Category Archives: Uncategorized

Working Hard to Stand Still; Or “COME THROUGH, IMMUNOCYTE!”

A dear friend of mine who is an intrepid post-doctoral researcher in the often murky, and full of much flow cytometry field of haematopoiesis sent me the following text from a recent gathering of some of the foremost immunologists in the field:

“People are now realizing that nutrition and immune function are closely linked. What a shocker!”

My friend comes from a nutritional biochemistry background, so this idea that the abilities of one’s immunocytes are closely linked to what you put in your body wasn’t especially mind-blowing to her. However, I could see why this could be so for others.

See, we think of the immune system as something that fights, kills, protects. It’s almost as if these cells are divorced from any other roles. However, that mindset is changing. And why not? The immunocytes in our body are inspiring: they make a variety of different pleiotropic factors, they are activated by many, many ligands/metabolites, they network with multifarious cell types like it was their job (it kinda is!), and so why wouldn’t they be involved in—wait for it—homeostasis?!

Because immune cells recognise that host defence and homeostasis are different games. Both of which they play well!

I recently read a piece about how γδ T-cells rely on recognizing metabolites from the mevalonate pathway to recognise rapidly proliferating cells—potential tumours—and kill them, thereby exerting tumour control. Inflammatory events are involved in the regulation of insulin responses and obesity. Phagocytes and  a class of Treg cells regulate homeostatic responses and prevent autoimmunity and pathology at the level of the skin. Innate lymphoid cell classes provide a protection against immunosuppression and subsequent bacterial infections in the gut by modulating their functions under conditions of nutrient depletion. Interferon γ, that paragon of antiviral responses, also helps out in maintaining skin pigmentation. Alternatively-activated macrophages show up, and help regenerate muscle after acute muscle damage (think: exercise).

Immune cells: working hard so things “stand still.”

Why am I sharing these examples? Etymology tells us that “homoestasis” means “standing still.” We think of immunocytes as warriors, not a meditative, “standing still” population. That they do the legwork in processes that enable “standing still” can be thought of as, in a way, prophylactic. Immunocytes would seemingly be involved in making sure that things remain normal, happy and homeostatic rather than mobilizing a big immune response if/when something goes even slightly wrong, physiologically speaking. This makes sense because launching an immune response is costly to the body. In many ways, it is like going to war. Your legions of immunocytes are your troops, you have to feed them, keep them functional. This is energetically expensive, and makes you feel like crud most of the time. So why not ensure that things “stand still” rather than deal with hourly fresh Hells of physiological dysregulation?

To put it another way: the immune response will turn up when needed, but have you ever partied for 4 days straight, and then gone on a weekend binge? Hurts, don’t it? Turn up, and be legendary rather than being in a constitutive state of turnt! 🙂

