iactaaleaest asked:

Can you please explain VDJ recombination to me? I'm a first year medical struggling with immunology!

Hi! I have a test coming up and I do not have the time to make comics and explain it to you like I usually do =)

I’ll explain it to you later, I promise (Just please remind me if I forget!)

Here is a great post on VDJ recombination for now —> http://immense-immunology-insight.tumblr.com/post/84724911095/b-and-t-cell-maturation

I reblogged it myself for you.

Hope you get comfortable with immunology and rock it this year!

julieyumi

B and T cell maturation

julieyumi:

Let’s start with B cell maturation. Our location: the bone marrow.

You are a stem-cell who has a choice in becoming a B or T cell. As in elections, since you’re for becoming a B cell, you’re pro-B, however, to become pre-B, you need a heavy chain to whip away your political opponents (jk, but you do need a heavy chain). Just like how you need a strong base when building a house, you’ll need a heavy (as opposed to light) chain to start building a receptor/antibody/immunoglobulin(Ig). To do this, you have to go through somatic recombination of VDJ segments.

What are VDJ segments? On a chromosome, there are multiple V (V1, V2, V3…), D (D1, D2, D3…), and J genes (J1, J2, J3…). It’s important to know that the heavy chain can be considered “heavy” because it expresses three (V, D, and J) genes while the future light chain only expresses two (V and J) genes. The heavy chain likes to think of itself as a cool “Puff daddy” or “Big daddy” or the like, so it gets its “DJ” genes rearranged before recombining with the V gene. How does it do that?

Think of the (V)DJ gene sequence as a long piece of tape. The RAG enzymes randomly choose two spots (one random D gene and J gene) on the piece of tape to stick together and makes a loop. Artemis comes along and cuts out the loop and there’s a repeat of this loop-snipping upstream with the V-segment. Then you end up with a unique VDJ recombination (e.g., V3-D7-J5 gene combination) attached to a full sequence of constant regions (mu, delta, gamma...). Then TdT comes along, thinking that the VDJ combination isn’t random enough, and vomits random nucleotides all over its ends until it’s satisfied. Ligase just wants to get work over with, so it glues everything together, and voila! You have the DNA blueprint for the heavy chain.

Okay, that’s all and well. Now that you have a heavy chain, you are now officially pre-B! But, wait!! Rather than just being pre-B cell, wouldn’t it be better if you were actually a B cell?! So, let’s do it. All, you’ll need is a light chain.

Uh-oh. If you’re like me, you have a difficult time making choices. Your mom and your dad both have lamda and kappa chains. Each different chain has a VJ segment that you can rearrange. This means you have four choices (and consequently, four chances) to recombine a great light chain. Okay, once you finally make your decision, you undergo somatic recombination again with the RAG, TdT, and ligase enzymes to create your very own “VJ + nucleotide vomit” light chain blueprint.

Now, before we go any further, why did you need both light and heavy chains and what does idiotype and isotype mean?

To simplify things, the constant region of the heavy chain determines the isotype of the receptor/antibody/immunoglobulin (I think the the “S” in isotype occurs later in the alphabet than the “D” in idiotype and so the S occurs in the chain with more letters (V, D, and J)) and the variable regions on the light chain determines the idiotype. You can think of the heavy chain/isotype as being a car and the light chain/idiotype being an undercover officer. Now the undercover officer has been given a case to catch a very specific criminal. In fact, this undercover officer is actually a Terminator and was built solely for catching this one person (antigen). It’s in his robotic DNA, which cannot be reprogrammed. Meanwhile, he owns a Transformer disguised as a default police car (IgM). Once he spies the criminal, if occasion calls for a faster or more bad-ass vehicle, then he can isotype switch his Transformer to a boat (i.e., IgA which is secreted with mucus, etc) or submarine (i.e., IgG which can cross the placenta).

I think I may have lost you, so let me reexplain here.

The light chain’s VJ—the somatic recombination that determined the antibody’s specificity for a certain antigen—has been set in stone (because it was a DNA recombination). Meanwhile, although the heavy chain’s VDJ has been set in stone, it still contained the full sequence of constant regions (mu, delta, gamma…). You know that DNA is just a blueprint. It’s the RNA that determines what proteins will be made. So, when the initial mRNA was made from the heavy chain blueprint, only the mu and delta regions were expressed as IgM/IgD. When certain conditions are met, it can go back to the DNA blueprint, and using “switch regions”, selectively splice out the constant regions it no longer wants to express (i.e., police car mode). In doing so, it can now be a boat (IgA) or sub (IgG), etc. However, now that we’re rearranging DNA, once the antibody becomes IgA, it can no longer become an IgM. That part of the blueprint for it is gone forever.

