T-Cell Receptors

I've been thinking about T-cell receptors (TCRs) a lot lately, primarily because they're a delicious, tangled little knot of wonderful complexity. Some (Sciliz, I'm looking at you) call them fickle, but no, they're far tastier than that. Synaesthetic metaphors aside, TCRs are the gate-keepers between strong and solemn anti-pathogen protection and a raging inferno of doomy autoimmunity. More specifically, the genes that encode TCR are divided up into Lego-block-like segments [V, D, and J segments] that are sorted more-or-less-at-random*. This happens in each developing T-cell, and the genes undergo some further random mutagenesis via the RAG proteins to generate completely unique receptor specificities. In turn, this means that each TCR is unique, like a precious little snowflake or puppy nose, and it guards the body against its cognate antigen vigorously**. However, much unlike a snowflake or puppy nose, the mechanism by which TCRs generate useful signals and screen out non-specific noise is absolutely badass. In fact, rather than naming battleships after dead guys, who are no longer badass, perhaps we'd be better suited to name warships after T-cell receptor clone lines: Jurkat, D0.110,...others?

Anyway, I've been thinking a lot about the applications of network information theory to TCRs lately. But that's not what I'm going to talk about today, because in thinking about TCRs like that I've recently come to appreciate just how absolutely unrefined, perhaps even crass, my initial understanding of TCRs was.

Back when I first took an immunology course through my university's medical school extension thing, this was the impression I got of TCRs. G-protein coupled receptors (GPCRs) had been beaten into our skulls with the Alberts' Molecular Biology of the Cell text and as such I figured it worked a lot like a GPCR. This turned out to be rather incorrect. In fact, I was also under the impression that almost everything in the world was some sort of GPCR***. Fortunately, this too turned out to be incorrect.

The CD4/8 molecule pictured above is a rather handy cell-surface marker that is expressed, respectively, on CD4+ and CD8+ T-cells, which in turn respectively recognize antigen in MHC-II and MHC-I proteins. If that didn't make any sense, don't worry about it, what's important here is that CD4 or CD8 help the T-cells see the antigen that elicits a signal. CD4 and CD8 are co-stimulatory molecules without which antigen-presenting cells cannot effectively transmit information.

Anywho, as evolution would have it, there are more proteins involved in TCR signal transduction.
At the time I learned of the existence of CD3 and CD28, I had absolutely no clue what they did, so I merrily accepted that they were part of the TCR complex and moved on. Why I didn't look further into them is currently beyond me, but the most likely answer is that I was distracted at the time by free cookies. As such, I thought that signal transduction just carried on with CD3 and CD28 as handsome bookends.

Little did I know of the strange superpowers these two molecules have. Eventually, because science enjoys knocking over the obelisks of my ignorance despite how hard we've labored to keep them intact****, I gained that knowledge.
I couldn't believe it. It was like when I found out that I couldn't eat clouds. Signal transduction WITHOUT antigen stimulation? What sort of stochastic heresy was this? This shattered the beautifully deterministic world-view that my undergraduate education had instilled, that every receptor has a ligand that can be defined and that the cell is a place of beautiful complacency and order. I had known that ligands::signals weren't always 1::1, and I had accepted that, but this, this was somehow darker and more malevolent, and the knowledge that TCRs could be so deftly manipulated and easily fooled was tantalizing. This assumption, also, turned out to be wrong. TCRs are stubborn little bastards.

