Molecular Biology and Oncology
(summary)
Theme 1...................................................................................................................................................................................................... 1
SSA1 Molecular Basis of Cancer......................................................................................................................................................... 1
SSA3 The Nature of Cancer................................................................................................................................................................. 4
Theme 2...................................................................................................................................................................................................... 5
SSA4 Tumor Viruses and Oncogenes.................................................................................................................................................. 5
SSA5 Growth Factors and Receptors - Chapter 5............................................................................................................................... 8
SSA6 Signal Transduction - Chapter 6...............................................................................................................................................10
Theme 3................................................................................................................................................................................................... 13
SSA7 Tumor Suppressor Genes (Sidebars al gelezen)..................................................................................................................... 13
SSA8 Rb and the Cell Cycle...............................................................................................................................................................15
SSA9 p53 and Apoptosis....................................................................................................................................................................18
Theme 4: Change of a Cell into a Tumor Cell........................................................................................................................................22
Flow cytometry Supplement............................................................................................................................................................... 22
SSA10 Cell Immortalization and Tumorigenesis................................................................................................................................ 23
SSA11 Multi-step Tumorigenesis and Cancer Stem Cells..................................................................................................................25
SSA12 Maintenance of Genomic Integrity..........................................................................................................................................29
Theme 6.................................................................................................................................................................................................... 33
SSA13 The Tumor Microenvironment: Not an Innocent By-stander...................................................................................................33
SSA14 Invasion and Metastasis......................................................................................................................................................... 37
SSA15 Cancer and the Immune System............................................................................................................................................ 41
SSA16 Cancer immunotherapy.......................................................................................................................................................... 44
Chapter 17 - Treatments.....................................................................................................................................................................47
,Theme 1
SSA1 Molecular Basis of Cancer
Mutations
● Euploid: normal configuration of chromosomes
● Aneuploid: deviation from the normal configuration, in 90% of cancer cells
○ (reciprocal) translocation: exchange of arms
○ homogeneously staining region (HSR): fusion of extra copies from a segment
○ double minutes: cleaved segment that replicates as an autonomous entity
○ interstitial deletion: flanking arms of a deleted segment fuse
● Germline mutation: the mutation must be present in sperm/egg or their precursors
● Somatic mutations: can not be transmitted to offspring
Gene expression
● Transcription: transcriptome
○ splicing: during elongation the introns are cleaved → exons are fused to form mature DNA
○ regulators of splicing favor transformation to a cancerous state
● Translation: proteome
○ post-translational modifications (PTM): chemical groups are attached