Okay, so right now we have this highly specific Terminator currently driving a Transformer in its default IgM police car mode. He then gets a call from officer TH1 from the lymph node germinal center, and there, the officer presents to him the finger he shot off the criminal/antigen. The Terminator alarmingly eats the finger and then begins to divide. Let’s briefly switch back to medical terminology here.

After the B-cell comes in contact with the antigen, it can do multiple things.

  1. If triggered by TH1’s CD40L, it can undergo isotype switching (we’ll address TH1 later). This is what I said earlier about the Transformer changing shapes. This means that the heavy chain undergoes DNA splicing of the constant regions and expresses gamma or alpha or other constant regions such as IgG or IgA, etc instead of IgM and IgD. Now it can chase after the antigen wherever it goes (as opposed to being a huge, chunky IgM pentamer that’s stuck in one spot).

  2. The B cell can undergo somatic hypermutation. HYPERMUTATION, NOT RECOMBINATION. Remember, somatic recombination occurs in the bone marrow, where V(D)J’s recombined. This hypermutation is also exactly what it sounds like. The variable regions (the regions that are selective for the antigen) are randomly mutated to try become more adept (“sticky”) at catching the antigen. Of course this could fail and the antibody could become less selective for the antigen, but those are quickly discarded. It’s survival of the fittest, and the B-cell that has the mutation that produces the immunoglobulin that’s best at catching the antigen, can further become:

    1. Plasma cells: these B-cells produce antibodies/immunoglobulins to secrete all over the place (like those robotic spiders in Minority Report)

    2. Memory cells: these B-cells are very long-lived and help defend against reinfection. They keep immunoglobulins on their surface as receptors (as opposed to antibodies which are released).

We’ll go more into the mechanism of B cell activation later. For now, we’ll say that Plasma-Terminator is on the move, secreting tons of antibodies. What do these antibodies do?

  1. They swarm and bind to the antigen and prevent it from damaging or binding to cells.

  2. They coat the antigen and alert macrophages and other proper immunological authorities to remove or destroy the antigen

  3. They trigger the complement pathway to also remove or destroy the antigen

They’re pretty much a swarm of target-locked, heavy flags.

Now onto T cell maturation.

We shall start once again at the bone marrow. This time, you want to be a T-cell, so you’re pro-T cell. The requirements for being a pre-T cell are similar to being a pre-B cell: you need a heavy chain, except in this case, it’s called a β chain. I hope I explained somatic recombination well to you earlier, because that’s exactly what you do here with V, D, and J gene segments. It should be no surprise to you that to become an immature T-cell, you also need your light chain, in this case called an α chain, also achieved via somatic recombination of the V and J genes. α and β chains combine to form something known as the T-cell receptor (as opposed to a B-cell receptor/immunoglobulin/antibody). Along with the T-cell receptor, the CD3 (basic signaling), CD4, and CD8 receptors are attached to the immature T-cell. Now are where things get different. Let’s move over to the thymus.

In the thymus, starting from the cortex, our immature T-cell is confronted by multiple TEC cells bearing both MHC1 and MHC2’s. We’ll get to how MHC’s present antigens in a bit, but first let’s learn the rule of 8’s:

  • CD8 binds to antigens presented on MHC1 (which is found on all nucleated cells) because 8*1=8

  • CD4 binds to antigens presented on MHC2 (which is found only on antigen presenting cells) because 4*2=8

Now, whichever receptor, CD4 or CD8, binds first to a TEC cell, basically decides what kind of T cell it will become. Unsurprisingly, if CD4 binds first, the T cell will become a CD4 cell (and CD8, then CD8 T cell) and the unbound receptor will “fall off.” However, if the T cell fails to bind to a TEC, it’s destroyed. This is called positive selection (because it had to bind to an MHC to live).

The survived T cell migrates down to the cortico-medullary junction inside the thymus and is confronted by dendritic cells which present our own antigens (self-antigens) to the T cell. Our body doesn’t want T cells that attack our own cells, so if these T cells bind too strongly to these dendritic cells, then these T cells are also destroyed. This is called negative selection (because it had to not bind too strongly to live).

So in short, positive and negative selection are used to select for T cells that are able to recognize antigens (positive), but not attack its host (negative).

There are two types of T cells now, CD8 and CD4. CD8 cells (aka “cytotoxic T cells”) kill infected cells in order to destroy the pathogens within (like viruses or intracellular organisms). CD4 cells (aka “helper cells”) help infected cells destroy the cells they ingested (inside phagosomes) and also help B cells isotype switch and produce more antibodies.