Nonetheless, I set aside my beloved copy of Janeway's Immunobiology and leaped into the scientific literature face first. I read cell biology papers, I read biochemistry papers, I read biophysics papers, I read autoimmune pathogenesis papers, I read genetics papers, I may have read some enzymology papers, and I know I read a bunch of computational biology papers. I emerged with a mouthful of bistable switches and nonlinear dynamics, and I believe that my understanding of molecular biology as a whole was greatly enhanced by it. Cells weren't orderly little machines, they were complex and messy tiny mechanisms that had error and chaos built in as part of their very functions. And that chaos and nonlinear responses can be harnessed by evolution to increase the sensitivity, response range, and efficiency of cells was absolutely beautiful in its inhumanity. Humans build orderly structures, boxes and flat surfaces and well-engineered machines, but cells don't given a damn! Cells get by, thrive, and capture the very entropy we try so hard to scrub out of our lives, and that, that right there was something that I didn't appreciate until I wound up climbing up atop the tallest stuff at hand one night (Halloween, exactly) and laid sprawled out on top of it watching the sky. Seeing the moon reel about the sky and the stars wheel away above it while the earth beneath me tangibly spun made me feel so very small and tiny and insignificant in the face of such a vast expanse as the universe. But then, at the same time I knew that I was composed of billions of microscopic cells to the point where we are complex molecular galaxies unto ourselves and that, too, made me feel small and insignificant. And lastly, knowing that the stars in the sky and the cells in my body will get by without giving a damn about whether I know they exist or appreciate them was a sort of beautiful thought that has remained with me, probably as the closest thing to faith that I've found.

Epic literature reading aside, the mechanisms of TCR activation as I now envision them are rather complex to draw, so I am going to use art instead.

Apotheose der während des Befreiungskrieges für das Vaterland gefallenen französischen Helden, by Anne-Louis Girodet-Trioson

This isn't meant to be tongue-in-cheek about it being epic*****, but more that it is incredibly crowded and busy and spatial location matters a LOT. You see, resting T-cells have TCRs scattered across their cell surfaces more or less at random, and each of those TCRs is identical. But once 1 of those is conjugated with the triggering antigen at just the right specificity, they all suddenly (within a matter of mere minutes) condense over to the site of that triggering and form an immunological synapse.

The synapse polarizes the TCRs all to 1 side of the cell and clusters them together. Actin also gets rearranged. This provides a cell surface anchor point for intracellular proteins to begin forming a complex cascade. The TCR proteins themselves change shape and CD3's intracellular domains are released from the cellular membrane where they were held. CD3 can then serve as a scaffold for effector kinases such Lck and Fyn. Some JAK/STAT scaffolding proteins eventually transmit the signal from Lck/Fyn/Zap70 to ERK and JNK, which in turn then affect transcription of NF-kB and other response genes such as IL-1b. At the same time, there is a massive calcium flux across the cellular membrane.

Like this. I had to take considerable liberties in omitting details to make this fit on one slide.

However, the synapse is presently more interesting than its effector functions. The immunological synapse is actually composed of 2 parts, the central supramolecular activation complex (cSMAC) and the peripheral supramolecular activation complex (pSMAC). As you might have already imagined, the cSMAC is surrounded by the pSMAC. Within the synapse, many T-cell surface proteins are able to interact with their ligands on the surface of the antigen-presenting cell and vice versa. The SMAC structures are stable (relatively for T-cells) and allow the antigen-presenting cells to properly stimulate the T-cell with both its cognate antigen and some pro-proliferation cytokines such as IL-2.

Now here's where I really have no idea how to visually illustrate it. Within the cSMAC, TCRs are systematically obliterated as the activated, presumably phosphorylated?, TCRs get pulled into the cell and chewed through proteasomes to allow fresher TCRs to get at the antigen-presenting action. This degradation of activated TCRs from the cSMAC is essential for proper T-cell activation (if you block it the T-cells keel over and die, as they are wont to do). And this is what is really frackin' cool: bistable switch behavior in the activation kinetics of TCRs is mediated first by formation of the immunological synapse, and then sustained by endocytosis and degradation of activated TCRs.

Toaster, what the blugoon is a bistable switch?

Hysteresis can be found in a lot of situations, including magnetization, memristors, and a whole lot of very useful electronics and materials sciences.

A bistable switch exhibits the property of hysteresis, which is rather awesome. Hysteresis essentially means that a signal going 1 way across some response action (sensor) doesn't necessarily get the opposite response when the signal goes the other way.

