Part 1 Introduction to modular organization of the networks of gene functions and cancer
Chapter 1 Systems biology of cancer progression
Multi-modular molecular networks of cancer progression depict heterogeneity in genetic and epigenetic alterations
Driver versus passenger alterations
Role of the microenvironment in cancer progression
Chapter 2 Lessons from cancer genome sequencing
Next-generation sequencing technologies
Sequencing template preparation
Sequencing through DNA observation
Analysis of sequencing information
Single nucleotide variations
Somatic mutations and inheritance
Cancer genome sequencing strategies
Single nucleotide polymorphism profiling
Chapter 3 Application of bioinformatics to analyze the expression of tissue-specific and housekeeping genes in cancer
Genomic technology for identifying tissue of origin for metastatic cancer
Expression of tissue-specific genes in tumors
Hepatocyte-specific expression signature and dedifferentiation of liver cancer
Identification of tissue-specific genes
Expression of neuron and glia-specific genes in brain tumors
Breast tumors with two distinct types of differentiation
The remarkable heterogeneity of lung cancers
Expression of maintenance genes in tumors
Maintenance genes frequently under-expressed in cancers: tumor suppressors?
Genes always expressed in tumors define a minimum set of survival genes
Part 2 Alterations in the regulatory networks of cellular and molecular events
Chapter 4 Events at DNA replication origins and genome stability
The cell cycle and genome stability
Positive regulation of origin licensing factors
Negative regulation of origin licensing factors
CDK-mediated phosphorylation
Inappropriate origin licensing
Consequences of CDT1 over-expression
Cell cycle-dependent degradation of CDT1 and geminin prevents re-replication
Consequences of geminin depletion
Consequences of re-replication
Acute consequences of re-replication: DNA damage and checkpoint activation
Long-term consequences of re-replication: induction of genome instability and cancer
Insufficient origin licensing
Origin licensing checkpoint
Origin licensing defects in higher eukaryotes
G1 arrest in normal cells
Apoptosis in cancer cells
Origin licensing defects in yeast
Chapter 5 Systems biology approaches bring new insights in the understanding of global gene regulatory mechanisms and their deregulation in cancer
The high-throughput revolution
Monitoring global gene expression levels: from cDNA arrays to RNA deep sequencing
Genome-wide mapping of binding sites: from PCR microarrays to high-throughput sequencing
Bioinformatics approaches: in silico deciphering of transcriptional networks
Transcription as a complex gene expression regulatory system
Systematic annotation of the genome, or find the common marks for regulation
Annotation of functional elements
Pol II promoter characterization
Structural and mechanistic insights from genome-wide studies
Genome-wide chromatin architecture
Histone marks and histone variants: transcription in the context of chromatin
Mechanistic insight of transcription regulation processes
Mechanisms of action of the transcriptional machinery
Non-productive PIC formation
Transient and permanent regulation of expression
TFIIB new function: gene looping
New insights brought by systems biology in the understanding of transcription deregulation in cancer
Decipher the oncogenic TF network
The network of the Myc family proteins
Expected application of the high-throughput technology in cancer research
Chapter 6 Regulation and dysregulation of protein synthesis in cancer cells
Mechanisms of regulation of protein synthesis
Update on protein synthesis factors and cancer
Initiation factor eIF4E and the 4E binding proteins
Other protein synthesis factors and cancer
Signal transduction pathways for control of protein synthesis
Significance of mRNA structure
Part 3 Events responsible for aberrant genetic and epigenetic codes in cancer
Chapter 7 Genomic instability and carcinogenesis
Genetic alterations in cancer
The scales of instability
Mutation, insertion, and deletion
Chromosomal rearrangements and aneuploidy
Intermediate-scale rearrangements
Causes of genetic instability
Oncogenes and tumor suppressors
Genomic integrity during the cell division cycle
Translocations, chromosome loss, and mutation
Effects of genetic instability