Let’s start with CD8 T cells.

CD8 T cells currently have a T-cell receptor, CD3 (for signaling), and CD8 receptor (among others unnamed). They go through the medulla, through the HEV, and to the lymph nodes. In the lymph node’s medulla, they meet with an antigen presenting cell (APC) that, well, present antigens to them. What happens next?

The immature CD8’s T-cell receptor and CD8 receptor bind the APC’s MHC1 just like it did with the TEC in the thymus. However, the CD8 matures when its CD28 receptor binds the APC’s B7 receptor (aka CD80/86). This second signal stimulates CD8’s maturation and allows CD8 to kick ass. The T cell then secretes a whole bunch of IL2 to replicate itself, then its clone army leaves the lymph nodes and travels to the site of the infection. There, they bind infected cells and release perforins and granzymes to aid in cellular destruction. No cell = no home for the intracellular pathogen.

Now for CD4 T cells.

Likewise in the medulla of the lymph nodes, the immature CD4 cells encounter an APC presenting an antigen on their MHC2. Like with CD8, the CD4 matures when both the CD4 receptor and the CD28 receptors bind the APC’s MHC2 and B7 receptors, respectively. The T cell then can secrete IL2 to form another clone army. Here, the APC decides which of two types of CD4’s the T cell will become:

  1. If the APC secretes IL12, the CD4 will become a TH1 cell.

    1. TH1’s go to the site of infection and latch onto an infected cell’s MHC2. By releasing interferon-γ, the target (infected) phagocytes release toxins to destroy bacteria trapped inside their vesicles.

    2. TH1’s CD40ligand (CD40L) can also attach to a B-cell’s CD40 receptor inducing B cell isotype switch!!

    3. They can also upregulate the B cell’s B7 (CD80/86) receptors. Remember that when B7 binds an immature B or T cell’s CD28 receptor, the B or T cell matures!

  2. If the APC secretes IL4, the CD4 will become a TH2 cell.
    TH2’s secrete IL5 and IL6, which stimulate B cell antibody secretion. TH2’s can also make more of itself by secreting IL4. Since TH2 stimulates antibody production, it’s the best T cell to prevent future reinfections. It should also be noted that the secretion of IL4 decreases the secretion of IL12 and consequently decreases the production of TH1’s; likewise, the secretion of IL12 suppresses the secretion of IL4 and decreases the production of TH2’s.

Okay, now for MHC’s.

I already mentioned this before, but:

  • MHC1 is found on all nucleated cells and presents antigens to CD8. CD8 T cells kill infected cells and intracellular, cytosolic pathogens (i.e., viruses).

  • MHC2 is found on APC’s and presents antigens to CD4. CD4 T cells help infected cells kill ingested, vesicle-contained pathogens (i.e., bacteria).

Let’s start with MHC1. MHC1 is expressed via HLA-A, HLA-B, and HLA-C. Here is how it presents an antigen.

  1. Say a virus injects itself into a cell and gets broken down into pieces by proteases.

  2. The viral peptides enter the cell’s endoplasmic reticulum (ER) through a TAP channel.

  3. MHC1 stored inside the ER bind the peptides.

  4. The bound MHC1 moves from the ER to the Golgi and is packaged in a vesicle.

  5. The vesicle floats to the cell-surface like a balloon, where the receptor is released and presents the bound viral peptide for CD8’s to see.

Now for MHC2. MHC2 is expressed via HLA-DP, HLA-DQ, and HLA-DR. See how it has an extra letter? Well, consider that extra letter an extra component of the MHC2, because unlike MHC1, MHC2 has a clip. Here is how MHC2 presents an antigen:

  1. Say a bacterium gets engulfed by a phagocyte and is trapped inside a vesicle.

  2. A lysosome comes along and fuses with that vesicle and chews up the bacterium.

  3. MHC2 gets notice of entry and is moved from the ER to the Golgi, where it’s packaged into a vesicle.

  4. The MHC2 floats up with its clip and its vesicle fuses with the phago-lysosome.

  5. The clip is acidified off and MHC2 binds the chewed up bacteria.

  6. The MHC2 floats up to the surface and presents its antigen to CD4’s.

Okay, I think that’s enough for both you and me. I hope this helps you and if you have any questions, just ask. :) phew!

VDJ recombination simplified.

dac1958 asked:

Is it possible to receive a liver transplant for Chronic Hep B, only to find out 2 yrs later (ALT and AST were at 400 and 500) that you had an underlying primary immunological disorder that is now manifesting as autoimmune hepatitis. This is what the transplant doctors are telling me, but I have the gut feeling a mistake was made during the surgery which caused graft dysfunction. They won't give me access to my records and my new liver (2 yrs old) is completely cirrhotic, due to AIH.

