Advances in Cancer Research -

Advances in Cancer Research (eBook)

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2007 | 1. Auflage
450 Seiten
Elsevier Science (Verlag)
978-0-08-055651-2 (ISBN)
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The Advances in Cancer Research series provides invaluable information on the exciting and fast-moving field of cancer research. This volume presents outstanding and original reviews on a variety of topics including RUNX Genes in Development and Cancer, The RNA Continent, The c-myc Promoter, Designer Self-Assembling Peptide Nanofiber Scaffolds for Study of 3-D Cell Biology and Beyond, and Dendritic Cells in Cancer. Immunotherapy
The Advances in Cancer Research series provides invaluable information on the exciting and fast-moving field of cancer research. This volume presents outstanding and original reviews on a variety of topics including RUNX Genes in Development and Cancer; The RNA Continent; The c-myc Promoter; Designer Self-Assembling Peptide Nanofiber Scaffolds for Study of 3-D Cell Biology and Beyond; and Dendritic Cells in Cancer. Immunotherapy

Front Cover 1
Advances in Cancer Research 4
Copyright Page 5
Contents 6
Contributors 10
Chapter 1: Foundations in Cancer Research The Turns of Life and Science 11
I. To Write or Not to Write? 12
II. Boys and Resurrection of Czechoslovakia 12
III. University 13
IV. Virogenic Cells and Provirus Integration 16
V. Virus Rescue 20
VI. Prague Spring 1968 25
VII. Dark Years 27
VIII. Partial Thawing and Molecular Biology 30
IX. Silencing the Provirus and the Red Power 33
X. Epilogue 36
References 39
Literary Works 39
Scientific Works 39
Chapter 2: RUNX Genes in Development and Cancer: Regulation of Viral Gene Expression and the Discovery of RUNX Family Genes 43
I. Introduction 44
II. EC Cells (Teratocarcinoma Stem Cells): The Biological Model That Led to the Identification of PEBP2 46
III. Infection of EC Cells with Retroviruses 47
IV. Infection of EC Cells with Py 48
V. Isolation and Analysis of PyEC Mutants 49
VI. Isolation of PyTr Mutants 49
VII. The Molecular Implications of PyFL and PyNB Mutants 52
VIII. Dissection of the Py Enhancer 53
IX. Developmental Regulation of Py Enhancer Subfragments in F9 and dF9 Cells 54
X. Responsiveness of Py Enhancer a Element to Activated Ras and TPA 56
XI. Identification of PEA2/PEBP2 56
XII. Why We Decided to Study PEBP2/RUNX Further? 57
XIII. Purification of PEBP2 Revealed That It Is a Heterodimer Composed of Two Subunits 58
XIV. cDNA Cloning of PEBP2alphaA1 61
XV. cDNA Cloning of PEBP2beta 63
XVI. Identification of the Runt Domain: Comparison of Drosophila Runt, Human AML1, and Murine PEBP2alphaA 63
XVII. Identification of the CBF and cDNA Cloning of CBFbeta 65
XVIII. Involvement of PEBP2beta/CBFbeta in Human Leukemia: cDNA Cloning of the inv(16) Chimeric Gene 66
XIX. Discovery of RUNX3 67
XX. RUNX Genes in Different Organisms: Evolutionary Conservation 70
XXI. Disruption of Runx1 and Hematopoiesis 70
XXII. Disruption of Runx2 and Osteogenesis 71
XXIII. Knockout Phenotype of Runx3: Gastric Cancer Tumor Suppressor 72
XXIV. The Knockout Phenotype of Runx3: Regulation of Axonal Projections of TrkC-Expressing DRG Neurons 74
XXV. Knockout Phenotype of Runx3: CD4 Silencer 74
XXVI. Knockout Phenotype of CBFbeta/PEBP2beta 75
XXVII. Perspectives 75
XXVIII. Conclusion 77
Acknowledgments 77
References 78
Chapter 3: The RNA Continent 87
I. Introduction 88
II. Which Technique Is Suitable to Analyze Mammalian Transcriptome? 89
III. CAP Trapper and Full-Length cDNA Cloning System 91
IV. CAGE and GIS/GSC Ditags 94
V. The Structure of the FANTOM Datasets 95
