5-4-2018 Summary course
BBS2004, Cell
signalling
Cases, lectures, practicals and JC
Hermans, Sammy (Stud. FHML)
,Contents
Cases ....................................................................................................................................................................... 3
Case 1 the cellular intra- and internet ................................................................................................................ 3
Case 2 secretary molecules used in cell signalling .............................................................................................. 9
Case 3 signalling to degradate mRNA .............................................................................................................. 16
Case 4 from the outside to the inside without entering.................................................................................... 20
Case 5 what happens when signals go nuclear? ............................................................................................... 27
Case 6 How to deal with foreign chemical exposures? ..................................................................................... 31
Case 7 Signalling now for in the future ............................................................................................................. 36
Case 8 Oxidative stress, the good, the bad and the ugly .................................................................................. 41
Case 9 incoming and outgoing signals .............................................................................................................. 49
Case 10 CRISPR, genome editing ...................................................................................................................... 58
Case 11 biomedical techniques in cell signalling research ................................................................................ 63
Case 13 from mutations to cancer .................................................................................................................... 67
Lectures................................................................................................................................................................. 77
Lecture 1: cellular communication routes ......................................................................................................... 78
Lecture 2 cell derived signalling molecules ....................................................................................................... 82
Lecture 3: Signal transduction routes ............................................................................................................... 88
Lecture 4 introductory lecture on long and short term consequences of alterations in external signalling
molecules .......................................................................................................................................................... 93
Lecture 5 Redox aspects of cell signalling ......................................................................................................... 99
Lecture 6 pathway analysis ............................................................................................................................. 104
Lecture 7 signalling at network level .............................................................................................................. 107
Lecture 8 biotechnology in cell signalling research ......................................................................................... 110
Lecture 9 cancer and altered cell signalling .................................................................................................... 115
Practicals ............................................................................................................................................................. 124
Practical 1: TCDD and Ahr signalling .............................................................................................................. 124
Practical 2: Measurement of anti-oxidant induced lowered oxidative stress via H 2O2 detection in exhaled air.
........................................................................................................................................................................ 124
Practical 3: wikipathways, insulin phosphoproteomics & effect of Akt inhibition .......................................... 125
Journal clubs ....................................................................................................................................................... 128
Journal club 1 .................................................................................................................................................. 128
Journal Club 2 ................................................................................................................................................. 129
Journal Club 3 ................................................................................................................................................. 132
Journal club 4 .................................................................................................................................................. 136
Journal club 5 .................................................................................................................................................. 138
2
,Cases
Case 1 the cellular intra- and internet
How are the cells in an organ
organised? How are the cells
connected to each other?
Epithelial tissues
cells are tightly bound together in
sheets called the epithelia, underlying
these sheets there is a thin layer of
specialised extracellular matrix, called
the basal lamina or basement
membrane. Below the basal lamina,
there is connective tissue. Functions
of the basal lamina are:
• The basal lamina, attaches
and anchors the cells to the
underlying connective tissue. Integrins Junctions in an simple columnar epithelial cell
and proteoglycans, attach the cell membranes to the proteins in the basal lamina, which is in
turn linked to the connective tissue.
• Limits contact between epithelial cells and other cell types in the tissue.
• Acts as a filter: only water and small molecules are able to pass.
Within the epithelium, cells are attached to each other by cell-cell junctions. Cell-matrix junctions link
the cytoskeleton of epithelial cells to the basal lamina. The apex of the cell (upper surface) is exposed
to the extracellular matrix. At the basal side, epithelia are anchored to other tissue (basal lamina), at
the apical side not. Epithelia are thus polarised.
cell-cell junctions
Anchored cytoskeletal filaments transmit stresses across the interior of the cell, from adhesion side
to adhesion side.
• Lateral side of the cell: anchoring junctions: adherens junctions, which link actin filaments of
both cells and desmosomes which anchor intermediate filaments of the cell. The main
function of desmosomes is to provide mechanical strength. Therefore they are present in a
lot of numbers in tissues subjected to a lot of mechanical stress. The cadherin superfamily is
involved in these junctions.