I am sorry to hear about your diagnosis.

Yes. It is possible for autoimmune hepatitis to be diagnosed after the transplant.

I can not be too sure, but I think the condition you are talking about is De Novo Autoimmune Hepatitis. It typically shows up 12 months after transplant. Source: http://graft.edina.clockss.org/cgi/reprint/6/2/120.pdf

It must be hard, but I strongly recommend that you trust your doctors. I am not an expert, but as far as I know, surgical mistakes don’t cause autoimmunity or graft dysfunction.

About accessing health records: The Health Insurance Portability and Accountability Act (HIPAA) Privacy Rule gives you, with few exceptions, the right to receive a copy of your medical records held by health care providers. If you want a copy, you may have to apply in writing, pay a fee and wait (up to 40 days).

Diagnostics can be a tricky little place to be in. Consider this, Your patient has been coughing his lungs out and you can’t quite put a finger on what’s causing it. A la house M.D., you have 20 different differentials scribbled on a white board/notepad. But the question still remains: What is the mysterious little creature coursing the airway of your patient? A zillion coffee mugs later you are not very much closer to IDing the rogue.Phew! There there. Enter Mr.(Ms./Mrs./ Dr.? ) Microbiologist to the rescue. A few diagnostic procedures and voila, he presents to you the little tyrant. You thank your stars for LabDs and move on to the next patient.Now that we’ve established the importance of lab diagnostics, you must also know that there are many procedures involved. However few of these tests are as sensitive, economic  and as easy to perform as the Enzyme immunoassay (EIA). ELISA ( Enzyme linked immunosorbent assay), an heterogeneous EIA, is quite a popular diagnostic method. The principle behind it is fairly simple and easy to grasp.Whenever you have an infection, the B-lymphocytes in your body produce antibodies which then bind to the antigen (infection causing agent) and a series of events ensue which eventually help in getting rid of the infection. These antibodies are specific to the antigen that has opened attack, which means, it will bind to that infectious agent and none other (most of the time). Thus, If an antigen is exposed to its specific antibody, they are bound to bind!This insane specificity is what drove scientists to develop the ELISA. A fairly easy concept which gave rise to a fairly easy lab procedure. Coat a plate with the antigen, put a patient’s serum in it. Add a substrate and some enzyme tagged anti-antibody. If this magic diagnostic mix develops/changes color, antibodies are swarming the serum in significant quantities. As with other procedures there are errors involved. However, most of these are overcome by setting up positive and negative controls which help you to know if the color has actually changed and to what extent. To quantitatively analyse, color intensity meters are available. Infections are sometimes missed if the concentration of antibodies is not significant enough or if antibodies have not yet been formed. This is overcome by repeating the test at regular intervals in suspected patients.However, modifications in the ELISA (ALL HAIL SUPERELISA) leave little scope for false negatives. ELISAs and modified ELISAs are very rampantly used now to detect anything from adulterants to pregnancies. This only proves that even a very basic concept if understood can go on to create a revolution, also millions in patent rights.So hit the books hard, who knows you might just create the next ELISA.Some terminologies (roughly put);Sensitivity:  The ability of the test to detect even the most minute quantities. A very sensitive test will not give you any false negatives.Specificity: This basically means that the test will give a positive for only that antigen and none other. This means no cross reactions and thus no false positives.
This post was written by a friend of mine. Since it was her first blog post, she was very nervous. Please say something nice and encourage her to write more! =)

Diagnostics can be a tricky little place to be in. Consider this, Your patient has been coughing his lungs out and you can’t quite put a finger on what’s causing it. A la house M.D., you have 20 different differentials scribbled on a white board/notepad. But the question still remains: What is the mysterious little creature coursing the airway of your patient? A zillion coffee mugs later you are not very much closer to IDing the rogue.

Phew! There there. Enter Mr.(Ms./Mrs./ Dr.? ) Microbiologist to the rescue. A few diagnostic procedures and voila, he presents to you the little tyrant. You thank your stars for LabDs and move on to the next patient.

Now that we’ve established the importance of lab diagnostics, you must also know that there are many procedures involved. However few of these tests are as sensitive, economic  and as easy to perform as the Enzyme immunoassay (EIA). ELISA ( Enzyme linked immunosorbent assay), an heterogeneous EIA, is quite a popular diagnostic method. The principle behind it is fairly simple and easy to grasp.