VI. The Landscape of the Mouse Transcriptome: ncRNA, Transcription Forest, and Transcription Desert 96
VII. Abundant Natural Antisense Transcripts and Their Biological Significance 100
VIII. Interesting Features of the Mouse Transcriptome 101
IX. CAGE Tag and Promoter Analysis: The Diversity of Transcription Regulation 102
X. Alternative Usage of the Promoters: 5' Variation and 3' UTR Promoter 104
XI. Characteristics of the CpG Island and Bidirectional Promoters Revealed by CAGE Analysis 105
XII. Summary of the Physical Map of the RNA Continent 105
XIII. The Functional Aspect of the RNA Continent in Cancer Research 106
XIV. miRNA and Other Small RNAs in Cancer 106
XV. Epigenetics and ncRNA in Carcinogenesis 109
XVI. The Telomerase RNA Component and Small Nucleolar RNA 110
XVII. Recently Characterized Functional ncRNAs in Mammalian Cells 111
XVIII. Conclusion: Functional RNA and Cancer 112
Acknowledgment 113
References 113
Chapter 4: The c-myc Promoter: Still MysterY and Challenge 123
I. Introduction 124
II. c-Myc: Transcription Factor and Oncogene 124
A. c-Myc Function and Biology 124
B. c-myc Expression 127
III. Regulation of the c-myc Promoter 128
A. The c-myc Locus 128
B. The c-myc Promoter Structure 131
C. Regulation Levels of c-myc Transcription 132
D. Chromatin Structure 156
E. c-Myc Autosuppression 161
IV. Control of the c-myc Promoter 162
A. Transcription Factors That Directly Bind to the c-myc Promoter and Their Partners 162
B. Transcription Factors That In Vivo Occupy the c-myc Promoter 225
C. Other Transcription Factors That Regulate the c-myc Promoter 234
D. Additional Transcription Factors That Directly Bind to or/and In Vivo Occupy the c-myc Promoter 239
E. Signal Transduction Pathways 244
F. Deregulation of the c-myc Promoter in Burkitt's Lymphoma 255
G. c-myc as Target for Anticancer Therapy 259
V. The c-myc Promoter: Black Box and.Enigma? 262
A. Feedback Loops 262
B. A Concept for Regulation of the c-myc Promoter 264
VI. Summary and Perspectives 278
Acknowledgments 279
References 279
Chapter 5: Designer Self-Assembling Peptide Nanofiber Scaffolds for Study of 3-D Cell Biology and Beyond 345
Prologue 347
I. Introduction 350
II. 2-D or Not 2-D 350
III. Micro- and Nanoscales, Why They Are Important? 351
IV. The Ideal Biological Scaffolds 354
V. Discovery of Self-Assembling Peptide Scaffolds 354
VI. Self-Assembling Peptide Nanofiber Scaffolds 355
VII. Dynamic Reassembly of Self-Assembling Peptides 356
VIII. Kinetics of Nanofiber Reassembly and a Plausible Reassembly Process 359
IX. Self-Assembling Peptides Nanofiber Scaffold 3-D Cell Culture 361
X. Designer Peptides Scaffold 3-D Cell Cultures 362
XI. Designer Peptide Scaffolds for Bone Cells and 3-D Migration 366
XII. Why Designer Self-Assembling Peptide Scaffolds? 366
XIII. Beyond 3-D Cell Cultures 368
XIV. Concluding Remarks 369
Acknowledgments 369
References 369
Chapter 6: Dendritic Cells in Cancer Immunotherapy 373
I. Dendritic Cell Biology 374
A. Human DC Origin and Subsets 374
B. DC Function in Healthy Individuals 374
C. DCs in Patients with Cancer 376
D. The Immune Response in Cancer Patients 378
II. DCs and Their Use in Immunotherapy 378
A. DC Type 380
B. DC Differentiation and Activation 381
C. Antigen Choice 382
D. Antigen Loading 384
E. Vaccine Administration 384
F. Immunological Responses 385
G. Clinical Responses 386
III. Future DC Vaccines 387
A. DC Activation 388
B. DC Cotransduction 388
C. DC Gene Silencing 389
D. Targeting DCs In Vivo 390
E. Patient Selection and Timing of Vaccination 390
F. DC Vaccines Combined with Other Immunotherapies 392
G. DC Vaccines Combined with Conventional Treatment 396
IV. Conclusion 399
Acknowledgments 400
References 400
Index 419

