CLASS: 10:00-11:00
DATE: 9-27-10
PROFESSOR: Dr. Burrows
Antibody and T Cell Receptor Genetics
Scribe: Eric Larson
Proof: Lauren Morris
Page 1 of 4
I. Title [S1]
II. Learning Objectives [S2]
a. Basically this lecture will cover the mechanisms for generating the great amount receptor diversity we see in
immunoglobulins (Ig)
b. After that we’ll discuss the mechanism for switching isotypes
c. Then we’ll talk a little about the difference between T cell and B cell antigen receptors
III. Antigen Receptor Diversity [S3]
a. The process of generating antigen receptor diversity is critical to our survival
b. Pathogens can mutate very rapidly, so we’re always being presented with new pathogens we’ve never seen
before
c. Our immune system must have a wide spectrum of cells with various receptors waiting for new pathogens to
come in, so that one can hopefully be able to recognize nearly any pathogen
d. This enables your immune system to be prepared to respond to pathogens it’s never encountered
IV. Generation of Diversity – Cellular Solutions [S4]
a. Diversity begins at the lymphocyte, because each lymphocyte has a receptor which is unique for a particular
antigen
b. We produce these lymphocytes in our bone marrow, and make about a million new lymphocytes every day
c. An antigen can come in contact with one of those lymphocytes, which will induce an immune response
V. Antigen Selects Lymphocytes [S5]
a. Here we see how an antigen comes in contact with a B cell, and how the B cell then rapidly divides and
specializes
b. Obviously though, since we produce so many new lymphocytes that never come in contact with an antigen
those that aren’t used must die so that we don’t become a big bag of lympocytes
c. It may be a wasteful strategy, constantly getting rid of lymphocytes making a million new lymphocytes each
day, but it works
VI. B Cell Production and Proliferation [S6]
a. The process of proliferation and switching which occurs in the peripheral lymphoid tissue is dependent on
antigen
i. An antigen must interact with a receptor on a lymphocyte
b. What we’ll talk about today is happening in the bone marrow and doesn’t require antigen
i. It is a developmental process that has no need for antigen
VII. Antigen-Antibody Binding [S7]
a. Each one of the lymphocytes has a different receptor which can bind to different epitopes
b. The reason that they are different is because they are encoded by different genes
VIII. Generation of Diversity [S8]
a. Here is where we run into a serious problem
b. We accept the idea that we need to be able to respond to a wide variety of pathogens
c. This is accomplished by having the ability to produce up to 100 million antibodies
d. However, we can do some quick math and figure out pretty easily that we don’t have enough DNA to directly
code for that many different antibodies
i. We’d need about ten billion base pairs of DNA, but we only have three billion
e. So the immune system has had to figure out a way to make all these receptors without taking over our whole
genome
IX. Anatomy of a Typcial Gene [S9]
a. Here’s a quick review of what a typical gene looks like in humans
b. If you look at the mRNA it is pretty much colinear with the protein - you start reading at the one end and read
to the other end when making the protein
c. The DNA is expressed in different exons which are transcribed into the mRNA, which is spliced, which is then
translated into a protein
d. That’s how you make a protein from a typical gene
X. Anatomy of Immunoglobulin Genes in B Lymphocytes [S10]
a. B cell genes look just like regular genes
b. The protein corresponds to the gene directly for both the light and heavy chains, which is pretty normal
c. But if we want to make 10 million receptor genes, we can’t do it this way
XI. Generation of Diversity – Genetic Solutions [S11]
a. What we find is that the variable region genes for antigen receptors don’t exist anywhere in the body, until
they are generated during B cell development in the bone marrow
b. The variable region exons are what must be spliced together to make the functional gene segments
CLASS: 10:00-11:00
Scribe: Eric Larson
DATE: 9-27-10
Proof: Lauren Morris
PROFESSOR: Dr. Burrows
Antibody and T Cell Receptor Genetics
Page 2 of 4
c. These parts of the gene are inherited through the germline, but are not functional until they are spliced - you
only inherit the potential to make the genes, but do not inherit the genes themselves
d. This whole process of splicing segments is called immunoglobulin or TCR (in the case of T cells) gene
rearrangement
e. This is what allows us to generate such great diversity without monopolizing the entire chromosome
XII. Variable Region Genes are Constructed from Gene Segments[S12]
a. Here again we’re looking at the B cell DNA
b. On the left if you look at the germline DNA you can see how variable (V) and constant (C) gene segments are
separated
c. From that DNA you can’t make a light chain directly because the segments are separated, but that’s the
configuration you inherit
d. So somehow in the process of becoming a B cell, the segments must join together to make a functional
variable region exon which produces the light chain
e. The same thing is true for the heavy chain
f. Again, if you look at the exon segments for the heavy chain, they are separated on the germline DNA
g. The question now is: how does simply joining genes together create diversity?
