Download Genomics, Proteomics and Vaccines

Genomics, Proteomics
and Vaccines
Editor
Guido Grandi
Chiron Vaccines,
Siena, Italy
Genomics, Proteomics
and Vaccines
Genomics, Proteomics
and Vaccines
Editor
Guido Grandi
Chiron Vaccines,
Siena, Italy
Copyright # 2004 John Wiley & Sons, Ltd. The Atrium, Southern Gate, Chichester,
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ISBN 0 470 85616 5
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Contents
Preface
xi
List of contributors
xix
PART 1: INTRODUCTION
1
Vaccination: Past, Present and Future
3
Maria Lattanzi and Rino Rappuoli
1.1
1.2
1.3
1.4
1.5
2
Introduction
Vaccination: the past
Vaccination: the present
Vaccination: the future
Conclusion: the intangible value of vaccination
References
Bioinformatics, DNA Microarrays and Proteomics in Vaccine
Discovery: Competing or Complementary Technologies?
3
4
6
12
14
15
23
Guido Grandi
2.1
2.2
2.3
2.4
2.5
Introduction
From genome sequence to vaccine discovery
A case study: the anti-meningococcus B vaccine
Comparison of the three approaches
Conclusions: a ‘nomics’ approach to vaccine discovery
References
Genomics, Proteomics and Vaccines edited by Guido Grandi
# 2004 John Wiley & Sons, Ltd
ISBN 0 470 85616 5
23
25
28
34
37
40
vi
CONTENTS
PART 2: TECHNOLOGIES
3
Genome Sequencing and Analysis
45
Hervé Tettelin and Tamara Feldblyum
3.1
3.2
3.3
3.4
4
Introduction
Genome sequencing
Genome analysis
Conclusion
References
Understanding DNA Microarrays: Sources and Magnitudes
of Variances in DNA Microarray Data Sets
45
46
60
65
65
75
She-pin Hung, Suman Sundaresh, Pierre F. Baldi and
G. Wesley Hatfield
4.1
4.2
4.3
4.4
4.5
5
Introduction
DNA array formats
Data analysis methods
Sources and magnitudes of noise in DNA microarray experiments
Conclusions
Acknowledgements
References
The Proteome, Anno Domini Two Zero Zero Three
75
76
79
84
97
100
100
103
Pier Giorgio Righetti, Mahmoud Hamdan, Frederic Reymond
and Joël S. Rossier
5.1
5.2
5.3
5.4
5.5
5.6
5.7
5.8
Introduction
Some definitions
What methods exist to tackle the proteome complexity?
Quantitative proteomics
Pre-fractionation in proteome analysis
Multi-dimensional chromatography
Protein chip arrays
Imaging mass spectrometry
Acknowledgements
References
103
105
107
112
117
120
123
126
127
127
CONTENTS
6
Mass Spectrometry in Proteomics
vii
135
Pierre-Alain Binz
6.1
6.2
6.3
6.4
7
Introduction
MS technology
Principle of protein identification based on MS data
Proteomics workflows
References
High Throughput Cloning, Expression and Purification
Technologies
135
136
147
155
155
171
Andreas Kreusch and Scott A. Lesley
7.1
7.2
7.3
7.4
7.5
7.6
Introduction
Gene cloning
Protein expression
High-throughput protein purification
Validation of the pipeline and outlook
Conclusion
References
171
172
174
175
178
179
180
PART 3: APPLICATIONS
8
Meningococcus B: from Genome to Vaccine
185
Davide Serruto, Rino Rappuoli and Mariagrazia Pizza
8.1
8.2
8.3
9
Meningococcus, a major cause of bacterial meningitis
Group B meningococcus as an example of reverse vaccinology
Conclusions
References
Vaccines Against Pathogenic Streptococci
185
190
200
201
205
John L. Telford, Immaculada Margarit y Ros, Domenico Maione,
Vega Masignani, Hervé Tettelin, Giuliano Bensi and Guido Grandi
9.1
9.2
9.3
9.4
9.5
Introduction
Comparative genomics of streptococci
A vaccine against group B streptococcus
A vaccine against group A streptococcus
Conclusions
References
205
206
208
215
218
219
viii
10
CONTENTS
Identification of the ‘Antigenome’ – a Novel Tool for Design
and Development of Subunit Vaccines Against Bacterial
Pathogens
223
Eszter Nagy, Tamás Henics, Alexander von Gabain
and Andreas Meinke
10.1
10.2
10.3
10.4
10.5
10.6
10.7
11
Introduction
Small DNA insert libraries – a tool to cover a pathogen’s ‘antigenome’
Proper display platforms
