Friday, September 05, 2008

TLR, PPR, cytokines and signaling

I am a microbiologist. The last couple of weeks however (ah, who am I kidding – lots of months of my post doc stint) I have been trying to become more of an immunologist. Let’s just say that I have never really been a fan of signaling pathways. And what is immunology? That’s right, signaling and reactions to that (inflammation and activation of different parts of the immune system).

My latest thing is TLRs*… or really, trying to figure out why this TLR # is involved in this, and why it isn’t. The hypothesis was “it should be a better outcome, let’s just try it”. The outcome turned out to be the complete opposite. (Not really surprising to anyone who has done those “this is the last control experiment, let’s just confirm the hypothesis”.) Don’t get me wrong. I am all fun and games about this since it means that I might have discovered something really new. Then again there is always this thing that I have misunderstood something. Since we are talking about TLR, PPR**, PAMP***, MyD88****, NfKb***** and the lots of the rest of the proinflammatory cytokines - and last but not least T cell activation and MCH recognition – this is not at all something impossible.

Personally I find it interesting that my reaction to signal pathways (let’s be honest here – mainly immunology and T cells, CD4, CD8, TLR, Il12, Il1, TNF-a and all the other abbreviations and letters that immunologist throw around for fun) is similar to the majority of adolescent students when presented with math and math problems. “I can’t do this. Huu… let’s run away and not think about it. Really, who need this anyway.”

Anyone with a brain can see though that this approach isn’t really helping me get any closer to finishing the paper/project and understanding the bigger picture. Hence, what to do? Well, I guess the drawing I am doing at the moment with the nice little receptor on the cell membrane getting attacked by parts of TLR# activation parts from the bacteria is one way. The other? Use the lovely [true] immunologists who scurry around me in the corridor of the Big Institute.

Here is one of the pictures I am trying to interpret and build on…. Can someone say “black box” and “we don’t know if this is an indirect activation or a direct activation of NfKb”… but sure enough, it is interesting. To a point.
(courtesy of wikipedia and not really a picture I am using but it seems better to use this one due to copyright and journals etc...)

*Toll like receptors, membrane spanning receptors
that recognize structurally conserved molecules derived from microbes once they have breached physical barriers such as the skin or intestinal tract mucosa, and activate immune cell responses. They are believed to play a key role in the innate immune system and are conserved in all vertebrates as well as invertebrates. (Even in some part as smaller molecules in bacteria and plants – although not complete and functional.)

Some of these TLRs are found on macrophages, monocytes and dendritic cells and are receptors for interleukins…. And this is in part why they are called TLRs, they give rise to a signal cascade and in the end usually cytokines are produced. There are 13 known TLRs, numbered TLR1 – TRL13.

TLRs got their name (and was discovered) partly by Christiane Nüsslein-Volhard who received the Nobel prize in 1996.

Personally, I read about her when she started the Christiane Nüsslein-Volhard foundation in 1994 to support German female Scientists with children… it is mainly childcare and stipends to facilitate some kind of maternity leave and having children as a researcher without a stay at home wife.

**Pattern recognition receptor; are proteins
/receptors expressed on the surface of cells of the immune system.They recognize molecules that are produced by pathogens (and shared between many speices) although different from molecules made by the host as well as molecules produce by cellular stress. TLRs are a type of PPRs, although all PPRs aren’t TLRs.

***Pathogen-associated molecular patterns, are molecular motifs that are found on pathogens. TLRs, and other PPRs, recognize these PAMPs. LPS would be a typical PAMP from a Gram negative bacteria. Lipoteichoic acid (try pronouncing that if you can) and peptidoglycan would be typical Gram postivie PAMPs. And then of course viral and bacterial DNA and RNA are PAMPs as well.

****Myeloid differentiation primary response gene (88); a universal protein that is used by all TLRs
(except TLR3 which is a tad bit different and therefore is called the MyD88indepoendent activation pathway) to activate the transcription factor NfkB.
My personal note would be, an important part of the signaling pathway I am trying to understand. There are interesting deficient mice … and MyD88, as far as I understand, is important to apoptosis and pretty much lots of cell signaling.

*****nuclear factor-kappa B is a transcription factor
that is found in almost all animal cell types. It is involved in cellular response to stimuli like cytokines (my thing at the moment), bactieral and viral antigens and stress. NF-κB plays a key role in regulating the immune response to infection.

So, back to drawing the signal pathway and trying to get why on earth removal of one TLR would make the outcome worse… it seems a little counter intuitive at the moment, I must say.


Dr. A said...

Now you are talking MY language!! I am a microbiologist turned immunologist and TLRs are my life at the moment.

Cath@VWXYNot? said...

Immunology is one of those things that I've always had to learn afresh every time I come across it. It just doesn't seem to stick in my brain the way other parts of biology do!

chall said...

Dr A> did you choose that? ;)
I might see if I can find your email and maybe quiz you about a certain TLR (TLR 4 and 2)...

Cath> see, that's me in a nutshell. I need to reread it every time. THose TLR 7 and 9, what do they do? What was with the proinflammatory thingy.. ahh.. TNF-a ... etc...

I can still tell all the amino acids and their side chains even thoughm I haven't done that in three years... something is obviously filling the brain space needed for immunology.

microbiologist xx said...

Immunology doesn't stick with me either. Every time immunology enters the picture, I know that a never-ending parade of looking things up is fast approaching, and if I am looking things up, I am probably not getting data. ;)

Cath@VWXYNot? said...

But I can still pull a Jun protein binding site out of lines and lines of DNA sequence within a matter of seconds... and I haven't had to do that since 2002!

TGA G/C TCA, since you ask. Yes, it's palindromic