government was not suited to further develop
technologies, Bayh–Dole allowed Academia to retain ownership of inventions
developed with federal funds, the expectation being that the turnover of ownership
would spur the commercialization of inventions that would in turn benefit the
public with new drugs and therapies.
The third event at the start of the 1980s was the development of recombinant
DNA technology, which involves the altering of the genetic information of cells
by combining the DNA of different organisms. In the case of the mouse, this
allows for the creation of transgenic mice. The term “transgenic mouse” tech-
nically means a mouse that has a foreign gene introduced randomly into all of
its cells, but it has commonly been used to describe any genetically altered
mouse. This technology has been succeeded by the ability to target specific genes
to “knock-in” or “knock-out” activity of these genes in mice as well as many
other technologies, such as the so-called “gene switch” systems where genes
can be turned on or off in specific anatomic sites. These new technologies have
made the laboratory mouse an even more powerful research tool for studying
human diseases.
mice, with the assurance by Jackson that these new models would be made available
to the whole research community with as few restrictions as possible.
CRE-LOX
While the resistance by Academia to the license terms for Oncomouse® was still
unresolved, another technology, Cre-lox, was developed and patented by Dupont.6
Cre-lox proved to be a very powerful and ubiquitously used technology because
it allowed a researcher to knock out genes on a tissue-specific basis. This tech-
nology involves flanking the gene of interest with Lox sites, and when Cre is
introduced with a tissue-specific promoter, it deletes the flanked DNA. Cre-lox
allows researchers to knock out genes in selective tissues when otherwise knock-
ing out all expression would be embryonically lethal. Later developments allowed
a researcher to turn gene expression on and off at will. Dupont’s terms for a
license to use and share mice made with Cre-lox included an advance view of
Sharing Research Tools 15
any publications resulting from using the technology and unspecified royalties
on any products resulting from the use of mice containing Cre or Lox.
recipient institutions of federal grants. The MOUs provide that Dupont shall under
separate license agreements make the patent rights available to nonprofit grantees
“... in accordance with the terms and conditions …” of the MOUs. The MOUs
were and remain a unique example of a resolution by government, Academia,
and a company addressing the tension between availability of, and proprietary
rights to, research tools.9
NIH POLICY
No doubt prompted by the issues surfaced by the P53 Mouse, “Harvard Mouse”,
and Cre-lox controversies, Dr. Varmus requested that a Working Group of the
Advisory Committee to the Director look into concerns over the dissemination
and use of unique research tools, the competing interests of the owners and users
of these tools, and how the NIH might provide a policy response. The Report of
the Working Group found that patent and licensing restrictions could stifle the
broad dissemination of research tools and thereby frustrate basic research and
the development of products for the benefit of public health. The Report found,
on the other hand, that reasonable restrictions might be necessary to protect
intellectual property rights and preserve incentives for further research and com-
mercial development. The challenge, of course, was to balance these competing
interests. After submission for public comment of a draft policy, the NIH adopted
a final document entitled “Sharing Biomedical Research Resources: Principles
and Guidelines for Recipients of NIH Research Grants and Contracts” (hereafter
“NIH Sharing Policy”),10 setting forth four basic principles.