Selected human sera to provide imprints of pathogen encounters
Cognate antibodies reveal the ‘antigenome’ of a pathogen
How to retrieve from the ‘antigenome’ the candidate antigens for vaccine
development
Summary and discussion
References
Searching the Chlamydia Genomes for New Vaccine
Candidates
223
227
230
231
234
235
237
239
245
Giulio Ratti, Oretta Finco and Guido Grandi
11.1
11.2
11.3
11.4
12
Old problems and new perspectives for chlamydial vaccines
Post-genomic approaches
Genomic screening results
Concluding considerations
References
Proteomics and Anti-Chlamydia Vaccine Discovery
245
250
251
262
263
267
Gunna Christiansen, Svend Birkelund, Brian B. Vandahl
and Allan C Shaw
12.1
12.2
12.3
12.4
13
Introduction
Proteome analysis
Proteomics as a complement for genomics
Benefits that proteomics provide for vaccine development
References
267
269
277
279
280
Proteome Analysis of Outer Membrane and Extracellular
Proteins from Pseudomonas aeruginosa for Vaccine Discovery 285
Stuart J. Cordwell and Amanda S. Nouwens
13.1
Introduction
285
CONTENTS
13.2
13.3
13.4
13.5
Index
Membrane proteins in P. aeruginosa
Extracellular proteins in P. aeruginosa
Immunogenic proteins and vaccine discovery
Conclusions
References
ix
286
292
296
298
299
305
Preface
I have always been fascinated and intrigued by the history of human cultures
and civilizations and how they have emerged and disappeared since 11 000
B.C., the date corresponding to the beginning of village life and the start of
what geologists term the Recent Era.
In mathematical terms, the complex function describing how prosperity of
a given society has varied with time is defined by several variables, often
interlinked. These include the availability of domesticable plant and animal
species (indispensable to trigger the passage from a hunter-gatherer to an
agricultural lifestyle), climate, richness of the territory occupied and the
appearance of individuals with strong personality and leadership. An additional
important variable, which is often surprisingly neglected even in history textbooks, is human susceptibility to microbes and infectious diseases. Indeed,
epidemics caused by a variety of human pathogens have often been associated
with, if not responsible for, major changes in human history. The eminent
bacteriologist Hans Zinsser once wrote: ‘Soldiers have rarely won wars. They
more often mop up after the barrage of epidemics. And typhus with his brothers
and sisters, – plague, cholera, typhoid, dysentery, – has decided more campaigns than Caesar, Hannibal, Napoleon, and the inspectors general of history’.
There are several well documented examples supporting Zinsser’s position and
highlighting how the fate of human populations has often been dictated by
epidemics.
In 430 B.C., Sparta and its Peloponnesian allies engaged in a bloody war
against the Athenians, whose culture and power were at their height at that
time. The Spartan invasion forced an uncounted number of villagers to find
protection within Athens’ city walls. As the war’s great chronicler Thucydides
wrote, the crowded city was soon scourged by a plague that killed a huge
Genomics, Proteomics and Vaccines edited by Guido Grandi
# 2004 John Wiley & Sons, Ltd
ISBN 0 470 85616 5
xii
PREFACE
number of Athenians. The plague weakened Athens to such an extent that,
despite its great naval power, it took more than thirty years to defeat Sparta,
and the city never regained its political and cultural glory.
The dissolution of the great Roman empire has always been attributed to the
decadence of the pagan lifestyle that led people to indulge in the pleasures of
life rather than to protect the empire’s borders from barbarian invasions.
However, historians seldom highlight the fact that from the second century on,
new diseases appeared in Europe with increasing frequency and devastation.