■ glycosylation and proteases
● Modifications
○ transcription factors: bind to a sequence motif and provide or block access for RNA polymerase
■ the sequence motif is an enhancer or silencer
■ pleiotropy: one TF can elicit many changes within a cell
○ transcriptional pausing / promotor-proximal pausing: physiologic signals allow some to continue
■ The Myc-Max heterodimer can release RNA polymerase from its pause site
Chromosome structure
● Specialized nucleotide sequences
○ Replication origin: starting site for DNA replication
○ Centromere: site for the kinetochore complex formation, mitotic spindle pulls them apart
■ contains specialized histones (CENP-A) for very dense structures
○ Telomeres: repeated nucleotide sequences, protects the ends of chromosome (would otherwise be
mistaken as a broken DNA molecule)
● Chromatin organisation (chromatin = DNA + histone + non-histone proteins)
○ Modifications: replacing histones or modifying existing ones
○ nucleosome: histone octamer with a DNA stretch
■ histone subunits: H2A, H2B, H3 and H4, each contains a histone fold
■ many hydrogen and polar bonds between histone core and DNA (histone = +)
■ bends in the minor groove in order to wrap around
■ histone tails: extend from the histone core and can be modified
■ main histones are synthesized during S phase, the others throughout interphase
○ Chromatin remodelling complexes: with the energy from ATP hydrolysis it slides DNA along the histone
core → nucleosome sliding
■ together with histone chaperones they can remove histones
○ Nucleosomes are stacked: using histone tails and histone H1 (linker histone)
● Epigenetics:
○ Position effect: spreading of the heterochromatic state to a normally euchromatic region
○ Histone modifications: acetylation (lysines), methylation (lysine), phosphorylation (serine)
■ HATs add acetyl groups and HDACs remove them
■ acetyl group on lysine removes the negative charge → less affinity histone
■ histone code: covalent additions to histone tails that dynamically signal to different cell
processes, tails remain accessible in condensed structures
■ trimethylation of lysine on H3 → HP1 protein that characterizes heterochromatin
○ Spreading of modifications: reader complexes can bind to newly modified histones and activate a writer
complex → chain reaction of reading and writing
■ eraser enzymes work in the opposite way
■ barrier sequences prevent unlimited spreading; used in genetic engineering to prevent silencing
Andrea Kloen - 2024 - 1
, ● contains histone acetylase enzyme binding sites
○ Inheritance: daughter cells have the same silenced genes as their parents
○ Lampbrush chromosomes: large chromosomes that have loops with a determined gene
■ genes within the loops are actively expressed
miRNA: primary microRNA is transcribed → Drosha protein cleaves the segment with the hairpin formation → transferred
to Argonaute 2 (Ago2) → one strand is broken down → RISC complex → binds to mRNA resulting in degradation or
blockage of translation
long noncoding RNAs (lnRNA): HOTAIR
Transcription
● RNA: thymine (T) is replaced by uracil (U) and contains ribose instead of deoxyribose
○ RNA polymerase does not need a primer
● Initiation
○ Prokaryotes: RNA polymerase holoenzyme (plymerase + σ factor) slides along genome until promotor
→ binds tightly (bonds between exposed bases) → transcription bubble → scrunching mechanism
(polymerase pulls DNA in) → release promotor and σ factor → elongation → stops at terminator
sequence (hairpin formation)
○ Eukaryotes: RNA polymerase II + many general transcription factors → assemble at the TATA box within
promotor (starts with TFIID binding → distortion in DNA) → transcription initiation complex → TFIIH
unwinds with DNA helicase → polymerase binds template strand and synthesizes short strands → until
conformational change → elongation and dissociation from transcription factors
■ enhancer: can bind transcriptional activator to attract RNA polymerase
■ mediator: helps the transcription factors and polymerase to communicate
■ chromatin and histone modifying enzymes: access to DNA in chromatin
■ RNApol C-terminal domain (CTD) is phosphorylated
■ TATA box is 25 nucleotides upstream of transcription start site
● Elongation
○ Prokaryotes: no elongation factors, DNA gyrase removes supercoiling → facilitates opening
○ Eukaryotes: elongation factors prevent dissociation → chromatin remodelling complexes and histone
chaperones, DNA topoisomerase enzymes remove supercoiling
■ enzymes leave a trace on histones, leaving a record of where it has been
■ RNA processing
1. 5’ capping: removal of phosphate group → addition of GMP → methylation of guanosine;
cap distinguishes mRNA from other RNAs and binds CBC
2. splicing: spliceosome (small nuclear RNAs) recognizes the splicing sites
○ DNA supercoiling: polymerase creates superhelical tension as it moves along
■ in eukaryotes may help to unwrap DNA in nucleosomes
■ topoisomerases remove this helical tension
● RNA processing