Foundations in Cancer Research The Turns of Life and Science


Jan Svoboda    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic

Abstract


This chapter provides a personal insight into the scientific and social atmosphere in former Czechoslovakia. It covers the period of the rise of Hašek's immunologic school and application of immunologic tolerance to Rous sarcoma virus (RSV) heterotransmission. These approaches permitted establishment of a new model of mammalian cells transformed by RSV (virogenic XC cells), where the noninfectious viral genome was kept indefinitely as new genetic information (provirus). RSV was rescued from nonpermissive mammalian cells by fusion (complementation) with permissive chicken fibroblasts; this opened the way to understanding virus nonpermissiveness. Mammalian cells transformed by the reverse transcript of v-src mRNA were characterized, and the resulting provirus was shown to be highly oncogenic for chickens and to carry tumor-specific transplantation antigen. Other areas covering epigenetic reversion of RSV-transformed cells and long-term persistence of chicken leucosis viruses in foreign avian species are discussed.

Comme Sodome et Gomorre puissez tomber en soulfre en feu & abysme, en cas que vous ne croyez fermement tout ce que je vous racompteray en ceste presente chronicque.

Rabelais, F.: Gargantua and Pantagruel

Like those of Sodom and Gomorrah, may you fall into sulphur, fire and bottomless pits, in case you do not firmly believe all that I shall relate unto you in this present Chronicle.

Rabelais, F.: Gargantua and Pantagruel (translated by Sir Thomas Urquhart of Cromarty and Peter Antony Morfeus)

I To Write or Not to Write?


Since I received the invitation from George Klein to write my recollections, I have been postponing my final decision for 12 years. Several factors influenced my hesitation. I did not feel old enough to undertake such an enterprise, but unfortunately I had been learning about departures, either physical or mental, of my colleagues who were younger than me. The biological clock is ticking in everybody, and the longer the distance from past events, the worse their memory is kept.

In fact, I am going to write about a nonexistent country, Czechoslovakia, which was dissolved at the beginning of 1993, in the absence of any referendum, and which gave rise to the Czech Republic and Slovakia. However, strong ties among intellectuals of both newly established twin countries (who, according to my knowledge, would have preferred to stay together) remained viable and even formalized into joint scientific societies.

Encountering Western colleagues, we often discussed the unpredictable turns of the fate of this country, which at first glance appeared to be fatal for its culture and science. However, this was finally modified and regulated by our national sense of humor, heresy, and free thinking, traditions deeply rooted in our culture. I realized that despite the fact that some of the escapes from and solutions to absurd situations look strange to straightforward Anglo-American thinking, they bemused and sometimes even attracted the listeners. This aspect represents an additional excuse for writing further pages.

II Boys and Resurrection of Czechoslovakia


Being a boy after the end of Second World War was a great privilege for several reasons. At the age of about 10 years, I was not deeply marked by the Nazi occupation like my older mates, who were expelled from the universities and in many cases sent to forced labor. The first 3 years after the liberation of the country in 1945 were extraordinarily fruitful and inspiring. There was general enthusiasm and willingness to catch up again with the civilized world. There was a plurality of views, a richness of information from both the East and West, and many opportunities to learn about and love nature—being a boy scout—or to try to understand human thinking by joining discussion clubs or the academic YMCA. To me it has been highly attractive to collect natural objects and to try to learn about their origin or function. I loved amphibians and to some degree also snakes (as viper) that I bred at home. These years formed my generation, which later had to live, for such long years, out of this crop of these seasons.