h. The answer is that there is more than one copy of each of the gene segments
XIII. Germline Ig Genes [S13]
a. Again we have the constant region sections, the J gene segments (5 of them), and a lot V gene segments
b. Since we have multiple segments for each group we must now pick out one segment from each group, which
is where the diversity comes from
c. By the way, V gene segments are genes that are not functional - don’t get it confused with the variable region
exon which is functional - if I talk about segments I mean something that isn’t functional yet
d. So what happens is that during the development of B cells, these segments undergo Ig gene rearrangement
XIV.
Joining of V-Region Segments by Somatic Recombination [S14]
a. So here’s the light chain again
b. You take this long strand of DNA and bring together the V and J regions, you then cut the DNA and stick the
V and the J segments together
c. Now you’ve made a functional variable region exon for the light chain
d. This process is a little weird because you break up chromosomes to mix and match and stick things together,
when typically you want to keep your genome stable and not cut it to pieces in order to prevent mutations
e. This is the same process that’s happening for the heavy chain locus and T cell receptor only with different
genes
f. The process can be called somatic recombination, or Ig gene rearrangement
XV. Somatic Recombination at the Ig Heavy Chain locus [S15]
a. This recombination process begins with picking one particular D segment and attaching it to a separate J
segments
b. That results in a D to J rearrangement
c. Next, you rearrange one of the V segments to contact the D-J segment
d. Once those segments are attached, you’ve made a functional exon for an Ig heavy chain which can then be
transcribed
e. The two processes of light chain gene rearrangement and heavy chain gene rearrangement take place
sequentially in the bone marrow
f. Keep in mind that between each process the cell is proliferating, which allows for a further increasing of
diversity
i. More diversity because each proliferated cell can pick different gene segments in the subsequent
recombination process, resulting in greater variety
XVI.
Benefits of Antigen Receptor Gene Rearrangement [S16]
a. It’s not important to know the specific numbers shown here, just the principle behind the numbers
b. So by random picking you can make over 2 million IgM  antibodies and just under a million IgM  antibodies
c. The immune system uses this multiplication of possibilities to generate a lot of diversity
d. Remember that each B cell only makes one type of antibody
XVII. Isotype Switching [S17]
a. Isotype switching uses somatic recombination as well
XVIII. Isotype Switching [S18]
a. Here we see a mouse B cell that has been produced to make IgM
b. But then the B cell leaves the bone marrow, becomes stimulated by antigen and T cells, and undergoes
isotype switching
c. This particular B cell switches to IgG3
CLASS: 10:00-11:00
Scribe: Eric Larson
DATE: 9-27-10
Proof: Lauren Morris
PROFESSOR: Dr. Burrows
Antibody and T Cell Receptor Genetics
Page 3 of 4
d. The switching is accomplished by the same steps we’ve seen before: looping out a large portion of DNA,
deleting what’s in between and joining the important parts of DNA
e. Now you’ve created a new gene which encodes for a new isotype protein
f. Again, this diversity was accomplished by the process of somatic recombination
XIX.