Hystersis can be found in TCRs at several levels. First, it is part of the kinetic proofreading that occurs at TCRs prior to cSMAC formation. TCRs have to be extraordinarily sensitive to their cognate antigen and must be vigilant in screening out false positives. Therefore it takes a stronger signal to activate TCRs than it does to deactivate them. Second, use of hysteresis in this is an efficient way of screening out false positives; the formation of the cSMAC and subsequent degradation of activated TCRs both help to sustain hysteresis behavior. Condensation of TCRs into a cSMAC requires a stronger activating signal than deactivating signal, which means it will remain active at a signal weaker than that which activated it. Thirdly, degradation of activated TCRs helps sustain hysteresis by ensuring that the signal is propagated into the cell at a proper rate. Too fast and the T-cell's built-in anti-autoimmunity mechanisms will kill the whole cell, and too slowly risks death by anergy, while still the net signal from an antigen presenting cell must be higher to activate the T-cell than to deactivate it.

There are many finer details of TCRs that I did not cover here, and still more that I probably don't yet know about. T-cells are an essential part of the immune system, able to differentiate into several different useful phenotypes. CD8+ cytotoxic T-cells can circulate around the body and survey for viral infection or cancerous abnormalities. CD4+ Th1 cells secrete massive amounts of IFNg and help direct innate immune effector cells to combat bacterial infections. CD4+ Th2 cells secrete lots of IL-4 and are involved in battling away parasites or, more relevantly in the Western world, causing allergies and asthma. CD4+ CD25+ regulatory T-cells shut down the immune response by secreting IL-10 after the pathogens have been cleared away to prevent Th1 T-cells from tearing up the place (see: cytokine storm). Memory T-cells lurk around and provide lasting immunity to previously encountered pathogens. And Th17 T-cells do something, they seem to be involved in protection against autoimmunity but we're not quite sure yet. Each of these T-cell phenotypes relies upon the TCR to detect their cognate antigen and help defend the body against the invading microbes that find its squishy, nutrient-rich nooks so very appealing. At the population level, I sometimes think of T-cells as a library of exquisitely-finely-tuned peptide detection machinery that we all carry around with us, and I find that chaos they usefully harness in hysteresis to be beautiful and captivating. There may be other, as of yet, undiscovered T-cell phenotypes and functions despite an already broad and deep literature, and that is an exciting prospect. T-cells and the exact mechanisms of their TCRs remain a relatively open biological frontier, and the best we can do is to dive in face-first.

*Not quite, but explaining it goes beyond the scope here. Look here for more information.
**If it doesn't get killed off first, as the grand majority of developing lymphocytes do, due to anergy or too strong a reaction against self.
***I really liked imagining that there were little Ggamma subunits shuttling around everywhere, all the time, in absolutely everything making a "BlootablootalootaLOO!" burbling sound as they went, with tiny ADP bubbles behind them.
****This is an obligatory joke notification footnote.
*****Also to help break up large blocks of text.

Microcluster Condensation in Immunological Synapses 1

I remember reading one of the popular science magazines I subscribed to back in high school, probably either Popular Science or Discovery, and coming across a brief article on the discovery of the immunological synapse. It included pretty pictures. I was intrigued by the spatial and sequential alignment of disparate signaling effectors, even though I knew absolutely nothing about the context at the time. Now, I know more about the molecules and pathways involved in dendritic cell::T-cell signaling than I am able to concisely put down here in words without rolling myself up in a cloak of jargon, and even so I barely know anything (with comparison to both the experts in the field and the scale of the unresolved questions). The immunological synapse is fascinating, and to me it is beautiful in its absolute parsimony (that's a whole other post for later).