However, disaster was looming and fell in February 1948 as a communist coup d'état. Boys at the lyceum were not affected directly, but the freshly released high-school graduates who in spring tried to enter university often reappeared with pale faces, commenting on their nonadmission simply: “La politique.”

However, for younger boys, the situation also became more difficult. Good teachers started to make far less comments and some of them invited selected students to their homes to discuss history and other topics freely. Having reached the last year of the lyceum, I learnt that I would not be recommended to enter any university. Being educated in the spirit of liberalism by my father and inclined to comment on what was going on, I finally faced real trouble. Several factors had been involved, but the most peculiar one stemmed from my friendship with one of my classmates. He had become seriously ill, and I taught him what he missed at school, for free of course, just on a friendly basis. By such occasion, I was also commenting critically public affairs. When he recovered, he converted to orthodox communism and became a leading person of the Party at school. Evaluating me, he postulated that although I was a good human being, I was an enemy of the working class. Such is, sometimes, the end of an open mind.

Again, the opportunity to study fortunately came about in 1951, when the political pressure was decreasing. Finally, I got notice that there was a chance for me to enroll, not in the humanities or at the highly desirable medical faculty, but with two provisions. The first was to get excellent notes in all subjects, which was against my mind and nature, so that I had to strongly force myself to comply with this unpleasant goal. The second condition was easier and involved labor work at the so-called Constructions of Youth, which included just digging and digging, however with a beautiful view of the hills of central Slovakia.

III University


Vždyt' také je mnohem větší nebezpečenství při koupi nauk než při koupi jídel.

Platon: Protagoras, aneb o výchově a občanské zdatnosti

For there is far greater peril in buying knowledge than in buying meat and drink.

Plato: Protagoras (translated by Benjamin Jowett)

Avšak správná filosofie a věda žádá pro všecky obory, aby lidé myslili, aby nastřádali co nejrozsáhlejších zkušeností (indukce), aby pozorovali a srovnávali všecko, co dáno v přítomnosti a minulosti, a aby své výsudky ze zkušenosti ověřovali zkušeností další, aby se nedostali dedukováním z malé zkušenosti, dedukováním ukvapeným, do říše fantastiky.

Masaryk, T. G.: Světová revoluce za války a ve válce 1914–1918

However, the true philosophy and science requires of all its branches to make people think, to let them accumulate all possible experience (induction), to make them observe and compare all of the present and the past, and to make them verify the conclusions drawn from their experience by the new one, not to let them get, due to deducing from too little or too hasty experience, into the world of fantasy.

Masaryk, T. G.: The World Revolution during and in the War, 1914–1918

Finally, I safely matriculated at the Faculty of Science of Charles University that offered my particular choices. In those days, biology was taken as a preferential subject, thanks to Lysenkoism, which for ideological reasons was implemented as the leading genetic teaching. However, in contrast to the humanities and social sciences, professors who did not fit with the forced ideological views were not removed but silenced. They were—even by their mere presence—a reminder that there was a wealth of genetic knowledge based on the Mendelian laws. I should add that in secondhand bookshops, one could still find books dealing in detail with classical genetics, and these became the source of solid information to any one wanting to pay attention to them.

From the beginning, I should have been interested in cytology, which, unfortunately, was viewed only as a morphological discipline. I got essential training in methods of plant anatomy; but in those days, there was almost no way to grow and influence living plant cells. Therefore, I requested and succeeded to get volunteer training in animal tissue culture in the laboratory of cell metabolism created by Dr. Keilová at the Academy of Sciences. This laboratory was interested in the study of possibly differing metabolic requirements between tumor and normal cells. I easily fell in love with tissue culturing and acquired my first experimental experience with the characterization of the growth properties and morphology of tumor cells. A great stimulus for my activity was represented by the arrival of a highly motivated, but to some degree eccentric, Ph.D....

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