Multi-hit hypothesis and clonal selection
Chapter 8 Epigenomic code
Techniques to study the epigenome
Epigenetic marks in normal cells
DNA hypomethylation in cancer
Gene silencing in cancer by DNA hypermethylation
Mechanisms leading to DNA hypermethylation in cancer
Cancer as a genetic and epigenetic disease
Histone modifications in cancer cells
Chapter 9 MicroRNA epigenetic systems and cancer
MiRNA biogenesis and mRNA targeting
Impaired miRNA biogenesis and cancer
MiRNAs as tumor suppressor genes
The miR-15a/miR-16 cluster
MiRNAs play a direct role in cancer progression
MiRNAs as metastatic inducers
MiRNAs as metastatic suppressors
MiRNAs and epigenetic machinery
MiRNAs as effectors of the epigenetic machinery
MiRNAs as targets of the epigenetic machinery
MiRNAs and systems biology
Chapter 10 Dietary and environmental influences on the genomic and epigenomic codes in cancer
Nutritional genomics and cancer
Nutritional epigenomics and cancer
Nutrition and epigenetic modifications
Epigenetic impacts of dietary bioactive components on cancer
Epigenetic impacts of food contaminants and environmental factors on cancer
Critical periods for stable epigenetic aberrations
Summary and future directions
Part 4 Functional networks of events that modulate phenotypic manifestation of cancer
Chapter 11 Regulatory signaling networks in cell transformation and cancer
Signaling pathways involved in cancer
Technical tools for the discovery of oncogenes and tumor suppressors
Integration of genomic approaches
Chapter 12 RAS signaling networks
RAS isoforms and their homologies
Post-translational modifications for membrane trafficking
Regulation of RAS protein activation and inactivation
RAS activity regulatory mechanisms
RAS-guanine nucleotide exchange factors
Signaling networks initiating RAS activation
RAS-GTPase-activating proteins
Downstream signaling by activated RAS
Signaling through PI3Kinase, influencing cell survival and protein translation
Signaling through RAF, influencing cell cycle progression and transcription
Signaling through PLCepsi, influencing calcium signaling
Signaling through RAL GDS, influencing vesicle transport, and cell cycle
Mechanisms of aberrant RAS signaling in cancer
Mutation or amplification of RAS effectors
Growth factor receptor activation
Current anti-cancer therapeutics targeting RAS signaling networks
Antisense oligonucleotides
Farnesyl transferase inhibitors
Kinase inhibitors of RAS effectors
Interference with survival pathways (AKT, PKC δ)
Inhibitors of upstream activators of RAS (receptor tyrosine kinase inhibitors)
Chapter 13 PI3K pathway in cancer
Chapter 14 TGFβ
and BMP signaling in cancer
Smads mediate TGFβ
signaling
TGFβ
synthesis and activation
TGFβ
signal transduction pathway
The bone morphogenetic protein (BMP) signaling pathway
TGFβ
in cell proliferation and apoptosis
TGFβ
in development - mouse models
TGFβ
in immunosuppression
TGFβ
signaling in cancer progression and metastasis
Context and tissue-specific Smad signaling alterations and defective cytostatic responses
TGFβ
in epithelial to mesenchymal transition (EMT) and cancer stem-like cells (CSCs)
The TGFβ
signaling pathway as a therapeutic target in cancer
Antisense oligonucleotides
Small-molecule inhibitors
Chapter 15 The Wnt signaling network in cancer
Wnt signaling components and pathways
Canonical or Wnt/β-catenin
pathway
Extracellular and membrane-bound modulators of Wnt signaling
Non-canonical or
β-catenin-independent Wnt pathways
Wnt pathway specificity and Wnt pathway network
Tumorigenic potential of Wnts in animal models
Upregulated Wnt/β-catenin
signaling in human tumors
Upregulated
β-catenin-independent Wnt signaling in human tumors
Wnt signaling activation and Wnt network in cancer
Delineating the Wnt signaling network through large-scale genetic screens
Wnt/β-catenin
assays and readouts
Applications to Wnt/β-catenin
signaling
Defining the Wnt signaling network through interaction proteomics
Affinity-purification mass-spectrometry (AP-MS)
Protein-protein interactions and complexes
The targetome of the
Wnt/β-catenin pathway
Methods: how to identify
Wnt/β-catenin target genes
Differential display PCR (DDRT-PCR)
Next-generation sequencing
Results of exemplified
Wnt/β-catenin targetome studies
The transcriptomic side of Wnt
The Wnt/β-catenin
pathway has a multi-level targetome
Target genes differ in time point after activation