• Tight junctions, hold the cells close together at the apex, which makes it possible for the
epithelial cells to perform the barrier function. They lie mostly apical (above) the adherens
and desmosome junctions. All these junctions together form a junctional complex. Tight
junctions seal the gap between the cells and prevent leaking of molecules (sealing function).
Transport across epithelium can happen via transcellular transport and paracellular
transport. The tight junctions can be permeable for small ions, but their permeability differs
per tissue. This difference results from the difference in proteins that form the tight junction.
Tight junctions are strands of transmembrane adhesion molecules, mainly claudin. Claudin is
important in the formation and function of the tight junctions. Occludin is important in
regulating the permeability of the tight junctions. Tricellulin is important for sealing the
membranes together and preventing trans epithelial leakage.
3
, Zona occludens (ZO) proteins play a major role in the organisation of tight junctions. They are
scaffold proteins that provide support while the tight junctions are build. They have PDZ
domains, which are sequences of amino acids that are able to bind a specific partner protein.
• Gap junctions: at the basal end of the cells, channel forming junctions which create pathways
to the cytoplasm of adjacent cells. The gap (1,4nm) is spanned by channel forming proteins:
connexin (vertebrates) and innexins (invertebrates). Small inorganic ions and water soluble
molecules are able to pass through these junctions (NO macromolecules such as proteins and
nucleic acids). This electrically couples adjacent cells, and is able to synchronise contractions
of heart muscle cells e.g. connexins are 4 transmembrane proteins together, and 6 connexins
are able to form a connexon. When two connexons in two adjacent cell membranes are
aligned it forms a connection between the interior of the two cells. Channels can differ in
permeability and regulation. Different types of connexin proteins can form heteromeric
connexons with specific properties. Gap
junctions can switch between open and
closed states, by various stimuli (e.g.
voltage differences). Connexin molecules
have only a half life time of a few hours:
there is constant turnover (adding (via
exocytosis) and removing) of the gap
junctions.
Transmembrane adhesion proteins:
Cadherin superfamily(require Ca2+): involved in adherens junctions & desmosomes.
Cadherins depend on Ca2+, they remove Ca2+ from the extracellular matrix, which
causes strong adhesion. Classical cadherins include E-cadherin, n-cadherin and P-
cadherin. These all have a similar structure (they are closely related in sequence)
in their intracellular and extracellular domain. Adhesion by classic cadherins is
involved in signalling pathways (Wnt e.g.). Nonclassical cadherins are more
distantly related in sequence, under which protocadherin.
Cadherins mediate homophilic adhesion, symmetrical anchoring junctions.
Cadherins will bind to the same/similar subtype of cadherin on the adjacent cell.
They thus bind cells of the same cell type together and segregate them from
other cell types. During development they play a crucial role in cell sorting.
Cadherins bind their partner with low affinity. Many parallel bonds result in strong attachments.
The intracellular domain of cadherin interacts with actin or intermediate filaments, the extracellular
domains mediate the homophilic bindings. Adaptor proteins are needed to actually bind the cadherin
to the cytoskeleton: catenins. (Β-catenin, p120-catenin in adherence junctions).
• Junction assembly and maintenance;
Mechanotransduction: mechanical signals are transduced and able to change junctional
behaviour. Most adherence junctions are subjected to pulling forces since they are bound to
actin and non-muscle myosin II. Disruption of myosin activity will result in the disassembly of
many adherence junctions. The contractictile forces on both sides of the junction are balanced,
so that no cell pulls another cell towards it. This ensures equal distribution of a cell throughout a
tissue. Large actin based forces, are able to pull two cells apart from each other.
