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The Spectrum of Cells
A single fertilized egg develops into a
human body, brain and all. During this
process perhaps 300 different types of cells
arise. Understanding and controlling this
process of development is critical for stem
cell based medicine.
For some animals, such as C. elegans, the complete lineage and
type of every cell is worked out.
Cell Lineage Tree of C. elegans, focusing on the gut.
Full cell lineage for C. elegans, worked out by John Sulston and
colleagues using microscope, eye, sketchbook and patience.
Vertebrate development is too
complex to work by hand
Mouse embryos days 7 - 10
Some cell lineages, such
as those leading from
the hematopoietic stem
cell to the various types
of cells that make up the
blood stream and much
of the immune system
are well worked out in
vertebrates.
A good deal of stem cell
research involves finding
marker genes that
distinguish between
different cell types at
various branches in the
differentiation tree. In
many cases the discovery
of new markers has
resulted in the definition
of new cell types.
Blood cell lineages
were worked out
with surface markers
and a cell sorter.
Many types of cells
don’t sort so easily,
but usually cell
nuclei can be
resolved even in
fairly complex
embryos by
microscopy,
especially confocal
microscopy.
Multiple markers can be used to classify cells into different
types with microscopy as well as with sorters. Using quantum
dots it is now possible to label simultaneously with a dozen
markers.
Cell 450
nm
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nm
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nm
525
nm
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nm
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nm
600
nm
3
1
650
nm
1
5
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625
nm
8
1
1
7
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3
9
5
5
Note: last two might look same to eye but not to sensors, which have more than three
channels.
Next cells would be clustered into
groups that share similar color
values across all channels.
Several algorithms exist to do this.
These algorithms are used on
microarray data and elsewhere.
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540230053
671330063
780341073
440120164
570340063
000300010
000301000
000400020
000300010
010058001
000057002
020168002
700000100
900100100
800100200
Trails in color space between clusters, and to a certain extent
proximity of clusters in color space, could be used to define edges
in cell type lineage graph
Information about
where cells are
located and in what
embyronic stage
could also come in
helpful here.
Ideal Markers
• Unlike cell sorting experiments, would try to pick
markers that are each present in 1/3 to 2/3 of cell
types rather than markers present in only one cell
type.
• The markers would be chosen so that their
expression patterns were relatively independent of
each other, using resources such as Allen Brain
Atlas
• In ideal world, 8 perfect markers expressed at two
different levels could distinguish 256 cell types.
In real world we’d hope 12 or 15 well chosen
markers at three or four distinct levels would be
enough.
Cell Spectrum Summary
1) Use brain and gene atlas data to find 10 to 20
nuclear markers with distinct but overlapping
expression patterns.
2) Label antibodies with quantum dots.
3) Stain thick slices with labeled antibodies.
4) Capture images with multichannel confocal
microscope.
5) Identify nuclei and assign colors to them.
6) Cluster based on color to define cell types.
7) Construct tree of cell types by looking at spatial
and temporal data, and looking for intermediate
forms.
The End