Take care,



The Scent of a T-cell…

Everyone has one of these, right? A signature scent. It’s that little something that alerts the senses that you have entered the room. Mine signature scent entails the woodiness of bergamot which, as the day continues, gives way to an enlivening flash of violet and nutmeg. It’s perfect! It’s me. My days begin with smoky, woody flavours of coffee, and eventually give way to endorphins and a furtive energy which gets the cytometer running, the cell cultures going and the ELISAs flashing the lemon-lime joy of a successful experiment.
I like to think that T-cells have their signature scents, too. Those little somethings about the cells that alerts the body that these particular cells have entered a particular compartment, and are ready to do work. I speak, via metaphor, of transcription factors.
One hears, of course, of T-Bet, GATA-3, RORγ and their indispensable impacts on the cytokine profiles of CD4+ T-cell subsets, these scents of a T-cell that dictate the outcome of an infection, an insult or, well, just the regulation of physiology in general. The one transcription factor that I am *obsessed* with of late is Promyelocytic Leukaemia Zinc Finger-1 (PLZF-1) which is a transcription factor of the Bric-a-brac Tramtrack Broad-complex Pox Virus Zinc Finger (BTB-POZ) family of transcription factors. The BTB-POZ’s, if you will, are known to be transcriptional repressors and, they find themselves at these exciting points-of-inflexion in the developmental biology of adaptive cells. As an example, the BTB-POZ protein Bcl6 regulates affinity maturation of B-cells. Th-POK (this protein, I kid you not, is sometimes called “Pokemon”) controls the T-cell decision of going CD4 or CD8.
PLZF, encoded by the Zbtb16 gene, is the “signature scent” of iNKT cells. It’s moments like these that keep me in awe of biology: a family of transcriptional factors whose affairs are deeply entwined in those of adaptive cells have a member who controls the development of a unique subset of T-cells that has both innateness and adaptivity. Features that are conferred upon these cells by this transcription factor.
The development of iNKT cells itself is a bit of a trip. We start, as we always do in such tales, in the thymus. “Stage zero” iNKT cells are positively selected via a recognition event facilitated by presentation of CD1d-borne alpha-linked glycosylceramides. What is “stage zero” for iNKT cells, for conventional T-cells, is the stage when they are CD4+.Stage “zero” iNKT precursors downregulate their CD69 and CD24. These cells, which are CD69lo CD24lo CD4+, do not join other CD4-expressing naïve T-cells in the periphery, but stay in the thymus. In the thymus, the iNKT cells proceed to stage two of their development which entails the upregulation of CD44—a cell-surface marker one associates with T-cells who’ve “seen” antigen, and also start transcribing genes for IL-4, IL-10 and IFNγ production. At stage two, these cells are ready to leave the thymus, and so they upregulate their S1P receptor, and hearken to the siren song of sphingosine-1-phosphate, and exit the thymus. Stage three of their development occurs in the periphery wherein they begin to upregulate cell-surface markers associated with NK cells (think NK1.1, NKG2D, NKG2A and such).

A summing up of iNKT cell development in the presence of PLZF-1

A wonderful, pioneering paper by Derek Sant’Angelo et al first identified PLZF as the signature transcription factor which is absolutely imperative for iNKT cell development. Compared to other αβ T-cell populations, PLZF seems restricted largely to iNKT cells, the proverbial signature scent, and a blockade of PLZF results in a strange, troubling reversion in phenotype: cells lacking PLZF Benjamin Button’d themselves back to a state in which some of them expressed CD4, had a pittance in the name of CD44 surface expression and literally no NK1.1., much like iNKT cells in an earlier stage of development. What was worse is that these PLZF-deprived iNKT cells secreted a whimper of IFNγ and a pathetic sigh of IL-4. So you see, without the signature scent, PLZF, the iNKT cells are, literally, not themselves!

iNKT cells without PLZF.

There has been recent evidence to fortify the “signature scent” idea of iNKTs and PLZF. While the immensely clever Dr. Seddon Thomas has shown that the expression of LFA-1 on iNKT cells is under control of PLZF-1. My inventive and astute predecessor here in the Gumperz lab showed that iNKT cells can, under conditions of weak TCR stimulation, can produce a cytokine while maintaining mobility—a feature that is likely under the control of PLZF as well.

Because, really, the lack of effector functions can be…disorienting. COME BACK, PLZF!

It is my hope that my work, too, will tell us more about the innate innateness of these cells: their ability to make cytokine under conditions that are thought to be anergizing for “conventional” T-cells, their ability to use integrin signaling to enliven the activities of antigen presenting cells, and, ultimately, how this adaptive innateness and innate adaptivity relate to the signature scent of iNKT cells.
Take care,

5 Cytokines That Are Just Ballin’

I blame Buzzfeed. I really do. But, really, why not have a GIF-studded listicle of cytokines? Am I crazy? 🙂

1) IL-10

You know how inflammation can be a clusterf**k sometimes? Well, IL-10, and the other cytokines of that family are the ones that lay down the law. When inflammation needs to be quieted, IL-10 will insert its bad 18.5 kDa self into the fray, and, via a JAK1-STAT3 signaling axis will induce the anergy of IL-2 dependent Th1 cells. IL-10 is the friend who knows when your rager of a party has run its course, the friend who will save your IL-2-drunk ass from alcohol poisoning. In a nutshell, this is IL-10.

IL-10 wants you to know that the party is over.

