Stem cell sharing – part 2

Last week, I wrote about my experience of being a potential stem cell match for someone suffering from leukaemia or other blood disorder. Today, I’ll explain how someone is a “match” and the technology used to test this.

The theory

The surface of every cell (except red blood cells) is decorated with a cluster of proteins known as the major histocompatibility complex (MHC). In the event of infection, the invader (pathogen) is chopped up and parts are stuck onto the MHC. This serves as a signal to immune cells that a response is required. For example, if a cell is infected with a virus, parts of the virus are displayed. An immune cell known as a killer T cell will come along, recognise the MHC with added viral fragment, and pass a signal to the infected cell to shut down and die to slow the advance of the invading horde!

If cells from another human are encountered by the immune system, a difference in MHC tells the immune system that the cell is foreign and an immune response is mounted. This is an understandable response; it’s what defends us from infection but is exactly what we don’t want to happen in a transplant scenario. Stem cell transplants are even more complex as the cells go on to produce the immune system. These could go on to attack the recipient’s existing cells in what is known as graft vs host disease.


To avoid this rejection of cells from other people, we need to pick the donor correctly and it all comes back to the MHC. We need the MHC of donor and recipient to be as similar as possible to give the best chance for the cells to accepted, and in the case of stem cell transplant, avoid graft vs host disease.

The practicalities

How do you go about testing the compatibility of donor and recipient? We need to compare the proteins that make up the MHC in the patient and all the donors on our registry.

My former lecturer has a memorable saying about biochemistry: “DNA is easy, protein is fun“. What Dr Cox means by fun is that working with proteins is difficult, unpredictable and frustrating compared the the simplicity of dealing with DNA.

Fortunately, we understand that proteins are the products of genes, which are comprised of DNA. Here’s a reminder of the central dogma.

DNA –> mRNA –> Protein

By comparing the genes that code for the MHC, we can compare the nature of the proteins. The genes considered important for matching are: HLA-A (1,833), HLA-B (2,459), HLA-C (1,507), HLA-DRB1 (1,047), HLA-DRB3 (46), HLA-DRB4 (8), HLA-DRB5 (17), HLA-DQB1 (337) and HLA-DPB1 (205). They are named HLA after Human Leukocyte Antigen, another term for the MHC. The numbers in brackets indicate the number of protein variants known in January 2014 (source).

As you can see, there are lots of different versions of the proteins and the chances of any two unrelated people being a match is low.

The technology

(The following is based on information from Anthony Nolan. I don’t know what techniques other registries use but they are likely to be similar.)

One benefit of carrying out analysis on DNA is that we know how to amplify it. We can take the enzymes used to replicate DNA in bacteria and use them for our own purpose of replicating DNA in a plastic tube! This technique is called polymerase chain reaction and is one of the fundamental techniques of molecular biology. It is to DNA what a photocopier is to information on a sheet of paper. Kary Mullis won the Nobel Prize for inventing this process. Once DNA is amplified, we have lots of copies to do testing on.

All samples from donors and patients are tested using a very clever fluorescence technique. Many, many different synthetic DNA molecules are attached to lots of tiny fluorescent beads. Each bead has a unique colour and is decorated with only one type of DNA. Elsewhere, the amplified DNA from the humans is labelled with a fluorescent molecule of a different colour. If the synthetic DNA and DNA from the human being tested are similar, they will stick together, known as hybridisation. Each bead is then looked at by a computer controlled microscope that identifies the colour of the bead, and if DNA has stuck. If you want more information about this remarkable machine, check out the product website. This method is used as a primary way to identify the type of MHC of the patient and potential donors, however it only gives a rough idea of similarity as DNA will still hybridise if there is a small difference.


This shows that the subject has DNA similar to the DNA immobilised on the cyan bead.

This is the technique used to test all donors and patients. Next week, I’ll talk about how higher resolution matching is achieved.

If you’re hungry for more information or interested in joining a stem cell registry, I hope these links to UK organisations will satisfy you.

