Monday, August 8, 2016

PTPN22 gene and type 1 diabetes: a short post about why the genetics of diabetes are so complex.

Apparently, this post has been sleeping as a draft for a while. Wrote it at the beginning of the year, never posted it...

The case of PTPN22

Outside of the major histocompatibility complex (yes, that HLA-DR... stuff), the PTPN22 gene that encodes a protein call Lyp (lymphoid protein tyrosine phosphatase) is one of the genes most associated with auto-immune diseases such as Type 1 Diabetes, RA, JIA, Addison, Psoriasis, etc... A single mutation in the coding part of that gene leads to an amino acid (the building blocks of proteins) substitution. We will call that "bad" mutation R620W.

Here's a short description of PTPN22, we'll talk more about the roles of the phosphatase it encodes a bit later.

You will note the phosphatase is a member of a sub-family (an indication that there are lots of them). You will also note the use of "may". Not necessarily the word you want to read when you are looking at a strong suspect... We'll also get to the reasons behind the uncertainty.

How do we know it is associated with auto-immune diseases?
There are a few "simple" cases where one single mutation in a single gene creates a well defined disease. Phenylketoneuria is the archetypal single gene disease. Certain forms of Type 1 Diabetes have a direct genetic cause. When the Human Genome Project started, we lived for a while under the illusion that we would soon explain hundreds of "genetic diseases". We were totally wrong! In most cases, when a genetic predisposition is present, the causal links are weak and many. Most of today's gene-disease association research is done through Genome Wide Association Studies. How do those GWAS work? Here is a simple analogy. Let's say that 50% of the citizens of the USA are republicans. Therefore, we know that 20%  of the US citizens (40% of 50%) vote for Donald Trump. We also know that only very few Muslims, a small percentage of Blacks and possibly a slightly bigger percentage of Latinos vote for our dear Donald. Crunch the numbers, and you will obtain the odds for each population category. In that simple case, you can safely say if you are Caucasian your risk of contracting Trumpism is higher than the general population. The danger is even worse if you are a Caucasian Republicans! Of course, Caucasian Democrats are less likely to contract the disease but some of them could catch it at some point. Calculate all the odds and predict the results of the elections. Not that simple, right?

But in fact, biology is even more complex than politics and the odds aren't always that clear. Consider that recent Chinese study for example.

The tiny genetic code modification in PTPN22 is more frequent in the T1DM patients population. But, and that is extremely important, approximately 80% of the T1DM patients and 92.5% of the healthy control do not carry that variation! In a nutshell, while more T1DM patients than healthy subjects carry that variation, the vast majority of the population does not carry it...

The risk factor is clear, but the big picture is extremely fuzzy.

The huge weakness of GWAS studies is that while they find a lot of strong or weak correlations, in most cases they do not help us much in terms of causal link. They are pointers that can help directing further research.

Another interesting link between the bad mutation R620W and auto immune diseases is that its geographic distribution mirrors the distribution of diseases (Finland for example has the highest T1D frequency in Europe and also the highest R620W frequency). 

What do we know about PTPN22?

We know an awful lot about PTPN22. In fact, we know almost everything there is to know about it. Here is a simpler description of the gene

It has been extensively studied. 437 citations in Pubmed. 309 Gene RIFs (roughly established connections to functions)

Note: the green rsxxxxxx numbers are the SNPs (single nucleotide polymorphisms) tested by the 23andMe version 3 chip. Our SNPs are constantly loaded as a browser extension and automatically highlighted on pages that I visit.

In fact, you could probably devote your life to the study of PTPN22, its product, the role of its product, its interactions and associations.

Now, lets interest ourselves with the product of PTPN22, the phosphatase itself. You'll find a good summary of what we knew in 2011 in the excellent article Why is PTPN22 a good candidate susceptibility gene for autoimmune disease? I will just summarize a few salient points below.


Lyp, the product of PTPN22, is a protein tyrosin phosphatase (PTP). We know more than 110 variations of which at least 57 of them are present in Lymphocytes ("white" cells, in general cells involved in the immune system). Phosphatase (PTP) and Kinase (PTK) are enzymes that control the activity of signalling transmitters, the messengers that will inform the cell of external changes and change the cell behaviour (they are the control switches inside of cells). In general PTP control the amplification of the signal, PTK control its tempo and duration. Again, you could spend a full life studying kinases and phosphatases without running of material...

Reaction to outside signals is obviously extremely important for immune system cells. It is no surprise that several of those phosphatases are associated with auto-immune diseases (PTPN2, PTPRC, UBASH3A, PTPN11, PTPRT and our PTPN22). PTPN22 was linked to Type 1 diabetes in 2004 (N. Bottini, et al., A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes, Nat. Genet., 36 (4) (2004), pp. 337–338)

Lyp, the member of a family of 100+ enzymes, a sub family of 57+ enzymes has three forms, independently of its eventual mutation.

The expression of Lyp varies, depending on the type of lymphocyte and cells.

Lyp inactivates some of the kinases of the Src and Syk families.

Lyp interacts with many other molecules. Here's a rough overview


and a closer view of one of the process. 


At this point, I can't resist a few direct (unlinked) quotes.

 The precise stoichiometry of the interactions that promote Lyp phosphorylation by Lck is complex and remains to be determined, but Csk micro clusters may facilitate this interaction through SH2 binding sites that allows the docking of Lck and subsequent phosphorylation and inactivation of Csk associated Lyp. Clarification of the sequence of events that govern inhibition of Lck by Csk and Lyp is also required, since Csk preferentially targets activated Lck that is phosphorylated at Y394, as demonstrated by in vitro kinase assays and phosphopeptide mapping [72]. The regulation of Lck has also been brought into question in recent years since it is becoming evident that acute dephosphorylation of Y505 may not be necessary for Lck activation and TCR signalling

 Studies have yet to address the contribution of Lyp in regulating Vav function.

Because B cells share much of their signalling machinery with T cells it is likely that Lyp may regulate proximal B cell receptor signalling in a similar fashion, but substrate trapping experiments have not been undertaken in B cells. There is some evidence that there may be impairment of signalling in human individuals carrying the R620W variant  

Despite these two molecules having opposing kinase/phosphatase activity, they both serve to inhibit T cell function, possibly synergistically

Together these studies flag up two important questions. First, how does a mutation outside the catalytic domain lead to increased enzyme activity? Second, how could an apparent attenuation of TCR signalling lead to autoimmune disease?

There is still no clear consensus as to whether R620W is a gain- or loss-of-function variant and there is a possibility that in the future there may be newly discovered functions of the mutant phosphatase. It is not inconceivable that R620W may exert both gain- and loss-of-function activity in different pathways but within the same cell. Another possibility is that the mutant Lyp may have different (or opposing) effects in cells of different lineages, or that the mutant has opposing activities in different pathways in the same cell.

Note: I stopped my draft at this point - probably out of despair.

Addendum: interesting papers

Staging Presymptomatic Type 1 Diabetes: A Scientific Statement of JDRF, the Endocrine Society, and the American Diabetes Association (

A convenient list of T1D SNPs and their weighted risk score

Genetics of Type 1 Diabetes (

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