In beginning the activation of the adaptive immune system, dendritic cells process and present sampled antigen in distinct molecules (MHC) that T-cells can recognize (via the TCR and CD4/8). Due to chunk recombination of V, D, and J regions of the TCR binding motifs and subsequent pre-programmed random mutagenesis* there is extremely high heterogeneity in the recognition cognates of the TCRs. So as dendritic cells (DCs) crawl through the thymus, lymph node, spleen, or other, they have many distinct antigens loaded into their surface display molecules, and every once in a while a TCR that has some binding affinity for that antigen will bind. What follows is the immunological synapse.

The immunological synapse starts out with the binding of the TCR and CD4/8 to the MHC, which nucleate the formation of the central supramolecular activation complex (cSMAC), when all of the TCR/MHC complexes from microclusters and merge into 1 more stable site. A lot of other things happen downstream of that, most of which are very interesting**, but what I find intriguing about this is: what sort of topology do the kinetics of microcluster condensation add up to?

All optimized networks have some sort of topology. This means the hierarchy of one node over another, because to have all nodes processing the same exact bandwidth is rather energetically inefficient. As such, there can be strictly hierarchical topologies like those found inside human corporations with management, there can be scale-free topologies in which hierarchy arises due to through-put optimization and is not strict (a good example of this is the server structure of the Internet), or others I don't know anything about yet.

Is microcluster condensation hierarchical or scale-free?

Unfortunately, it is extremely difficult to answer that question empirically because it happens so fast and because the cells involved are rather camera-shy unless given very exacting and munificent conditions. Therefore, this is more or less a thought experiment.

I posit that microcluster condensation is both hierarchical and scale-free, in turn; first, hierarchical and then, later, scale-free. Cook your noodle on that for a bit, and I'll explain my reasoning for why within the next few days.

*Not a contradiction of terms. The immune system allows for random mutagenesis of a restricted set of amino acids residues on T-cell receptors and B-cell receptors to greatly increase the range of possible binding motifs without great additional informational storage costs (DNA).
**E.g., I find the activation of such factors as NFAT, mTOR, et al to be interesting, but generally find the dynamics of histone deacetlyation to be rather dull.

Llamas Against Breast Cancer

We all knew llamas were kind of weird. They're fluffy. They're smelly. They spit. They're like Sanrio (the Hello Kitty company) tried to make over a camel. But that's not all. Llamas are also immunologically strange. Whereas most all other organisms with a humoral immune system produce large, multi-domain antibodies with several distinct genetic and structural motifs, llamas instead make nanobodies. Nanobodies are, basically, tiny little antibodies. Normal antibodies contain 2 heavy chains and 2 light chains, which each have V (variable, where the epitope binds) and J (joining) regions; and the heavy chains also have C (constant, these make up the Fc fragment) regions. All of those chains are bound together by disulfide bonds and the resulting antibody typically has 2 binding sites, each at the tip of the Y shape. Nanobodies dispense with all of that and only retain a functional binding site with a single variable light chain domain. As a result, nanobodies are much much smaller and can access and bind to sequestered epitopes or complex 3D epitopes that may otherwise be hidden inside a molecular cleft.

Figure A: Structual phylogenetic picture, much like a family picture. This is only an approximation as Good Images are copyrighted and Photoshopping ribbon-style molecules is difficult.

The point of this study is not that nanobodies are weird and cool. Instead, Alvarez-Rueda et al harnessed the complex 3D structural variability of nanobodies to mimic the immunogenic structure of HER2. HER2 is a surface protein normally only expressed in fetal development that is reexpressed in 20-40% of breast cancers and 30% of ovarian cancers. It is a member of the epidermal growth factor (EGF) family and is suspected to help cancerous cells proliferate more rapidly and aggressively. Tumor expression of HER2 correlates strongly with increased metastatisis and decreased survival. We've known about HER2 for a while now and it has been a target of intense research. There are now genetic tests available for HER2 alleles that correlate with increased morbidity from breast cancer. There was also a passive immunotherapeutic treatment against HER2 approved for use in combination with chemotherapy in 1998 called Trastuzumab (marketed as Herceptin(R) and manufactured by Roche). Trastumuzab is a humanized antibody therapy that targets HER2 directly; it is thought that it mimics the natural humoral immune response to HER2, which is observed to slow down tumor growth in early tumors but unfortunately sometimes fails to stop it. The primary problem with Trastuzumab is that it must be repeatedly administered over the course of cancer treatment to have any effect. While Trastumuzab is an invaluable tool in the fight against these cancers, it has long been recognized that inducing a robust host immune response would help to combat the tumor itself, and subsequent induction of a host immune memory against HER2 would help to prevent relapse of the cancer.