BBMR – Blood donors can join at next session if aged 18-49.

Anthony Nolan – People aged 16-30 can join.

DKMS – Accept people aged 17-55 (only 18+ called to donate).

If you’re in another country, take a look at this extensive list of stem cell registries from reddit.

This post is composed of my own views and opinions and not those of the above organisations.


Stem cell sharing – part 1

Some years back, I joined the British Bone Marrow Registry. It was a simple process, just an extra sample was taken during a blood donation session. A card with my registry ID number has sat in my wallet since then and I’ve thought little of it.

Last week: I received a letter from the BBMR saying I am a potential donor for a patient, likely someone suffering from leukaemia (leukemia for those in the US) or other blood disorder. Included was a booklet all about the process from Anthony Nolan.

You're a match booklet from Anthony Nolan

The booklet from Anthony Nolan. It’s a more in-depth version of this page.

I made a quick phone call to answer some health questions, and an appointment at my doctor’s surgery for a blood sample. A week later, I went to the nurse with the sample kit the BBMR posted out to me. After 2 minutes of painless blood sample collection, we packed up the tubes in a Special Delivery bag and I went for a coffee while waiting for the Post Office to open. The samples were destined for Anthony Nolan labs in London indicating the level of cooperation between the different registries.

Special delivery bag containing samples

Packaged samples and the edge of a flat white coffee

It will take up to 8 weeks for the testing procedures to be carried out to find the best match for the patient. Only then will I discover if I’ll play any further part in the process.  What is the process?

There are two ways that stem cells can be collected:

  1. Peripheral blood stem cell (PBSC) collection. The donor is given injections of a protein called granulocyte colony-stimulating factor (G-CSF) on 4 or 5 consecutive days. This signals to the bone marrow to make more haemopoietic (blood-making) stem cells which are released into the blood.  The donor is then hooked up to a machine and blood is removed, centrifuged to extract the stem cells and returned in a process known as apheresis. This is the most common method of stem cell donation; ~90% happen this way.
  2. Bone marrow extraction. Bone marrow is extracted directly from inside the hip bone (the iliac crest for the anatomists out there).

The choice of method is down to the donor but doctors will advise what is best for the recipient. My preference would be PBSC collection.

Regardless of the source, the collected cells are then transported to the recipient and given intravenously. The patient will have been prepared for this beforehand with strong chemotherapy and/or radiotherapy for three reasons:

  1. To destroy existing, faulty bone marrow.
  2. To destroy cancerous cells.
  3. To weaken the immune system to reduce the chance of rejection of the stem cells.


Cells will then travel into the bones, form the bone marrow and start producing healthy blood cells. This process is known as engraftment.

My thoughts:

  1. As a biochemist, it’s exciting to be part of a real life biotechnology meets medicine situation. I’ve enjoyed reading about the technology Antony Nolan use to match donor and patient.  The development of peripheral blood stem cell collection as a more pleasant method of donation and perhaps more effective treatment for patients (source) is the product of the work of biotechnologists (to produce and purify G-CSF), biomedical engineers (to design apheresis machines) and clinicians (to treat and monitor donors and patients).
  2. On a human level, I know there’s someone out there that needs some stem cells and I could be the person to provide them. I find it easier to understand the biochemistry and immunology involved than process this. Whatever the level of my involvement, I wish them all the best. I hope that a small amount of donor discomfort and disruption leads to a healthy life for the recipient.

Check out my whistle-stop tour of finding a match in part 2!

If you’re hungry for more information or interested in joining a stem cell registry, I hope these links to UK organisations will satisfy you.

BBMR – Blood donors can join at next session if aged 18-49.

Anthony Nolan – People aged 16-30 can join.

DKMS – Accept people aged 17-55 (only 18+ called to donate).

If you’re in another country, take a look at this extensive list of stem cell registries from reddit.

This post is composed of my own views and opinions and not those of the above organisations.

Grip Mod for Logitech iPad 2 Keyboard

Happy New Year!