○ 5’ Capping: distinguishes mRNA from other types of RNA, cap binding complex (CBC) for export
■ Phosphorylation of the CTD helps dissociate starting proteins and binding of processing proteins
■ Phosphatase removes one phosphate group, guanyl transferase adds GMP (5’ to 5’) and methyl
transferase adds methyl group
○ Splicing: two transesterifications that join the exons in mRNA
■ Splicing machinery recognizes 3 sequences: 5’ and 3’ splice site plus branch point (adenosine
nucleotide)
■ Spliceosome: consists of small nuclear RNAs (snRNAs)
■ ATP hydrolysis in RNA-RNA rearrangements: multiple checkpoints for the splicing signal and
formation of the catalytic sites → protein + RNA
■ After splicing, the exon junction complex (EJC) binds to mark the splicing event
■ Increase accuracy: 1. Directly coupled to transcription, 2. exon definition: exons are
approximately the same length and SR proteins bind
■ Chromatin structure affects RNA splicing: faster transcription along open chromatin can result in
alternative splicing and histones attract spliceosome components
○ 3’ polyA tail
■ CstF and CPSF bind to the consensus sequence → cleavage of RNA molecule from polymerase
→ polyA polymerase adds the A nucleotides (from ATP)
Andrea Kloen - 2024 - 2
, SSA3 The Nature of Cancer
Carcinomas - epithelial cells
Sarcomas - connective tissue cells
Hemapoietic - blood and immune cells
Neuroectodermal - neuronal cells
Transdifferentiation: the acquisition of a new set of differentiated characteristics
● Epithelial-mesenchymal transition → in carcinomas the cancer cells acquire mesenchymal properties
○ differences in gene expression programs, not necessarily genomic mutations
Dedifferentiation: tumors that are anaplastic, they do not have recognisable structures
● Cancer of unknown primary (CUP)
Stages of cancer cells
● Hyperplasia: excessive number of cells
● Metaplasia: cell layer is replaced by abnormal cell type
○ common in epithelial transition zones
○ Baretts esophagus → squamous epithelium is replaced by secretory cells of the stomach
● Dysplasia: cells with an abnormal cytology
○ nuclear size and shape, increased nuclear staining, mitotic activity, lack of cytoplasmic features
● Polyps: large growths that can be seen with the naked eye
○ contains all the normal cell types
● Invasion: neoplasms
Ames test: mutant Salmonella strain that is dependent on the amino acid histidine to grow, but mutant allele can be
reverted by a mutation → addition of possible mutagen to gauge the ability to provoke such a mutation
Andrea Kloen - 2024 - 3
(summary)
Theme 1...................................................................................................................................................................................................... 1
SSA1 Molecular Basis of Cancer......................................................................................................................................................... 1
SSA3 The Nature of Cancer................................................................................................................................................................. 4
Theme 2...................................................................................................................................................................................................... 5
SSA4 Tumor Viruses and Oncogenes.................................................................................................................................................. 5
SSA5 Growth Factors and Receptors - Chapter 5............................................................................................................................... 8
SSA6 Signal Transduction - Chapter 6...............................................................................................................................................10
Theme 3................................................................................................................................................................................................... 13
SSA7 Tumor Suppressor Genes (Sidebars al gelezen)..................................................................................................................... 13
SSA8 Rb and the Cell Cycle...............................................................................................................................................................15
SSA9 p53 and Apoptosis....................................................................................................................................................................18
Theme 4: Change of a Cell into a Tumor Cell........................................................................................................................................22
Flow cytometry Supplement............................................................................................................................................................... 22