The regulational side of Wnt
The biological side of Wnt
Wnt signaling results in a waterfall modification of the transcriptome
Wnt targetomes are specific for cell type
Wnt signaling as target for small interfering molecules
Exemplified molecules interfering with the Wnt pathway
Strategies to find new modulators of the Wnt/β-catenin
pathway
The Wnt pathway and clinical trials
Omics data analysis and integration
Clustering multidimensional data
In silico prediction of Wnt targets
Computer simulation of Wnt circuits
Simulation of the Drosophila segment polarity network
Simulation of the Wnt/β-catenin
pathway
Simulation of Wnt pathway oscillatory dynamics and pattern formation
Chapter 16 Apoptotic pathways and cancer
Death domain (DD) superfamily
IAPs and their antagonists
Regulation of the intrinsic pathway
Crosstalk between the intrinsic and extrinsic pathways
Regulation of the extrinsic pathway
Integration of proximal apoptotic signals
NF-κB
and cytokine-induced apoptosis
p53 and genotoxic stress-induced apoptosis
FoxO and growth factor deprivation-induced apoptosis
Deregulation of apoptosis in cancer
Alterations in the proximal regulators
Deregulation of the intrinsic pathway in cancer
Deregulation of the extrinsic pathway in cancer
Apoptosis modulation for cancer therapy
Exploiting the intrinsic pathway for cancer therapy
Exploring the extrinsic pathway for cancer therapy
Other proapoptotic cancer therapies
Chapter 17 Molecular links between inflammation and cancer
Orchestrating cancer-related inflammation: transcription factors
Orchestrating cancer-related inflammation: cytokines and chemokines
An intrinsic and an extrinsic pathway link inflammation and cancer
Chapter 18 Cancer metastasis
Metastasis as a complex, multistep event
Organ-specific metastasis
Cancer therapies directed at metastasis
Chapter 19 Cancer metabolism
Enhanced glucose metabolism is a central feature of cancer cell metabolism
Metabolic reprogramming mediates flux of glucose carbons to anabolic pathways for proliferation and survival
The fate of glycolytic metabolites
The pentose phosphate pathway
The impact of mitochondrial metabolism changes in cancer
Glutamine requirements for cancer cell proliferation
Analytical and computational frameworks for studying cancer metabolism
Chapter 20 Tumor microenvironment: blood vascular system in cancer metastasis
Blood vascular system in the pathogenesis of cancer metastasis
Blood vascular system in the spread of cancer cells
Blood vascular system in organ-specific metastasis
Blood vascular system associated factors/events that play a role in cancer metastasis
Cellular and non-cellular components of blood
Non-cellular components of blood
Neovascularization/angiogenesis
Endothelial basement membrane
Part 5 Current state of the evolving MMMN cancer progression models of cancer
Chapter 21 Genetic alterations in glioblastoma multiforme
Large-scale genetic changes
Mutations in genetic pathways
Receptor tyrosine kinase pathways
Newly identified pathways
Isocitrate dehydrogenases
Pathological classification of breast cancer
Molecular classification of breast cancer
Mutational landscape of breast cancer genomes
Chapter 23 The role of growth factor-induced changes in cell fate in prostate cancer progression
Prostate gland development and prostate cancer
Epithelial-mesenchymal transition (EMT)
Models to study EMT and invasion of prostate cancer
Aberrant expression of epithelial and mesenchymal markers in prostate cancer
Deregulation of EMT-inducing transcription factors in prostate cancer
Influence of growth factor-induced signaling on cell fates and prostate cancer progression
Transforming growth factor-ò family
Fibroblast growth factors
Insulin-like growth factors
Etiology, staging, screening, and therapy
Familial vs. sporadic colorectal cancer
Molecular basis of colorectal cancer
Genomics of colorectal cancer
Metabolomics of colorectal cancer
Proteomics of colorectal cancer
Transcriptomics of colorectal cancer
Conclusion and perspective
Chapter 25 Biology of human stomach cancer
Associated host genotypes
Hereditary diffuse gastric cancer (HDGC)
Hereditary non-polyposis colorectal cancer (HNPCC)
Li-Fraumeni and Peutz-Jeghers syndromes
Adenomatous polyposis syndromes
Microsatellite instability
Acquired somatic alterations
Apoptosis signaling alterations
Growth factor alterations