One of my Christmas/birthday presents this year was a Logitech iPad 2 Keyboard. Connects by bluetooth, acts as a stand and makes it much more pleasant to write on. One downside is that it is a little slippery on the underside. It tended to move around a lot on a recent coach journey. Here’s a cheap fix!

I bought some self-adhesive neoprene tape (10mm wide and 2mm thick), cut two ~17 cm strips and stuck them on.

No more slippage! Just need to decide what to do with the remaining 9.6 m of tape…

Bells and whistles in medical technology

At the recent Medtech Motions OBR event, Ian Oliver from Ernst & Young gave an overview of the current field of medical technology.

The idea of medtech companies offering stripped down versions of their devices with reduced functionality but at a lower price was discussed. Emerging markets are sensitive to price and healthcare providers in established markets aren’t exactly carefree when exercising their cheque books.

This made me realise that two types of development are going on in medtech companies:

1. We have people extending existing technologies and creating new ones. This can be guided by immediate needs of patients and practitioners, or be a little more speculative. One example of this is my friend developing new programs for MRI scanners to see processes in the body that are currently hidden (he’s doing this in a university but a medtech company is part-funding the research by providing cheap equipment and will eventually buy the technology).

2. There are others looking to remove superfluous bells and whistles from the device, guided by practitioners. They are also looking to economise on the manufacture of the device by reducing material and labour costs. This McKinsey report tells a good story of a “teardown” exercise where a company compares its device against that of the competition in minute detail.

I believe that the relative efforts put into the two processes above could tell a great deal about individual device markets (scanners, monitors etc.), whole companies and the industry as a whole.

Zopa’s seventh birthday

Early March brought the birthday of the peer to peer finance company Zopa. There was good news from CEO Giles Andrews as accounts released later this year will show a profit! 2012 has seen an increase in applications from borrowers and more loans are being disbursed each week than ever before.

This post serves to explain the Zopa basics.

I’ve been a member of Zopa since late 2006 when they gave me £30 to try it out. After seeing the results of this test I went in with some of my own funds in the middle of 2008.

What is Zopa?
The concept is simple. Zopa links those who want to borrow with those who want to lend. Zopa is a marketplace.  Since its birth over £185 million of loans have been arranged and only 0.9% of this has gone into default. It has won Moneywise’s ‘Most Trusted Personal Lender’ for the past two years. Lenders are making 6.2% per year on average after fees and before bad debt. Borrowers are receiving market-leading rates. Zopa accounts for 1-2% of the personal loan market.

How does it work?
1. Lenders set their desired rate and how much to lend to each borrower. Zopa give predicted bad debt rates and an indication of how competitive your offer is.
2. Potential borrowers apply and Zopa credit check them and give them a risk rating. They are then given a rate based on what lenders are currently offering.
3. If borrowers like the rate, they continue with the application. Zopa continue with credit checking.
4. A few days later, a final decision is made. If approved, borrowers receive the funds shortly after.
5. Repayments are returned to the lender to either withdraw or lend out again.

This sounds risky, what protection is there?
Zopa credit check all applicants and only prime borrowers are accepted. Should a borrower stop making repayments, Zopa deal with chasing. They also manage all the court business if it comes to it. Lenders can protect themselves by only lending a small amount to each borrower to minimise the effect of defaults. Newcomers needn’t lend more than £10 to each borrower!

How does Zopa make money?
Zopa charges a fee to borrowers when they are approved for a loan. There is no early repayment fee, which is quite a bonus for borrowers. Zopa also charge lenders 1% p.a.

My thoughts
Zopa was the first peer to peer  finance operation and I’m delighted to hear that it’s profitable. The timing of its launch was extremely lucky; sufficient reputation was build up when the financial crisis hit and the wave of anti-bank feeling certainly helped get media attention. The fact that Bank of England policymakers are talking about it makes me think disintermediated finance is hitting the mainstream in 2012.

Why not give it a try today? Sign up here and be part of the finance revolution.



