College aantekeningen

Lecture Notes - TBCB - week 1

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Vrije Universiteit Amsterdam (VU)

Lectures included: cancer histopathology, lab techniques in cancer research, mass spectrometry & proteomics, CRC biomarkers, cancer epidemiology, tumor profiling & biomarkers (case: hemato-oncology), NGS for personalized cancer treatment, prostate cancer profiling, microbiome & cancer

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Geschreven in 2018/2019
Type College aantekeningen
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tumor biology clinical behavior
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Tumor Biology & Clinical Behaviour Lecture Notes

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1. College aantekeningen - Lecture note - tbcb - week 3
2. College aantekeningen - Lecture note - tbcb - week 2
3. College aantekeningen - Lecture notes - tbcb - week 1
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Week 1: Tumor Biology & Clinical Behavior

LECTURE 1: HISTOPATHOLOGY – TUMOR STAGING (W.J. Mooi) Monday, 29/10/2018

Cancer detection & diagnosis (identification & determination of cancer cell type):

a. Screening: chance finding in asymptomatic patient

b. Index complaint (symptoms appear: e.g. lump, etc  set into motion the Dx cascade)

c. Phys Ex (symptoms +)

d. Radiologic investigation

e. Diagnostic nuclear medicine (radioactive trecer)

f. Clinical test: blood test, Dx microscopy/pathology (e.g. cytopathology exfo, FNA, histopathology of biopsy &
resection specimen)

Triple diagnosis of cancer: physical ex, histopathology, radiology

Exfoliative cytology

Exfoliative cytology (tissue brushing): looking at cells/group of cells outside the tissue context, may identify metastatic cells,
dysplastic cells, etc  non-intact tissue sample; Sources: body cavities, body fluids, etc

Fine needle aspiration/FNA

Method: palpation/USG-guided  benefit: no anesthesia, quick, small needle

Needle biopsy enables the examination of tumor cells from intact environment i.e. in the actual site

 Fine needle: cytology

 Thick needle: histopathology (more representative for actual tumor tissue compared to FNA)

Endoscopic biopsy

Endoscope + blade for tissue excision (“biting” the tissue at lump site)  disadvantage: should be anesthetized (performed in
OR/sterile room)

Other method of tissue procurement: punch biopsy (skin lesions), traditional biopsy (e.g. BMP), traditional excision biopsy for
superficial lesions

Pathologic tumor diagnosis

Routine light microscopy: staining procedures (HE, Giemsa, Papanicolau, etc)  differentiation of different cells

Histochemical stains

IHC: identifying antigens present in tissue samples  certain cells would bind more strongly to certain antibody

ISH

Molecular analysis: gene expression (microarray), mutation detection, CGH, LOH mapping

, Week 1: Tumor Biology & Clinical Behavior

Procedures of tissue sampling

Aim: determine the scope of disease in tissue sample & identify clinically relevant area of the biopsy sample, e.g. presence of
tumor cells in resection margins  Not all sample area gets analyzed, adjust with the needs of clinicians

Example: FFPE  Definition of FFPE: …?

Procedure: tissue taken out of patient  transferred to pathology  formaldehyde stabilization  wash off, replace with
paraffin (dehydration of sample & further stabilization)  cooling  tissue block  examination in microtome  slicing off
the tissue  rehydration  staining of sample  specimen analysis on microscope

Crosslink of molecules when treated with formaldehyde: …?

General histologic properties of cancer (“cardinal signs”)

Anaplasia (loss of differentiation) Pleomorphism of cells & nuclei  genetic mutations
result in presence of variants that present as different
Presence of keratin accumulation/“keratin pearl” cellular/nuclear morphology (small/large nuclei, heavily
indicates squamous differentiation, “undifferentiated” stained/unstained)
region of cells w/ aberrant differentiation
)

Disordered cellular architecture Abnormal mitosis

Conditions of basement membrane, presence of normal Presence of mitotic figures (double nuclei, abnormal
cellular structures, invasion, etc separation of cells, abnormal daughter cells/”triaster”)

, Week 1: Tumor Biology & Clinical Behavior

Tumor grading

a. Cytological atypia c. Presence of necrosis

b. Mitotic activity d. Degree of resemblance to normal tissue
(differentiation)
Invasive growth

Example: BCC cutaneous  spread down the subcutaneous, heavy staining of nuclei (abnormal mitosis)

Types:

a. Lymphogenic

b. Hematogenic

c. Direct seeding (e.g. to adjacent organ, through body cavities)

Angioinvasion: presence of tumor cells inside blood/lymph vessels on histology sample  most common route for metastasis
(e.g. loss of basement membrane underneath the vascular endothelium, rearranged stroma, tumor clones inside vessel)

Importance of pathological cancer classification

Tumors differ in growth rate, destructiveness for invasion, propensity for metastasis (regional, distant), response to Tx,
prognosis, family history, etc  complex classification in order to determine the therapeutic options to employ for certain
patient

1. Determining the main groups of
malignant tumors: carcinoma,
sarcoma, hematopoietic tumor, germ
cell tumor/GCT, lymphoma, brain
tumor

2. Cancer grading (low-grade/ well-
differentiated, high-grade/poorly
differentiated, undifferentiated) 
histopathological

3. Tumor spread/stage grouping (TNM
staging  Tumor, lymph Node, distant
hematogenous Metastasis; TNM later
utilized for stage-grouping 0-4, details
see slide)  clinical

LECTURE 2: LAB TECHNIQUES/TOOLS (S. Cilessen) Monday, 29/10/2018

Molecular detection techniques: DNA, RNA, protein, cellular functional assay, animal model, molecular imaging

Always perform validation (compare the preferred technique with easier, more large-scale techniques  e.g. PCR followed
by mRNA assay, IHC, etc)

, Week 1: Tumor Biology & Clinical Behavior

DNA Assay

a. NGS/MPS

Determine accurate order of nucleotides
(A/G/T/C) along chromosomes & genomes 
analyzing mutated pathways, resistance
mechanism, etc

Advantage: can be applied for many different
samples with low quantity of sample

b. Array CGH c. Methylated DNA immunoprecipitation (MEDIP)
Analyze CNV (gains/loss) Denature DNA  label w/ antibody  pattern formation by
antibody  immunoprecipitation  enriched Me-DNA
Extract DNA + digest  label tumor (Cy5) &
production  high throughput sequencing; can also use the
reference (Cy3) DNA  combine equal amounts of
denatured DNA for array hybridization
DNA  hybridization  image analysis in software
(spots)

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