Selectins require Ca2+
Carbohydrate binding proteins (lectins) that mediate transient cell-cell interactions in the
bloodstream. L-selectin on white blood cells, P selectin on platelets and endothelial cells that have
4
BBS2004, Cell
signalling
Cases, lectures, practicals and JC
Hermans, Sammy (Stud. FHML)
,Contents
Cases ....................................................................................................................................................................... 3
Case 1 the cellular intra- and internet ................................................................................................................ 3
Case 2 secretary molecules used in cell signalling .............................................................................................. 9
Case 3 signalling to degradate mRNA .............................................................................................................. 16
Case 4 from the outside to the inside without entering.................................................................................... 20
Case 5 what happens when signals go nuclear? ............................................................................................... 27
Case 6 How to deal with foreign chemical exposures? ..................................................................................... 31
Case 7 Signalling now for in the future ............................................................................................................. 36
Case 8 Oxidative stress, the good, the bad and the ugly .................................................................................. 41
Case 9 incoming and outgoing signals .............................................................................................................. 49
Case 10 CRISPR, genome editing ...................................................................................................................... 58
Case 11 biomedical techniques in cell signalling research ................................................................................ 63
Case 13 from mutations to cancer .................................................................................................................... 67
Lectures................................................................................................................................................................. 77
Lecture 1: cellular communication routes ......................................................................................................... 78
Lecture 2 cell derived signalling molecules ....................................................................................................... 82
Lecture 3: Signal transduction routes ............................................................................................................... 88
Lecture 4 introductory lecture on long and short term consequences of alterations in external signalling
molecules .......................................................................................................................................................... 93
Lecture 5 Redox aspects of cell signalling ......................................................................................................... 99
Lecture 6 pathway analysis ............................................................................................................................. 104
Lecture 7 signalling at network level .............................................................................................................. 107
Lecture 8 biotechnology in cell signalling research ......................................................................................... 110
Lecture 9 cancer and altered cell signalling .................................................................................................... 115
Practicals ............................................................................................................................................................. 124
Practical 1: TCDD and Ahr signalling .............................................................................................................. 124
Practical 2: Measurement of anti-oxidant induced lowered oxidative stress via H 2O2 detection in exhaled air.
........................................................................................................................................................................ 124
Practical 3: wikipathways, insulin phosphoproteomics & effect of Akt inhibition .......................................... 125
Journal clubs ....................................................................................................................................................... 128
Journal club 1 .................................................................................................................................................. 128
Journal Club 2 ................................................................................................................................................. 129
Journal Club 3 ................................................................................................................................................. 132
Journal club 4 .................................................................................................................................................. 136
Journal club 5 .................................................................................................................................................. 138
2
,Cases
Case 1 the cellular intra- and internet
How are the cells in an organ
organised? How are the cells
connected to each other?
Epithelial tissues
cells are tightly bound together in
sheets called the epithelia, underlying
these sheets there is a thin layer of
specialised extracellular matrix, called
the basal lamina or basement
membrane. Below the basal lamina,
there is connective tissue. Functions
of the basal lamina are:
• The basal lamina, attaches
and anchors the cells to the
underlying connective tissue. Integrins Junctions in an simple columnar epithelial cell
and proteoglycans, attach the cell membranes to the proteins in the basal lamina, which is in
turn linked to the connective tissue.
• Limits contact between epithelial cells and other cell types in the tissue.
• Acts as a filter: only water and small molecules are able to pass.
Within the epithelium, cells are attached to each other by cell-cell junctions. Cell-matrix junctions link
the cytoskeleton of epithelial cells to the basal lamina. The apex of the cell (upper surface) is exposed
to the extracellular matrix. At the basal side, epithelia are anchored to other tissue (basal lamina), at
the apical side not. Epithelia are thus polarised.
cell-cell junctions
Anchored cytoskeletal filaments transmit stresses across the interior of the cell, from adhesion side
to adhesion side.
• Lateral side of the cell: anchoring junctions: adherens junctions, which link actin filaments of
both cells and desmosomes which anchor intermediate filaments of the cell. The main
function of desmosomes is to provide mechanical strength. Therefore they are present in a
lot of numbers in tissues subjected to a lot of mechanical stress. The cadherin superfamily is
involved in these junctions.