2) IL-2

Interleukin 2 is a 133 amino acids of a roaring good time. IL-2 is the milkshake that brings almost all the important inflammtory cells to the yard. As antigenically/mitogenically stimulated T-cells crank out IL-2, it brings about its own proliferation by turning on IL-2 producing genes in T-cells and macrophages, but also causing IL-2 receptor upregulation on T-cells, B-cells, macrophages, and NK cells. Basically, IL-2 is what drives a robust adaptive response to any nasties who think they know what’s up. Really, bacteria/viruses/anything else, IL-2 always knows what’s up. Don’t even. Like, nope. “Cause IL-2 does not give a shit.

The World According to IL-2

3) TGF-β1

Transforming Growth Factor Beta is the belle of the ball, one of the reigning divas of the immune response, a major Prom Queen candidate… One of the reasons for this is that the cytokine is super-involved: it has important roles in cell fate determination, angiogenesis, morphogenesis and regulation of certain hormones, just to name a few things off of the top of my head. In the immune response, however, TFG-beta is involved in both the initiation and resolution of inflammation, like its buddy IL-10, up there. While TGF-beta has several productive interactions with T-cells, NK cells and macrophages, my favourite TGF-beta trick involves its interactions with the extra-cellular matrix wherein in brings about fibrosis. This is an important consequence for, say, wound-healing. The signaling axis involved is the sort of thing I want to party with forever.

TGF-beta1, telling it how it is.


TSLP is slowly emerging as THE Queen Bitch of the Th2 immune response–sorry, IL-4. Love ya, but, yeah…

Thymic Stromal Lymphopoeitin is involved in basophil development, the proliferation of dendritic cells armed with a Th2 programme or even a tolerogenic one, the homeostasis of NKT and CD4+ T-cell populations, and also this fascinating phenomenon known as The Atopic March. This is, well, “a process”, shall we say, that causes allergic diseases to progress: from, say, atopic dermatitis to allergic asthma or allergic rhinitis or both. TSLP is purported to be the one cytokine that fine tunes the Th2 response to seemingly leap from one organ to the next. Disclaimer: I don’t strictly understand the machinations of the Atopic March; take my explanation slightly salted! 🙂

Dear Th2 Response, Yep. Love, TSLP.

5) IL-33

Interleukin-33 is your epithelial cells’ way of letting you know that shit is going down. IL-33, under necrotizing circumstances, will be released from the dying cells and induce a potent cytotoxic T-cell response. IL-33 is one to watch out for, really, because, structurally, it has similarities with the IL-1 Family of cytokines, but it doesn’t *need* to be cleaved by Caspase 1 to be active. It also has a nuclear localization signal which suggests more “traditional” cytokine-y roles. But what are they, really? IL-33 is seen as important in both allergic diseases, as well as good ol’ antimicrobial defence. The destiny and secrets of this cytokine (alarmin?) seem very promising, indeed!

IL-33 is coming!

Take care now,


My Project, Myself

My project and I? We’re in a good place. We don’t hate each other. This isn’t like the Eminem-Rihanna thing that had begun to happen with my MS thesis. Oh, Lord. Those were dark, drunk days…

I will admit, I was a bit calculative when I picked my current lab: we work with NKT cells, a flavour of immunocyte that isn’t completely understood. Thus, there is a lot to do, lots of questions to ask, lots to answer, and lots of new questions to raise….However, real-talk: I don’t get these cells. I don’t understand them. I don’t understand where their so-called “self” antigens come from. I don’t understand how they get to, y’know, BE. This doesn’t bother me, though, because I imagine that this is part of the process of getting this here PhD. If I knew this already, why in the world would I be in the lab setting up experiments?

My work focuses on the adhesion and migration behaviour of NKT cells in response to differential integrin signaling. The project was born out of this brilliant paper by Dr. Seddon Thomas, whom I admire from afar. In truth, we don’t know what makes NKT cells wanna travel, and if they do, where do they go? Dr. Thomas’s work seems to suggest that NKT cells home to the sinusoids of the liver given the high concentration of ICAM-1 there. I’ll buy it. The paper also suggests that PLZF (zinc-finger protein, transcription factor, controller of cell cycles and fates) is the key regulator of LFA-1 abundance on the NKT cell surface. Sounds good to me…mainly because it opens up all these avenues for the impact of NKT chemokine and integrin/receptor profiles on pathogenesis of inflammatory diseases.