SSA10 Cell Immortalization and Tumorigenesis................................................................................................................................ 23
SSA11 Multi-step Tumorigenesis and Cancer Stem Cells..................................................................................................................25
SSA12 Maintenance of Genomic Integrity..........................................................................................................................................29
Theme 6.................................................................................................................................................................................................... 33
SSA13 The Tumor Microenvironment: Not an Innocent By-stander...................................................................................................33
SSA14 Invasion and Metastasis......................................................................................................................................................... 37
SSA15 Cancer and the Immune System............................................................................................................................................ 41
SSA16 Cancer immunotherapy.......................................................................................................................................................... 44
Chapter 17 - Treatments.....................................................................................................................................................................47
,Theme 1
SSA1 Molecular Basis of Cancer
Mutations
● Euploid: normal configuration of chromosomes
● Aneuploid: deviation from the normal configuration, in 90% of cancer cells
○ (reciprocal) translocation: exchange of arms
○ homogeneously staining region (HSR): fusion of extra copies from a segment
○ double minutes: cleaved segment that replicates as an autonomous entity
○ interstitial deletion: flanking arms of a deleted segment fuse
● Germline mutation: the mutation must be present in sperm/egg or their precursors
● Somatic mutations: can not be transmitted to offspring
Gene expression
● Transcription: transcriptome
○ splicing: during elongation the introns are cleaved → exons are fused to form mature DNA
○ regulators of splicing favor transformation to a cancerous state
● Translation: proteome
○ post-translational modifications (PTM): chemical groups are attached
■ glycosylation and proteases
● Modifications
○ transcription factors: bind to a sequence motif and provide or block access for RNA polymerase
■ the sequence motif is an enhancer or silencer
■ pleiotropy: one TF can elicit many changes within a cell
○ transcriptional pausing / promotor-proximal pausing: physiologic signals allow some to continue
■ The Myc-Max heterodimer can release RNA polymerase from its pause site
Chromosome structure
● Specialized nucleotide sequences
○ Replication origin: starting site for DNA replication
○ Centromere: site for the kinetochore complex formation, mitotic spindle pulls them apart
■ contains specialized histones (CENP-A) for very dense structures
○ Telomeres: repeated nucleotide sequences, protects the ends of chromosome (would otherwise be
mistaken as a broken DNA molecule)
● Chromatin organisation (chromatin = DNA + histone + non-histone proteins)
○ Modifications: replacing histones or modifying existing ones
○ nucleosome: histone octamer with a DNA stretch
■ histone subunits: H2A, H2B, H3 and H4, each contains a histone fold
■ many hydrogen and polar bonds between histone core and DNA (histone = +)
■ bends in the minor groove in order to wrap around
■ histone tails: extend from the histone core and can be modified
■ main histones are synthesized during S phase, the others throughout interphase
○ Chromatin remodelling complexes: with the energy from ATP hydrolysis it slides DNA along the histone
core → nucleosome sliding
■ together with histone chaperones they can remove histones
○ Nucleosomes are stacked: using histone tails and histone H1 (linker histone)
● Epigenetics:
○ Position effect: spreading of the heterochromatic state to a normally euchromatic region
○ Histone modifications: acetylation (lysines), methylation (lysine), phosphorylation (serine)
■ HATs add acetyl groups and HDACs remove them
■ acetyl group on lysine removes the negative charge → less affinity histone
■ histone code: covalent additions to histone tails that dynamically signal to different cell
processes, tails remain accessible in condensed structures
■ trimethylation of lysine on H3 → HP1 protein that characterizes heterochromatin
○ Spreading of modifications: reader complexes can bind to newly modified histones and activate a writer
complex → chain reaction of reading and writing
■ eraser enzymes work in the opposite way
■ barrier sequences prevent unlimited spreading; used in genetic engineering to prevent silencing
Andrea Kloen - 2024 - 1
, ● contains histone acetylase enzyme binding sites