The Oronius, Galen and Cyprian plagues (so called from the names of the
chroniclers who described them), together with the accompanying famines,
severely reduced the empire’s population and abated its morale. In 452 A.D.,
when the Huns, headed by their ferocious general Attila, reached the gates of
Rome, instead of entering the city, they halted and fell back. The withdrawal
has often been attributed to the persuasive power of Pope Leo I, but, in fact, a
severe epidemic, most likely smallpox, was raging within Rome, whose population, after subsequent epidemics, was soon to be reduced to a few thousand
people. The Western Empire (in the fourth century, the Roman Empire had split
into the Western Empire with its capital in Rome and the Eastern Empire with
its capital in Costantinople) finally crashed in 476 A.D.
During the following century, the great eastern emperor Justinian was
reconquering western territories. By 542 A.D., he had taken back much of
North Africa, Sicily and part of Spain. However, in the middle of his glorious
campaigns the first indisputably reported bubonic plague broke out, causing
one of the worst population crashes in human history. The Byzantine historian
Procopius described it as ‘a pestilence by which the whole human race came
near to being annihilated’. When the bout of plague ended, 40 percent of the
people in Constantinople had died. Plague returned frequently until 590 A.D.
and localized outbreaks occurred for another 150 years, halving human populations in many parts of the world. The Western Empire was never conquered
again.
In the 14th century, Europe was experiencing a period of cultural growth and
expansion. The population continued to grow; Crusades and trade routes put
Europe in contact with the Middle East, Arabia and China, favouring increasing
literacy and promoting what would have been later called Renaissance. This
flourishing expansion was dramatically slowed down by the worst disaster in
human history, the second bubonic plague pandemic, the Black Death. It was
brought into Europe in the summer of 1347 by Genoese traders who contracted
it in the Crimean city port of Kaffa when it was under siege by Janibeg, Khan
of Tartars (the legend says that before withdrawing because plague had started
killing the Tartars, Janibeg ordered plague-infected corpses to be catapulted
into Kaffa, thus spreading the epidemic within the city walls). The disease
PREFACE
xiii
rapidly reached all the main cities in Europe and it was estimated that up to one
half of the people in Europe, North Africa and Asia perished during the long
epidemics. All aspects of European life, from art to commerce, were severely
affected and the post-plague labour shortage was one of the main reasons for
European involvement in the slave trade.
The conquest of the Americas is usually attributed to the braveness, and
sometime ferocity, of the Spanish conquistadores and of the European immigrants who succeeded in defeating the aggressive native populations. However,
when Cortés attacked with his 300 soldiers the Aztec capital Tenochtitlán, he
found the city, originally inhabited by 300,000 people, slaughtered by smallpox
brought in by one of his African slaves who was affected by a virus strain to
which Cortés’ soldiers were immune. In his battle report, Cortés wrote, ‘A man
could not set his foot down unless on the corpse of an Indian’. Less than fifty
years after Cortés arrived in Mexico, of the original 30 million people, only 3
million survived, 18 million having been killed by smallpox alone. Similarly,
80% of the Inca population in Peru disappeared in the 200 years following the
Spanish invasion.
In North America, the natives suffered similar slaughter by pathogens
brought into their territories by European invaders. As in Latin America, it was
mainly smallpox and measles that kept killing Amerindians, reducing by about
90% the original population of 100 million. As a result, Europeans succeeded
in imposing their languages, religions, political power and what the historian
Alfred Crosby called ecological imperialism, whereby most of the original
ecosystems were completely europeanized by imported plant and animal
species.
Until the middle of the last century, infectious diseases were the first cause of
death in humans; they continued to influence human cultures and civilizations
and favoured the expansion of stronger, more immune-protected populations at
the expense of weaker, immune-susceptible ones.
In the second half of the 20th century, two extraordinary revolutions occurred,
which had no precedents in history in terms of prolongation and amelioration
of human life: the large scale availability of antibacterial drugs and the practice
of mass vaccination. For the first time, bacterial infections could be effectively
defeated and deadly viral and bacterial diseases such as smallpox, polio, rabies,
tetanus and diphtheria could be prevented. In the developed countries, where
antibiotics and vaccines were discovered and readily available, mortality rates
from infectious diseases rapidly declined and lost their first ranking in the
cause-of-death list, being overtaken by cancer and cardiovascular diseases.
Smallpox global vaccination eradicated this killer virus, which now exists in
only a few, well-contained laboratories, and anti-polio and anti-measles
vaccines are expected to have similar effects within the next few years.