Whenever you have an infection, the B-lymphocytes in your body produce antibodies which then bind to the antigen (infection causing agent) and a series of events ensue which eventually help in getting rid of the infection. These antibodies are specific to the antigen that has opened attack, which means, it will bind to that infectious agent and none other (most of the time). Thus, If an antigen is exposed to its specific antibody, they are bound to bind!

This insane specificity is what drove scientists to develop the ELISA. A fairly easy concept which gave rise to a fairly easy lab procedure. Coat a plate with the antigen, put a patient’s serum in it. Add a substrate and some enzyme tagged anti-antibody. If this magic diagnostic mix develops/changes color, antibodies are swarming the serum in significant quantities. 

As with other procedures there are errors involved. However, most of these are overcome by setting up positive and negative controls which help you to know if the color has actually changed and to what extent. To quantitatively analyse, color intensity meters are available. Infections are sometimes missed if the concentration of antibodies is not significant enough or if antibodies have not yet been formed. This is overcome by repeating the test at regular intervals in suspected patients.
However, modifications in the ELISA (ALL HAIL SUPERELISA) leave little scope for false negatives. ELISAs and modified ELISAs are very rampantly used now to detect anything from adulterants to pregnancies. This only proves that even a very basic concept if understood can go on to create a revolution, also millions in patent rights.

So hit the books hard, who knows you might just create the next ELISA.

Some terminologies (roughly put);
Sensitivity:  The ability of the test to detect even the most minute quantities. A very sensitive test will not give you any false negatives.
Specificity: This basically means that the test will give a positive for only that antigen and none other. This means no cross reactions and thus no false positives.

This post was written by a friend of mine. Since it was her first blog post, she was very nervous. Please say something nice and encourage her to write more! =)

Anonymous asked:

Hi, Can you explain why once you get an autoimmune disease you are more likely to get others? Thanks!

The specific cause of autoimmune diseases is not completely known.

Autoimmunity is thought to result from a combination of genetic susceptibility (what you inherit from your parents), breakdown in natural tolerance mechanisms (how your body decides what is harmful and what is not), and environmental triggers such as infections (that confuse your body about what is good or bad).

So we don’t really know what exactly causes it and hence we can’t really point out why once you get an autoimmune disease you are more likely to get others.

In some individuals, mechanisms that prevent autoimmunity like the central tolerance mechanisms that eliminate newly formed strongly autoreactive lymphocytes are impaired. (Your body allows lymphocytes that kill your cells to stay.) Obviously, you are more susceptible in such a case. In others, there are genetic risk factors like genetic variants of alleles of MHC class II molecules.

It’s complex and many factors play a role.

Hope you understand what lil explanation I gave you! =)

Anonymous asked:

I love this blog! I'm a freshman (in high school) and I'm taking an honors biology class right now! It's great to read things on here and bring them up it conversation with my teacher for some bonus points ;)

That’s amazing.. I love the passion you all have!

Do share with us and let us know if you learnt something new & unusual from your teacher as well ^__^

soundofaspark asked:

Hello, I'm a huge fan! Your posts are cool and helpful. I became interested in immunology when I was diagnosed with Rheumatoid Arthritis (and Crohn's disease) I have taken several anti-TNF biologics. Could you please illustrate how they work? Thanks!

Thank you for the compliments!

The pathogenesis of Crohn’s disease and rheumatoid arthritis is complex. If  I were to over simply it, I’d think of the disease as a type IV hypersensitivity in which the body is reacting to self antigens in rheumatoid arthritis and commensal bacteria in Crohns disease.

image

One of the principal cytokines secreted by activated macrophages is TNF-a. TNF-a is an inducer of a local inflammatory response that helps to contain infections.

Think of TNF-a as a key. It’s unlocks the door to many inflammatory processes, some of which may be harmful. Think of TNF-a receptor as the key hole.

Some anti-TNF biologics like Infliximab bind to the key and make them look funny! This prevents the effective binding of TNF-α with its receptors.

Other anti-TNF biologics such as Etanercept look like the key hole. They bind to it and prevent TNF-a to bind to the real key hole. It reduces the effect of naturally present TNF, and hence is a TNF inhibitor, functioning as a decoy receptor that binds to TNF. This is what complex terms like “soluble proteins that mimic the receptor” mean.

Tried my best not to make the explanation too science-y!

I hope that your treatments go well =)

linve94 asked:

Oh my god, I love your blog! I am a medicine student (2nd year). Your blog is awesome. I have understood much better the things I have studied today with your images. Thank you very much! You are the Tfh that activates my B lymphocytes! ;)

Haha I am so glad it helped!