NKT cells are a big deal in asthma. So, what causes them to home to or away from the lung? Is PLZF responsible, again? There are other things. Things I am not at liberty to speak of, but, needless to say, am chuffed about.

So, here we are: my project and I, eyeing each other gingerly, wondering what shall happen next…

Take care now,



It was with great disgust that I read the account of Dr. Danielle Lee being a called an “urban whore” for not wanting to write for an obscure science blog since they didn’t offer financial compensation to their bloggers.

Misogyny AND racism! Well done, Biology-Online! You stay classy!

What makes this situation even worse is that Scientific American, where Dr. Lee blogs, forfeited a wonderful opportunity to create a teachable moment out of this, one that highlighted the discrimination that women in science face, and further scientists of colour face.  They deleted Dr. Lee’s post, in what seems to be a move to protect themselves from negative publicity, and, perhaps loss of revenue.

Think of how dehumanizing Biology-Online’s editor’s words are: “urban whore” robs Dr. Lee of the science that she does. It robs her of her mind, and unflinchingly places the focus on her body, as if to say that her intellectual contributions are equivalent to what a prostitute working a corner does.

Why the hate, I ask? Just because she asked for compensation? We live in a world where advances in the biological sciences are happening at breakneck speed, and where there is a need for stellar scientists, there is also a need for stellar scientist-communicators who can share the wonder and awe of research with the common populace. Dr. Lee is one such writer. Her posts are that rare tonic of witty and edifying. Shame! Shame on Biology-Online for reducing one so brilliant to a slab of meat that gets traded on an ugly marketplace, and shame on Scientific American for not standing by one of their finest.

Take care now,


Narcissus, A Natural Killer, and His Self-love

If you are an old-school immunologist, you will probably accuse me of sacrilege if I revealed the focus of my graduate work to you. You see, I work on and with an innate T-cell population called the Natural Killer T-cells, or NKT cells. Yes, you read that right. Innate T-cell. Deal with it!

NKT cells were discovered 20-ish years ago and so you know that they aren’t a fad. They are a distinct population of T-cells that have the NK1.1 (CD161) marker (associated with NK cells), and, while some may express a semi-invariant version of the TCR one associates with conventional αβ T-cells using the Vα24-Jα18 and Vβ11 TCR genes, for example, others (Type II NKT cells) have more variety in the kinds of T-cell receptors they express. Both Type I and Type II NKT cells distinguish themselves from conventional T-cells by being CD1d restricted (as opposed to the MHC restriction we’ve come to know and love, but only as delimited by its strict 8-11-amino-acid-linear-peptide criteria!). However, the two types of NKT cells distinguish themselves from each other via a weird-ass, sponge-born lipid called α-galactosylceramide, or alpha-galcer. Type II NKT cells don’t respond to alpha-galcer, while Type I’s do.

What I like about NKT cells is that they represent the best kind of immunocyte: the kind that bridges the gaps of communication between seemingly “pureblood” populations of innate and adaptive cells. That NKT cells can be autoreactive but also respond to foreign, potentially pathogenic antigens, that NKT cells can secrete signature Th1, Th2 and Th17 cytokines are all signs that this is a cell type that can swing both ways, or as many ways as there may be.

The element of narcissism that NKT cells seem to come with is also a major turn on for this young experimental scientist, You see, NKT cells can respond to self-antigens as well. The means of doing this are, quite frankly, awe-inspiring. It makes sense that the CD1d receptor has evolved to enable the α-linked microbial glycolipids to fit perfectly perpendicularly in its groove for effiicient antigen presentation to the NKT TCR. That the NKT TCR manages to flatten the β-linked mammalian antigens to fit it is nothing short of, well, unexpected, Mainly, because you’d expect the TCR to be the one to make the structural compromise, as it were. Is this something that NKT cells learn as they terminally differentiate? Is this the test that they have to pass in order to be selected for? The jury is still out…