Switch Recombination [S19]
a. Isotype switch recombination is very efficient for two reasons:
i. There isn’t a separate VDJH recombination for each isotype
ii. We don’t do recombination for all B cells, we only do it to B cells that respond to an antigen
b. This process is irreversible because you’ve already tossed out DNA in between the regions spliced together
to make the isotype, which can’t be retrieved
c. And again, each plasma cell produces only one isotype of B cell with one specificity of receptor
XX. Primary and Secondary Antibody Responses [S19]
a. Isotype switching process actually explains some things we see in our immune response
b. If you look at this graph of serum Ig concentrations, you will see how first IgM concentration increases but
then decreases as the IgG concentration increases
c. Next, look at the second response and you can see how the IgG response increases more rapidly and to a
larger extent
i. This happens because the memory cells have already switched to the IgG receptor for this antigen on their
surface as a result of the first response and the subsequent isotype switching
XXI.
The T Cell Receptor for Antigen - TCR [S21]
a. We’re done with antibodies and will now consider T cells
XXII. Comparison of the TCR and BCR (Immunoglobulin) [S22]
a. Let’s examine how T cells receptors look like
b. This might be an IgG receptor on a B cell on the right, and on the left is the T cell receptor
c. What you’ll see is that the T cell receptor has two protein chains, an  and a  chain, as well as a variable
region and constant region just like Ig structure
d. The variable region on T cells is made by gene rearrangement, just like the variable region of Ig
XXIII. Structure of the T-Cell Receptor [S23]
a. See there are two transmembrane proteins held together by disulfide bonds
b. One ach chain there is also a variable region, constant region, and transmembrane region for both chains
c. The variable regions are the portions which interact with antigens
XXIV. The T Cell Receptor [S24]
a. Here are a few things to know about a T cell receptor
b. It is a heterodimer, and only ever exists as a transmembrane receptor
c. T cells don’t secrete their receptors like B cells do
d. The variable region exons are generated by gene recombination
e. And again, the process of recombination is identical to IG gene rearrangements, except that different gene
segments are used for T cell receptors
XXV. T-Cell Receptor V Regions are Generated by Gene Segment Rearrangement [S25]
a. This figure gives you the idea in a nutshell
b. The α chain only has two gene segments that need to be rearranged before it can be produced – the V and J
segments
c. The β chain has three gene segments that must be rearranged to make the protein - the V, D and J segments
d. So just like in B cells, you have a sequential rearrangement process
i. The  chain sequences are rearranged, then the  chain sequences, and then the whole receptor can be
produced and placed on the cell surface
XXVI. B Cells Recognize Intact Protein Antigens [S26]
a. The reason for the different receptors on T cells and B cells, is that they recognize antigen in a different way
b. B cells can recognize intact protein antigens, something T cells can’t do
XXVII. T Cells Recognize Processed (Degraded) Protein Antigens [S27]
a. What T cells do instead is recognize antigens that have been processed (degraded)
b. T cells can only recognize peptides of antigens that are being displayed by the MHC molecule on the surface
of its target cell
XXVIII. Dangers in Diversity [S28]
a. It’s good to know that all this diversity is not without risk
b. The mixing and matching of gene segments is random, and so by chance some of those receptors might
recognize self antigens
c. It is necessary to get rid of self-recognizing antigens
i. If you don’t you get autoimmune diseases
CLASS: 10:00-11:00
Scribe: Eric Larson
DATE: 9-27-10
Proof: Lauren Morris
PROFESSOR: Dr. Burrows
Antibody and T Cell Receptor Genetics
Page 4 of 4
d. The other issue is that when you break chromosomes for recombination or isotype switching you can get
chromosome translocations
i. This can produce oncogenes, which in turn can result in lymphoid malignancies
[End 44:34 mins]