Crowdsourced and gamified innovation from Marblar

This week I have been fascinated by a new website called Marblar. Inventors give details of a new technology and participants give suggestions for applications and improvements. Rewards are offered for the best ideas that come in and one metric for quality comes via upvotes and downvotes from other members. I can’t wait to hear the results of the first rounds of brainstorming.

This reminded me of James Gardner’s Sidestep & Twist where he states that companies must employ strategies for driving innovation internally and a suggestion box simply isn’t good enough. You have to agree and Spigit (where Gardner now works) provides a platforms for ideas to be voiced and evaluated across an organisation.

There are similarities between Spigit and Marblar but there is a difference in the nature of the crowd. Spigit enables a preexisting crowd in the form of a company whereas Marblar has assembled (and will go on accumulating) users to work on problems.

Back to Marblar, two very different technologies are up for discussion at the moment; a novel chemistry for linking DNA and RNA, and electricity generating pedals. Why not pop along to and have a go?

No Cell is an Island – What I Do All Day (Part II)

Ages ago I wrote about how the molecules that cells need (or need to get rid of) travel through the membrane. Now it’s time to consider the problem of transmission of information through the barrier.

First of all we should consider the type of information that a cell receives.

  • Hormonal signals e.g. insulin. This is released from the pancreas when blood sugar levels are high. It mainly acts on liver and muscle cells causing a increase of uptake of glucose and subsequent storage as glycogen within the cells.
  • Neurotransmitters e.g. acetylcholine. This is released from nerve cells and makes skeletal muscles contract. It also released into the synapase or between two nerve cell, transmitting the signal from one to the other.
  • “Environmental conditions” e.g. glucose. Bacteria are able to swim in the direction of increasing glucose concentration. The process of moving in a certain direction based on chemical signals is known as chemotaxis. Also, we can smell all sorts of different chemicals.

There are other classes too but these are the main types that I want to consider today as they illustrate the different mechanisms across membranes but also reinforce the fact that mechanisms are shared across a wide range of different functions.

A key, take home point is that every molecular signal has a receptor. This is a protein that binds the signalling molecule and then passes the message on to the rest of the cell.

Some signalling molecules are able to move through the cell membrane independently. These are generally lipophilic (lipid loving) hormones such as testosterone and cortisol. Once inside the cell, an intracellular receptor binds the hormone and a message is passed down a chain of more proteins until an effector protein is activated causing a response. This doesn’t really involve the membrane so this is as much as I’m going to say about this!

Most hormones and “environmental signals”, and all neurotransmitters bind their receptors at the cell membrane – the receptors are membrane proteins.

One way of getting a message across is through dimerisation, the coming together of two proteins which serves to bridge the inside and outside of the cell. Binding of the signal outside causes two proteins to interact and transfer chemical groups. This changes the structure and allows the binding of further “downstream” proteins and the signal is passed down a chain until the effector is reached. Insulin receptors are believed to act like this, leading to effects such as increased production of glucose transporters.

Another mechanism for signal across a membrane is to activate a enzyme that catalyses the production of a so called “second messenger”. One very large family of proteins that do this are called G-protein-coupled receptors (GPRCs). These bind the signalling molecule, change shape and activates G-protein allowing it to interact with other membrane proteins including adenylate cylase (which makes a chemical known as cAMP), phospholipases (which break apart membrane phospholipids) and ion channels (which allow the flow of ions into the cell). These secondary chemical then diffuses through the cell where it binds other proteins to cause effects. Smell sensors or olfactory receptors are GPRCs!

The final mechanism I’ll talk about today are ligand-gated ion channels (LGICs). These channels open in response to the direct binding of a chemical to the channel such as a neurotransmitter. Binding of acetylcholine to receptors on a muscle cell opens the channel and allows the exit of potassium ions but a much greater entry of sodium ions. This changes the electrical properties of the membrane opening voltage gated calcium channels, causing the muscle fibres to contract. Magic, and not possible without membrane proteins!