Clearly, the implications of self-antigen reactivity are amazing in terms of the roles that NKT cells may play in graft rejection, anti-tumor immunity and immunomodulation. It also these very roles that define what exactly NKT cells do in the larger picture that is The Immune Response. Tracing the thymic development of NKT cells tells us that three distinct lineages of NKT cells exist (so far, anyway!): you have your T-bet hi, PLZF low, IFNγ and IL-4-producing, IL2R-expressing, CD4 +ve or -ve, NKR+, NKT1 cells; the transcription factor that dominates the NKT2 type cells is GATA3 and these cells are CD4+ and crank out IL-4 and IL-13, while bearing the IL17 receptor Rb. And, finally, the NKT17 type that are both CD4 and NKR negative and sweat IL-22 and IL17 and express receptors for IL-17 and IL-23. Sound familiar?

Just think! In a system of cells so geared towards specificity and an efficient division of the labour that is the immune response, there exists a population dedicated to fluidity in terms of the things they respond to and the phenotypes they subscribe to. NKT cells, to me, represent exactly what makes immunology work for me. If biochemistry and such as the Romance Languages, immunology is like English in that there are more exceptions to rules than there are adherents. It is a field that enables you to dream big, because everything is possible, though, at first, nothing makes sense!

Take care now,



We Don’t SMAC and Tell in This Business…

The number of T-helper subsets is staggering.  Well, staggering compared to the initial See-Saw* relationship we envisioned existing between the Th1 and Th2 profiles. A lot is known about these subsets, their hallmark cytokines, the transcription factors they couple with, and what musical genres really get them in a mood for proliferation…not really.

What is not known, however, shockingly, is what exactly initiates signaling at the T-cell Receptor (TCR)?  Weird, isn’t it? We got so caught up with all the drama in the middle of the story that we never bothered to ask how the story began?

The TCR is as elegantly put together and enigmatic as Don Draper. It is a membrane-spanning heterodimer made up of an elaborate, two-layered bow-tie  of β-pleated sheets: the classical immunoglobulin fold, as it were. The variable regions of this heterodimer, the Vα and the Vβ, interact via their bottom β-sheets. The constant regions also conform to the immunoglobulin fold but with one distinction: the top-most β-sheet of the Cα region is replaced by two linker-like strands. The significance of this pocket is not known. Yet.  The extra-cellular domain of the TCR has the aspect of the antigen-binding fragment (or Fab) region of an antibody molecule. That the extracellular domain of the TCR is what sidles up to the edges of a peptide-loaded MHC (pMHC) molecule to sample said peptide, this structural feature, so adept at recognition, makes a world of sense.

A co-conspirator of the TCR is CD3. Or rather, the four polypeptide chains(ε, γ, δ and ε)  that make up CD3.  Sort of the Roger Sterling to the TCR’s Don Draper, the intra-cellular regions of CD3 bear  Immunoreceptor Tyrosine-based Activation Motifs (ITAMs), the phosphorylation of which is one of early moments of signal transduction that activates a T-cell. In a lovingly rendered and thoroughly detailed treatment of how the TCR and CD3 fit together, Dr. Mike Kuhns of the University of Arizona (whom I’ve had the pleasure of dining with!) describes how the CD3δε and the CD3γε, in an “open face orientation”, dock on either side of the TCR. This not only provides evidence for there being sidedness for the TCR-CD3 complex, but also that the clustering of the complexes isn’t a random pile-up of multimeric complexes that orgiastically make signalling happen.

Ah, yes, the clustering! So much contention with the clustering. Are the TCR-CD3 clusters pre-assembled or do they huddle together once the TCR is activated? But as Xie et al tell us, in the T-cell’s self-communion, LAT (Linker of Activated T-cells) and TCR microclusters just lurk beneath the cell surface membrane, ready to co-mingle with CD3 when the time is right, and migrate to what becomes the inner circle of the cluster of receptors on the cell-surface: the central supramolecular activation cluster (cSMAC). The TCRs of the cSMAC are, themselves, bedizen with a cluster of accessory molecules like LFA-1 which form the peripheral SMAC or the pSMAC. In a conversation between antigen presenting cells and T-cells: these interactions ask the rather pivotal question of, “Shall we dance?” If the answer is “We shall!”, we might see some cytokine action!

Take care now,