The best way to do this is with a vaccine.

Simply injecting HER2 with an adjuvant could produce a strong immune response, but the HER2 itself could make the cancer worse meanwhile. The ideal vaccine would be a molecule that mimics the structure of HER2 closely enough to induce cross-reactive immunity but that doesn't have the biological activity of HER2.

Enter the llama and its nanobodies.

Alvarez-Rueda et al injected Trastuzumab into a llama and the llama kindly produced nanobodies. Because Trastuzumab is an antibody against HER2, the llama's immune system produced a molecule against it that is somewhat structurally similar to HER2. When this nanobody molecule was isolated and expressed via transgenic clone library, it was found to strongly bind both Trastuzumab as well as isolated human anti-HER2 antibodies. So they then took the nanobody (called 1HE) and injected it into mice (along with Freund's adjuvant). As expected, the mice produced antibodies against the nanobody. These antibodies then, in turn, bound strongly to both 1HE and the HER2 protein. This strongly implies that immunization of a human with the 1HE nanobody and adjuvant would induce a strong anti-HER2 antibody response, effectively immunizing them against HER2-expressing breast or ovarian cancers or arresting the growth of existing tumors as part of chemotherapy*. Additionally, the polyclonal antibodies produced by the mice in response to the nanobody were found to inhibit growth of HER2-expressing carcinoma cell lines. The data have not yet been validated in vivo.

Either way, this is a cool advance in the fight against breast cancer, and I sincerely hope that something therapeutically useful in humans will soon come out of this. Thank you, llamas.

*This is technically known as an anti-idiopathic vaccine.

Alvarez-Rueda, N., Ladjemi, M., Béhar, G., Corgnac, S., Pugnière, M., Roquet, F., Bascoul-Mollevi, C., Baty, D., Pèlegrin, A., & Navarro-Teulon, I. (2009). A llama single domain anti-idiotypic antibody mimicking HER2 as a vaccine: Immunogenicity and efficacy Vaccine DOI: 10.1016/j.vaccine.2009.05.067

Obviously Not Quite Right

DAB stain, mouse stomach, 40X.

This particular staining protocol had diaminobenzidine, hemotoxylin, and McGill's modified EA solution as stains. The diaminobenzidine, from what I understand, was supposed to color neutrophils and monocytes varying shades of grey-black intracellularly. Light blue is supposed to correspond to basophils. Either I've discovered some new property of basophils in which they invade and form sheets in the connective tissues and basement membrane of the stomach (which'd be even weirder considering that the system in question skews to T_H1/T_H17-driven inflammation), or I've screwed up the staining protocol somehow. The latter is much more likely, and it also looks like I left the slides in the hemotoxylin for way too long.

I just wish I could remember where I'd put the Coplin jars, because this time around I was staining out of Petri dishes (Toaster does not recommend putting xylenes in a Petri dish, unless it is a fancy glass Petri dish).

Your Microbiome and You

You are never alone. Not even when you might want to be. Tucked away within the ~100m² of your bowels are ~10¹⁴ (there are ~10¹³ somatic and germinal cells in the human body) of your closest friends, collectively termed The Microbiota. They eat, spawn, conjugate, die, poop, fight, and secrete right there inside of you, unseen and mostly unthought of except when something is wrong. This system, the remarkably homeostatic mammalian gut, forms what is perhaps the densest and most complex microbial ecology on this planet.