• Tight junctions, hold the cells close together at the apex, which makes it possible for the
epithelial cells to perform the barrier function. They lie mostly apical (above) the adherens
and desmosome junctions. All these junctions together form a junctional complex. Tight
junctions seal the gap between the cells and prevent leaking of molecules (sealing function).
Transport across epithelium can happen via transcellular transport and paracellular
transport. The tight junctions can be permeable for small ions, but their permeability differs
per tissue. This difference results from the difference in proteins that form the tight junction.
Tight junctions are strands of transmembrane adhesion molecules, mainly claudin. Claudin is
important in the formation and function of the tight junctions. Occludin is important in
regulating the permeability of the tight junctions. Tricellulin is important for sealing the
membranes together and preventing trans epithelial leakage.
3
, Zona occludens (ZO) proteins play a major role in the organisation of tight junctions. They are
scaffold proteins that provide support while the tight junctions are build. They have PDZ
domains, which are sequences of amino acids that are able to bind a specific partner protein.
• Gap junctions: at the basal end of the cells, channel forming junctions which create pathways
to the cytoplasm of adjacent cells. The gap (1,4nm) is spanned by channel forming proteins:
connexin (vertebrates) and innexins (invertebrates). Small inorganic ions and water soluble
molecules are able to pass through these junctions (NO macromolecules such as proteins and
nucleic acids). This electrically couples adjacent cells, and is able to synchronise contractions
of heart muscle cells e.g. connexins are 4 transmembrane proteins together, and 6 connexins
are able to form a connexon. When two connexons in two adjacent cell membranes are
aligned it forms a connection between the interior of the two cells. Channels can differ in
permeability and regulation. Different types of connexin proteins can form heteromeric
connexons with specific properties. Gap
junctions can switch between open and
closed states, by various stimuli (e.g.
voltage differences). Connexin molecules
have only a half life time of a few hours:
there is constant turnover (adding (via
exocytosis) and removing) of the gap
junctions.
Transmembrane adhesion proteins:
Cadherin superfamily(require Ca2+): involved in adherens junctions & desmosomes.
Cadherins depend on Ca2+, they remove Ca2+ from the extracellular matrix, which
causes strong adhesion. Classical cadherins include E-cadherin, n-cadherin and P-
cadherin. These all have a similar structure (they are closely related in sequence)
in their intracellular and extracellular domain. Adhesion by classic cadherins is
involved in signalling pathways (Wnt e.g.). Nonclassical cadherins are more
distantly related in sequence, under which protocadherin.
Cadherins mediate homophilic adhesion, symmetrical anchoring junctions.
Cadherins will bind to the same/similar subtype of cadherin on the adjacent cell.
They thus bind cells of the same cell type together and segregate them from
other cell types. During development they play a crucial role in cell sorting.
Cadherins bind their partner with low affinity. Many parallel bonds result in strong attachments.
The intracellular domain of cadherin interacts with actin or intermediate filaments, the extracellular
domains mediate the homophilic bindings. Adaptor proteins are needed to actually bind the cadherin
to the cytoskeleton: catenins. (Β-catenin, p120-catenin in adherence junctions).
• Junction assembly and maintenance;
Mechanotransduction: mechanical signals are transduced and able to change junctional
behaviour. Most adherence junctions are subjected to pulling forces since they are bound to
actin and non-muscle myosin II. Disruption of myosin activity will result in the disassembly of
many adherence junctions. The contractictile forces on both sides of the junction are balanced,
so that no cell pulls another cell towards it. This ensures equal distribution of a cell throughout a
tissue. Large actin based forces, are able to pull two cells apart from each other.
Selectins require Ca2+
Carbohydrate binding proteins (lectins) that mediate transient cell-cell interactions in the
bloodstream. L-selectin on white blood cells, P selectin on platelets and endothelial cells that have
4