Methylation silencing alterations
Angiogenesis signaling alterations
Molecular profiling: prognostic and diagnostic markers
Chemosensitization markers
Potential targets for treatment and intervention
Chapter 26 Pancreatic cancer
The proposed progression model of pancreatic cancer
Molecular genetics of pancreatic cancer
The multimodal molecular network (MMMN) and pancreatic cancer
Impact of high-throughput genomic approaches on systems biology of PDA
Informatics support for systems biology of PDA
Future directions in PDA systems biology research
Chapter 27 Deregulated signaling networks in lung cancer
Lung morphogenesis and histopathology
Regulation of lung development
Lung cancer pathophysiology
Genetic driver mutations and alterations
Molecular subtype classification of lung cancer
Deregulated signaling networks in lung cancer
Developmental gene regulatory networks
Therapeutic strategies in lung cancer treatment
Exploiting oncogene "addiction"
Cancer genomics and personalized medicine
Chapter 28 Modular signaling in hematopoietic malignancies
Acute myeloid leukemia: a malignancy that requires the combined effect of at least two classes of mutations
AML fusion proteins: more than just arrest of differentiation
Role for HOXA homeobox proteins in MLL-translocation leukemias
Assessing response of AML blasts to cytokines by phosphoflow cytometry predicts response to therapy
Dyregulated NF-κB signaling in multiple myeloma
Dysregulated NF-κB signaling in DLBCL
Bcl6-mediated ATR and BLIMP repression critical for BCR-type DLBCL
Dysregulated NF-κB signaling in MALT lymphomas
Burkitt's lymphoma: escape from Myc-driven apoptosis
CLL tumor suppressors: the del13q14 controversy
CLL: poised for death, rescued by BCR signaling?
Part 6 Applications of comprehensive cancer progression models in the fight against cancer
Chapter 29 Role of network biology and network medicine in early detection of cancer
New era of molecular markers of early detection
Types of biomarkers for cancer research
Clinical validation of biomarkers
Predictive (stratification) biomarkers
Screening biomarkers (diagnostic)
Surrogate end point biomarkers
Importance of early detection
Overdiagnosis and risk stratification
Network biology, network medicine, and biomarker discovery
Cancer: a systems biology disease paradigm
Mode of action network identification
Role of modularity in biologic network connectevity
Sub-network approach to gene expression profiles
Chapter 30 Systems biology in cancer biomarkers for early detection, diagnosis, and prognosis
Definition of systems approach
What is systems biology now?
Systems approach to biomarker research?
Systematic approach to the development of diagnostic biomarkers
In silico discovery from data mining
Future roles of systems biology in cancer biomarker discovery and validation
Chapter 31 Prognosis of cancer
General prognostic factors
General prognostic histological biomarkers
Intra-tumoral lymphocytic infiltration
Epithelial-mesenchymal transition tumor phenotype (EMT)
KRAS (KI-RAS2 Kirsten rat sarcoma viral oncogene homolog)
BRAF (v-raf-1 murine leukemia viral oncogene homolog B1)
MYC (myelocytomatosis viral oncogene homolog)
Ataxia-Telangiectasia-Mutated (ATM)
Breast cancer susceptibility gene (BRCA) mutation
Excision repair cross-complementing rodent repair deficiency, complementation group 1 (ERCC1)
Altered cellular metabolism
Thymidylate synthase (TS)
Des-γ-carboxy
prothrombin (DCP)
Cell surface receptor expression
Epidermal growth factor receptor (EGFR)
HER2 (Human epidermal growth factor receptor type 2)
Oncofetal serum biomarkers
Cancer antigen 125 (CA-125)
Carcinoembryonic antigen (CEA)
Cancer antigen 19-9 (CA 19-9)
Human chorionic gonadotropin (hCG)
Role of imaging in cancer prognosis
Functional tumor imaging with PET (positron emission tomography)
Role of adjunct imaging with MRI
Chapter 32 Cancer pharmacogenomics: challenges, promises, and its application to cancer drug discovery
Recent advances in cancer genomics and pharmacogenomics
Advances in genomics data generation
Advances in data mining and exploitation
Cancer genomics' impact on disease understanding
Impact of cancer pharmacogenomics in drug discovery and developments
Cancer cell line panels as important discovery platform for personalized medicine strategy development
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