○ Inheritance: daughter cells have the same silenced genes as their parents
○ Lampbrush chromosomes: large chromosomes that have loops with a determined gene
■ genes within the loops are actively expressed
miRNA: primary microRNA is transcribed → Drosha protein cleaves the segment with the hairpin formation → transferred
to Argonaute 2 (Ago2) → one strand is broken down → RISC complex → binds to mRNA resulting in degradation or
blockage of translation
long noncoding RNAs (lnRNA): HOTAIR
Transcription
● RNA: thymine (T) is replaced by uracil (U) and contains ribose instead of deoxyribose
○ RNA polymerase does not need a primer
● Initiation
○ Prokaryotes: RNA polymerase holoenzyme (plymerase + σ factor) slides along genome until promotor
→ binds tightly (bonds between exposed bases) → transcription bubble → scrunching mechanism
(polymerase pulls DNA in) → release promotor and σ factor → elongation → stops at terminator
sequence (hairpin formation)
○ Eukaryotes: RNA polymerase II + many general transcription factors → assemble at the TATA box within
promotor (starts with TFIID binding → distortion in DNA) → transcription initiation complex → TFIIH
unwinds with DNA helicase → polymerase binds template strand and synthesizes short strands → until
conformational change → elongation and dissociation from transcription factors
■ enhancer: can bind transcriptional activator to attract RNA polymerase
■ mediator: helps the transcription factors and polymerase to communicate
■ chromatin and histone modifying enzymes: access to DNA in chromatin
■ RNApol C-terminal domain (CTD) is phosphorylated
■ TATA box is 25 nucleotides upstream of transcription start site
● Elongation
○ Prokaryotes: no elongation factors, DNA gyrase removes supercoiling → facilitates opening
○ Eukaryotes: elongation factors prevent dissociation → chromatin remodelling complexes and histone
chaperones, DNA topoisomerase enzymes remove supercoiling
■ enzymes leave a trace on histones, leaving a record of where it has been
■ RNA processing
1. 5’ capping: removal of phosphate group → addition of GMP → methylation of guanosine;
cap distinguishes mRNA from other RNAs and binds CBC
2. splicing: spliceosome (small nuclear RNAs) recognizes the splicing sites
○ DNA supercoiling: polymerase creates superhelical tension as it moves along
■ in eukaryotes may help to unwrap DNA in nucleosomes
■ topoisomerases remove this helical tension
● RNA processing
○ 5’ Capping: distinguishes mRNA from other types of RNA, cap binding complex (CBC) for export
■ Phosphorylation of the CTD helps dissociate starting proteins and binding of processing proteins
■ Phosphatase removes one phosphate group, guanyl transferase adds GMP (5’ to 5’) and methyl
transferase adds methyl group
○ Splicing: two transesterifications that join the exons in mRNA
■ Splicing machinery recognizes 3 sequences: 5’ and 3’ splice site plus branch point (adenosine
nucleotide)
■ Spliceosome: consists of small nuclear RNAs (snRNAs)
■ ATP hydrolysis in RNA-RNA rearrangements: multiple checkpoints for the splicing signal and
formation of the catalytic sites → protein + RNA
■ After splicing, the exon junction complex (EJC) binds to mark the splicing event
■ Increase accuracy: 1. Directly coupled to transcription, 2. exon definition: exons are
approximately the same length and SR proteins bind
■ Chromatin structure affects RNA splicing: faster transcription along open chromatin can result in
alternative splicing and histones attract spliceosome components
○ 3’ polyA tail
■ CstF and CPSF bind to the consensus sequence → cleavage of RNA molecule from polymerase
→ polyA polymerase adds the A nucleotides (from ATP)
Andrea Kloen - 2024 - 2
, SSA3 The Nature of Cancer
Carcinomas - epithelial cells
Sarcomas - connective tissue cells
Hemapoietic - blood and immune cells
Neuroectodermal - neuronal cells
Transdifferentiation: the acquisition of a new set of differentiated characteristics
● Epithelial-mesenchymal transition → in carcinomas the cancer cells acquire mesenchymal properties
○ differences in gene expression programs, not necessarily genomic mutations
Dedifferentiation: tumors that are anaplastic, they do not have recognisable structures
● Cancer of unknown primary (CUP)
Stages of cancer cells
● Hyperplasia: excessive number of cells
● Metaplasia: cell layer is replaced by abnormal cell type
○ common in epithelial transition zones
○ Baretts esophagus → squamous epithelium is replaced by secretory cells of the stomach
● Dysplasia: cells with an abnormal cytology
○ nuclear size and shape, increased nuclear staining, mitotic activity, lack of cytoplasmic features
● Polyps: large growths that can be seen with the naked eye
○ contains all the normal cell types
● Invasion: neoplasms
Ames test: mutant Salmonella strain that is dependent on the amino acid histidine to grow, but mutant allele can be
reverted by a mutation → addition of possible mutagen to gauge the ability to provoke such a mutation
Andrea Kloen - 2024 - 3