These teeming microbes are not mere freeloaders living off of your access at their own convenience, they are true symbionts. In exchange for a warm, wet home and nutritional supply, they break down starches for us, metabolize complex molecules, and synthesize some key compounds, such as Vitamin K. It has been found that gnotobiotic, or germ-free, animal models require ~30% more calories to develop normally without a microbiota to help them out. In humans that have been on a broad-spectrum antibiotics, hardier inhabitants (such as Clostridium difficile) can bloom when all of their more sensitive neighbors (such as Bacteroides spp. and Bifidobacterium spp.) are killed off, which causes very unpleasant colitis and diarrhea, that can then be cured by a transplant of fresh microbiota from a healthy individual (colloquially referred to as "poop soup"). Microbiome transplants can also transfer physiological characteristics from one individual to another. For example, the microbiomes of obese individuals have been found to have reduced numbers of Bacteroidales spp., and transfer of these microbiota via poop soup into germ-free mice resulted in obese mice, theoretically because these microbiota were more efficient at releasing calories from food.

Microbes exist, or can exist, in virtually every segment of the gastrointestinal tract from mouth to anus. In the mouth, a variety of Actinomyces spp. are associated with the formation of plaque. In the forbidding and harsh environment of the stomach, only Helicobacter pylori can thrive (it does so by hiding among the mucous lining the stomach and modulating the host immune response) and it has been found to directly cause stomach ulcers and has been further implicated in the formation of gastric cancers (it's the only organism classified as a BSL 2+ carcinogen). The proximal portion of the small bowel is relatively sparsely colonized at ~10⁴-10⁵ microorganisms/ml lumenal contents, which contrasts sharply with the densely colonized colon (~10¹⁰-10¹² microbes/ml contents).

In the human and other mammals, diverse and distinct microbial ecologies also exist in the sinuses, ears, genitourinary tract (largely Lactobacillus spp. in the vagina; the bladder is generally only colonized in disease states [long-term catherization and/or pyelonephritis] by uropathogenic Escherichia coli, Proteus mirabalis, et al), and on the skin as a whole (mostly Staphylococcus spp.). These others will, however, be excluded from the present discussion.

However, what's very puzzling about all of this is: how does the mammalian immune system manage to differentiate from the massive basal antigenic signals coming from the microbiome from pathogenic antigens? In other words, why isn't the immune system raging against the huge number of microbial signals in the gut?

One of the exquisitely elegant features of normal gut physiology is that gut-associated lymphatic tissues (GALTs) mediate fine-tuned hyporesponsiveness to commensal microbiota while remaining responsive to pathogenic microbes. This flies directly in the face of most immunology, which holds that microbial antigens will always provoke a stimulatory response when ligated to TLRs, CLRs, or NODs (conserved receptors of the immune system that bind conserved molecular patterns associated with pathogens). In vitro data support this. Physiology doesn't.

Physiologically, the germ-free mouse is weird. A germ-free animal is one that has been reared in an environment completely free of all microbes, fungi, and exogenous viruses and as such they have no native intestinal microbiota. Not only do they require more calories and vitamin supplementation, but they also tend to accumulate undigested fibrotic material in their ceca, which predisposes them to gut twists and bloat. Additionally, they feature underdeveloped Peyer's patches (distinct GALT sites on the gastric mucosa), altered CD4+ T-cell and IgA-producing B-cell population profiles, and the follicles in the spleen and lymph nodes where T- and B-cells mature are poorly formed. All of these abnormalities can be rescued by adding back microbial signals such as LPS, even without the microbes themselves. Due to these alterations, it is becoming accepted that the microbiome plays a crucial role in the normal development of the immune system. But to reconcile this with the dogma of microbial signal + PRR ---> inflammatory immune reaction is somewhat difficult, or at the very least complex.

