International MPN News, Science & Opinion

Genetics — Crash MPN course

Genetics for MPNs — the Crash Course

by Zhenya Senyak

(Note: Part one of the formal genetics on-line course offered on MPDchat and MPN-NET in 2010 can be found here. Part two is  here.  The final session, Part III was presented in June 2010 and can be found here.)

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Behold our DNA, how filled with beauty, this constellation, how cloaked in mystery.

This mass of six billion base pairs, a dense and cosmic secret is locked in the dark night of the cell nucleus.  In each cell in our body it expresses its only message. “It’s Me, Behold, Me!”

Our double helix DNA is our immutable calling card, recognizable wherever it is flashed, blood drop, cheek swab, hand scrape, tissue and organ all stamped with this endlessly repeated mantra. “It’s Me. Behold Me!”

In MPN disease, somewhere along that sugar-phosphate crystalline scaffolding strung with beads of linked nucleotides, is harbored the mutated instruction set that created our MPN.   These new orders from within our DNA set in motion a cascade of events that produce our blood cancer cells.

Our “Me” now includes the proliferation of a blood cell line, possibly insignificant, potentially catastrophic.  

Find and cancel that order, we are cured.  Find that order and interrupt it, confuse it, block  it….and for a time we are relieved of MPN’s worst excesses. Search and find.   But how?

What follows contains more detail than absolutely required to understand what challenges the MPNRF scientists face as they question our DNA. The bare bones version goes like this: Our DNA contains a long code.  When decoded proteins are made, cells created. Somewhere in that long line of code things got garbled up, mutated. As a result our blood producing system started chunking out far more of more or more blood lines than needed.  By sequencing the DNA of someone with our MPN, spelling out the code letter by letter, and matching it up against a healthy human we might discover the mutation — sort of a bug in a computer program — and fix it.

However, we can get a much clearer picture of the task with some description of how the sequence of DNA letters turns into proteins…and sometimes go terribly astray.

The code is simple enough.

DNA contains four bases, the purines  adenine (A), and Guanine (G) and the pyrimidines cytosine (C) and thymine (T).  (RNA contains the pyrimidine uracil (U)  instead of thymine (T)    The diameter of the double helix is 2 nM which is too small for two purines and too big  for two pyrimidines but, like the Three LIttle Bears, just right for a  pyrimidine-purine pairing Thus G can bond with C or T but not A.   Adenine, Guanine, Cytosine, , and Thymine.   Just four letters. The only reason you really have to know this is to understand what’s meant by a base pair, those linked nucleotides on the DNA helix.   Because of the rigid bonding rules, when you sequence a strip of DNA you know automatically what the sequence code on the corresponding strip should be.

In the six billion years on this planet, those pairs mount up.  Nothing is forgotten as over eons time hangs its permutations on the tree of our double helix  In our “Me,” it’s all there – bacteria, fish, frog.

Turning this  code into proteins that do something in the body is the work of  translation and transcription.  The  DNA helix separates and its coding strand is read and duplicated by messenger RNA (mRNA) three nucleotides at a time to produce the coding for amino acids.  The nucleotide triplets are called codons. These are the production orders read in protein synthesis. ( There are 64 codons and 20 amino acids.  61 codons  specify the amino acid,  two are Stop signals, one is an Initiation signal.

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  Together, these 64 codons — coding for 20 amino acids —  make up the Genetic Code, applicable to nearly all life from viruses to wooly mammoths and virtually unchanged over billions of years.

The search for the single or multiple mutation causing our MPNs takes place in an ocean of irrelevant and dynamic data, data that expands and shifts under the pressure of another complication:  Mutation.

Mutations are common.  They come about during the course of reproduction, through environmental insult, through chance or entropy.    

Any change in the nucleotide sequence of the genome – is a mutation.  Sometimes a singlebase pair substitution – an AT  substituted for a TA in DNA  can have deadly effect. That single substitution results in a GUA codon replacing GAA in the mRNA As a result, a valine replaces a glutamic acid.  The single amino acid change caused by the mutation of a single base pair affects the way hemoglobin molecules load into red cells and produce the damaged red blood cells of sickle cell anemia.

Sometimes a single or even multiple  amino acid change have no effect on a protein’s function. (Proteins are three dimensional, resulting from specific folding of the produced polypeptides or amino acids.  As long as the shape remains relatively unchanged, biological function is usually not affected.)

            Mutation makes the search for genetic causes of MPNs  easier.  We are now looking for something pathogenic, something that doesn’t appear in healthy humans without the mutation.  Even though a composite human genome was been fully sequenced a decade ago,  it hasn’t been fully analyzed – and may never be – and the functional analysis, the relationships between gene expression and disease states is still at the very beginning    So simply discovering a mutation – say the JAK2 v617F mutation – doesn’t automatically buy us much,\

In 2005, four separate laboratories working from different approaches uncovered the prevalence of a single mutation nearly universal in polycythemia vera and common in about 50% of other MPNs. This was a JAK2 point mutation at codon 617 resulting in G and T swapping places at nucleotide 1849  in an expressed segment of the JAK2 gene.  As a result, in its final form, phenylalanine substituted for valine at codon 617, and the infamous JAK2 V617F mutation was created.

After several false starts and failed clinical trials, it was those discoveries in 2005 that led in 2011 to approval of ruxolitinib as the first approved therapy for myelofibrosis  (LINK TO ..)

One of the principal authors of a key paper that year was Ross Levine.  Another, was Benjamin Ebert.  It is to their labs we now turn our attention, as they are one of the recipients of an MPNRF grant.

There are two main areas of MPN genetic research underway,  Heritable and sporadic.  Now that we know MPNs are clonal stem cell disorders, the question arises as to why?  Did we inherit the disease or at least a genetic weakness to develop the disease under circumstances others wouldn’t?  Or it it purely sporadic, a result of environmental misfortune, radiation, accident? The answer lies in our chromosomes.

            Chromosomes are strange and shape shifting beasts.  They emerge out of the sea of nucleic acid during times of reproduction, 23 paired chromosomes, diploid, mom and dad continuing their bond all the way into the heart of each cell. 

            Except the germ cells, the sperm and ovum cells, the X and Y cells which are singular.  In human reproduction, the union of germ cells joins two halves of haploid DNA into a new diploid being, and issues a unique calling card to the new born child “Behold, it’s Me!”

Is our MPN stamped on this new card?  Has this baby inherited familial MPN?   Or is this baby carrying a set of instructions that will make it likely or nearly inevitable the there is an MPN in the future?  Or is this a perfectly healthy baby who will never suffer an MPN unless some sporadic event occurs, radiation exposure for example?  We’re getting close to some definitive answers.

Meantime, here are some videos to fill in the blanks and extend our view of genetics in action.

Some v ideos

http://www.youtube.com/watch?v=N4i6lYfYQz

How to Sequence a Genome   cartoon

http://youtu.be/-gVh3z6MwdU

Human Genome Sequencing = Animated tutorial

http://youtu.be/WBE8Mn9ts6A

(What is a Genome )USC cartoon)

http://youtu.be/91294ZAG2hgNC

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Take me back to the Contents

© Zhenya Senyak and MPNforum.com, 2012. Unauthorized use and/or duplication of this material without express and written permission from this blog’s author and/or owner is strictly prohibited. Excerpts and links may be used, provided that full and clear credit is given to Zhenya Senyak and MPNforum.com with appropriate and specific direction to the original content.

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