Immune cells that reside in the lamina propria underneath the gastric epithelium generally show signs of recent activation and a particular subset of dendritic cells (CX3CR1+) has been found to extend dendritic processes up through the tight junctions binding gastric columnar epithelial cells together to directly sample the lumenal contents. M cells that cap the Peyer's patches have been found to shuttle lumenal contents, and any antigens contained therein, to the dendritic cells and lymphocytes underneath. These pathways of antigen exposure are thought to be involved in the induction of immunological tolerance to microbiotal antigens, which could explain why the immune system does not attack the commensal microbiota. However, it does not explain how pathogen antigens processed by the same pathways are recognized as pathogenic and stimulate the immune system to attack.

Recent evidence strongly suggests that the intestinal epithelium itself is responsible for the differentiation of nonpathogenic microbiota from pathogens. Canonically, the intestinal epithelium is thought of as a simple barrier that is involved in the absorption and transcytosis of metabolites and nutrients. But it seems that it is much more involved that we had previously believed.

It turns out that intestinal epithelial cells (IECs) express TLRs and directly modulate the composition of the microbiome itself as well as the responsiveness of immune cells. This ranges from TLR expression on Paneth cells in the small intestine that secrete potent antimicrobial molecules (RegIIIg) when ligated [Dr. Lora Hooper, in seminar given 11/19/08] to actual expression of MHCII and direct antigen presentation. It was previously believed that MHCII expression was restricted to antigen presentation by dendritic cells.

When investigators deleted TLR4, NOD1, or MyD88 (an adapter protein involved in many TLR-mediated NF-kB inflammatory pathways) in murine IECs they found that the mice were more susceptible to bacterial infections, which implies that the TLR signalling on the IECs is essentially to the development of normal protective immunity. A second feature of this is that IEC TLRs and NODs are located intracellularly, instead of on the cell surface as in immune cells, which means that they'd only be ligated and activated when an invasive pathogenic microbe breaks into the IECs themselves (e.g., Salmonella typhimurium, Vibrio cholerae) as opposed to the more peaceful commensals. It may be that noninvasive gastrointestinal pathogens are recognized by the proteins that they shoot into IECs via Type IV secretions systems (e.g., Tir and Escherichia coli O157:H7) in the same manner.

The commensal microbiota is also at work on the IECs themselves, actively acting against IEC-mediated inflammation. Bacteroides thetaiotaomicron has been found to induce the PPARg anti-inflammatory (acts by increasing cytoplasmic shuttling of pro-inflammatory NF-kB away from the nucleus) mechanism in vitro. Commensal-derived metabolites such as butyrate (a short-chain fatty acid) have been found to inhibit expression of pro-inflammatory cytokines and increase expression of anti-inflammatory cytokines in IECs.

It is now thought that IECs regulate dendritic cell function through secretion of thymic stromal lymphopoietin (TSLP) and modulate T-cell activity through expression of MHCII in the abscence of costimulatory molecules. TLSP acts directly on dendritic cells and inhibits their production of pro-inflammatory cytokines (such as IL-12), which in turn promotes dendritic-cell-mediated activation of regulatory T-cells. TSLP is also implicated in skewing the immune response to a T_H2-type T-cell response, which is implicated in both response to metazoan parasites and pulmonary atopy. If naive T-cells are being exposed to MHCII on IECs without co-stimulatory molecules, then the T-cells will either kill themselves off (anergy) or mature into tolerogenic T-cells that limit the immune response to those given antigens. This, combined with widespread TGFb secretion by IECs, directly indicates an active role for IECs in promoting immune system hyporesponsiveness to the antigens present in the gastrointestinal system. Without this direct suppression of active, inflammatory immune responses, the immune system would be in a continual inflammation state due to not knowing what to do with a safe commensal antigen vs. a dangerous pathogenic antigen. Indeed, emerging research indicates that dysregulation of this process may underlie the pathophysiologies of inflammatory bowel disease and Crohn's disease.

It'll be interesting to see what's found next.

Artis, D. (2008). Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut Nature Reviews Immunology, 8 (6), 411-420 DOI: 10.1038/nri2316

How Vaccines Work: An Immunological Primer

Vaccines prevent disease. They do so by causing you to develop immunity against an infectious organism before it gets a chance to infect you and cause disease. In essence, vaccines teach your immune system how to recognize infectious organisms and fight them off much faster. Without vaccination, exposure to an infectious organism is like being thrown into the deep end of a pool without water wings where your immune system thrashes around desperately trying to save you. But vaccines are like the shallow kiddie pool where you touch the bottom and your immune system gets acquainted with the water so that it will have a better idea how to handle it later on when you can't touch the bottom. Vaccines do this by exposing the immune system to dead, weakened, or pieces of infectious organisms, usually along with a signal molecule called an adjuvant, so that it can learn that the molecules associated with the infectious organism are bad and should be attacked if they're ever seen again. The adjuvant acts like a wake-up call to the immune system to make sure it takes a look and does what it's supposed to.

Vaccines are education for the immune system.

The human body has 2 different immune systems: the innate immune system and the adaptive immune system, and they talk to each other quite a bit. The innate immune system is the infantry of the immune system; it reacts rapidly to invading pathogens and can destroy most of them, but it can have a hard time telling exactly who to kill and when and how much firepower to use. Meanwhile, the adaptive immune system is more like a laser-guided cruise missile from a fighter jet that very specifically takes out invading pathogens and tags the enemies that the innate immune system should kill off. However, just like it takes time for jets to get to where they need to go, the adaptive immune system takes several days to warm up and start fighting.

The innate immune system is scattered throughout the body in circulating white blood cells, in the mucous membranes, in the skin, and in the gut; all places where invading pathogens are likely to try to enter. The adaptive immune system, when there's no infection present, generally hangs out in the bone marrow, thymus, and lymph nodes; but when there is an infection some of them will go out to the site of infection to join the battle while others will stay behind and direct subsequent reinforcements.

In an infection where there is no prior vaccination present, say S. aureus in a pimple, the innate immune system quickly (in minutes) recognizes many of the molecular patterns that are generally associated with all bacteria, including S. aureus. These patterns are signals for the innate immune system to kill and also go talk to the adaptive immune system. So the innate system goes to work blasting away as well as it can at the S. aureus, but it's good at hiding so the innate system doesn't see all of it and S. aureus is able to establish an infection.

So meanwhile, the innate immune system has gone off to the adaptive immune system and handed it the information it has gathered about the infection. The adaptive system examines it and then begins to multiply and specialize. Some of the multiplying cells get out to the site of infection and join the battle. Other cells make antibody against the S. aureus, which is then secreted into the blood and binds the bacteria, lighting them up brightly and saying "Destroy this now!" to the innate and adaptive system cells that are already there.

Once the infection is cleared, many cells of the adaptive immune system specialize again and become memory cells that wait out in the body, able to specifically recognize the same infection they just fought off. This means that if S. aureus tries to come back, the memory cells will see it very specifically and very quickly and they can then jump-start the rest of the adaptive immune system and mount a very rapid lethal attack against it.

The problem is that many infections are strong enough to kill, or do serious and permanent damage to, a human before the adaptive immune system is strong enough to fight it off. Although the innate immune system starts fighting quickly, it takes the adaptive immune system about 4 days to start responding very much and a full 7 days to really get into swing. Memory immune cells can bypass that waiting period and kick both immune systems into battle mode right away.

Vaccines are designed to skip the infection part and go directly to teaching the adaptive immune system to recognize the infectious organism and then form the memory immune cells that will kill the pathogen before it even has a chance to cause infection.

This is why vaccines are effective, useful, and necessary. They also happen to be quite safe*.



NOTE: This was largely inspired by Abel Pharmboy's guest post over at Dr. Isis' place. I left a long comment there and then realized that it wouldn't do very well for me to be a hypocrite. If you feel I've left anything out, or if there's anything you want to know more about please let me know. I tried to keep it simple because even the basics of how the immune system functions could keep me busy with posts for the rest of the year.

*Bears, however, are something you should worry about. Bears are crazy dangerous.