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Genetics and Myeloproliferative Neoplasms (MPNs)

Coming to understand modern genetics is a bit like learning a language.  It’s foreign and impenetrable at first. Over time, with study and exposure it becomes more familiar. The first steps are the most difficult, but if we persevere we can end up enriched by the wonders of molecular biology and the miraculous flow of cellular interchanges that make up life itself.

The course title for our colloquium defines the material we’ll be exploring together:  the life cycle and function of our genes and the nature of our myeloproliferative neoplasms.

Genetics is about DNA (deoxyribonucleic acid) and genes, about the transmission of traits and the functioning of each cell in our body. .Since we are concerned with the form and function of biological molecules, the focus of this seminar is on molecular biology.

A gene is a stretch of DNA that encodes data to produce a protein to perform an action.  DNA, in the nucleus of every cell in our body, contains the instructions necessary for the cell to perform its functions.  These instructions are encoded in the form of four nucleotides made up of base pairs G and C, A and T.(Guanine and Cytosine,  Adenine and Thymine) plus sugar and phosphate.  On average genes are about 1000 to 10,000 base pairs in size, but some genes are much larger.

Myeloproliferative neoplasms are genetic disorders affecting hematopoeisis, blood production. The genetic instruction set within the hematopoeic system has mutated to produce an excess of one or another blood cell lines or otherwise impair the proper functionality of blood cells.  Our practical object in learning how biology at the molecular level works is to help us understand and sort through the genetic discoveries designed to slow or reverse the progress of our MPNs.

There are seven elements to this first seminar module: 1. A graphic tour of concepts; 2. a DNA cartoon; 3. vocabulary building; 4. a summary printout of genetic terms; 5. an MPN application;  6. an exercise in building a DNA molecule; and 7.  concluding visual aids.

Suggestion:   Much material in this seminar will be opaque in the beginning and become clearer only as we move along. Best bet is to get a notebook to hold your notes on each module and write down the vocabulary. Repetition of these terms and seeing their interaction in future modules will eventually make them familiar.   In beginning this work, there are several aids available to us. :

(1) Start with the Genetic Science Learning Center site of the University of Utah. At http://learn.genetics.utah.edu/  When you arrive at this site:

Tour the BASICS (Click Upper Left)

Then choose each of these topics in turn.

What is DNA

What is A Gene

What is a Chromosome

What is a Protein

Note: You might have to click on NEXT in some cases to advance the narrative

===============================================================

(2) Look at DNA structure on DNA Tube, a short, technical cartoon.

http://www.dnatube.com/gvideos.php?viewkey=a1a4f25f62e0eb5261ca&urlkey=dna_structure&gid=26

===============================================================

(3) Vocabulary

Learning the vocabulary is made much easier by the talking glossary put together by the National Human Genome Research Institute. Here, you can hear  and see leading scientists present these words.. It’s important to learn the pronunciation of these unfamiliar terms so we can use them in talking with our hematologists…. and, of course, impress our friends.,

http://www.genome.gov/glossary/index.cfm?id=145   Learn and Review these 12 terms

Allele

Amino Acid

Base Pair

Cytosine

DNA

Gene Expression

Histone

Nucleotide

Ribosome

RNA

Telomere

Transcription

=================================================================

(4)  (Handout )

http://www.genome.gov/18016863

A brief guide to genomics fro NHGRI, downloadable.   Print this short guide and tuck it in your notebook as it will give us a common frame of reference.

=================================================================

(5)  MPN and genetics:  The HDAC Affair.

The current  MPD Foundation Newsletter as well as several postings to MPD-Net reported promising results on HDAC inhibitors. Instead of just sliding by that news, let’s try to figure out what it means.  HDAC is an abbreviation for  “histone deacetylase.”  Histones ,which act as a spool around which DNA is wound within the cell nucleus,  are small proteins electrically attached to DNA. Histones play a role in gene regulation. “De-acetylase” is to effect gene expression by reducing the acetylation of the histone thus “inhibiting” the expression of a target gene.  HDAC inhibitors also act on nonhistone proteins like gene transcription and growth factors.

Why this works:  Acetylation of the lysine residues at one end of the histone protein removes its positive charge reducing the affinity between histones and DNA.  In most cases histone acetylation enhances the ability for a gene to reproduce itself while histone deactylation represses transcription.

For a graphic look at the process go to http://www.youtube.com/watch?v=4b-NSWm24BA&feature=related

Vocabulary:  acetylation, inhibiting, gene transcription,

=================================================================

(6) Exercise:  Build a DNA Molecule.  Review material by playing this video game. http://learn.genetics.utah.edu/content/begin/dna/builddna/

===================

(7)  Videos

(Very brief and dramatic microscopic film, a must-see if you have ET)

http://www.youtube.com/watch?v=6R-ESPFiKbo

Megakaryoctyes breeding platelets

Dr, Stephen Sullivan, Bucks County Community College,

http://www.dnatube.com/gvideos.php?viewkey=deb67d7ce42d58fe5157&urlkey=dna_structure&gid=26

Very clear slide presentation, about 10 minutes, on DNA, proteins, cell division. Definitely do your vocabulary work before viewing this presentation.

Barry Schuler Introduction to Genomics http://www.youtube.com/watch?v=_xJXZBCOWMY&feature=related

A  21 minute visionary overview and projection of future genetic applications

==========================

Feedback, questions to incorporate in next week’s discussion, send to: zhenyasenyak@gmail.com.

Introduction…As patients or caregivers, we lack the narrative necessary to bring the names, acronyms, formulas and processes of genetics and gene therapy into focus.  Stories can be life changing and the story written in the multiple billion year strand of our DNA is filled with the letters and codes that tell those stories.  In the process of duplication, of translation and transcription of that code into proteins, mutations arise, sometimes for the good, sometimes not. Perhaps no one can tell this part of the story better than Professor Eric Lander, an MIT mathematician, scientists and geneticist, a teacher,  story teller and pioneer in sequencing the human genome. In this unit we are in Dr. Lander’s freshman genetics class at MIT.

    Starting with Unit Three, next week,  we explore some likely genetic causes and potential cures of our myeloproliferative diseases. The object is to convert some of the vital reports coming out of  labs and clinical trials from incomprehensible scientific abstracts into narratives we can understand and apply.  

====================================

Scope of Unit Two

In this second unit we complete the overview of the genetics portion of our seminar by considering how DNA moves from genes carrying the code of the genome to creation of the proteins needed for cell structure, function, and repair.

=====================================

This Unit has seven sections:

1. Vocabulary

2. The Central Dogma

3. Visual Aid: From RNA to Protein Synthesis

4 The Eric Lander MIT lectures

5. Test yourself

6. The BCR-ABL video (homework to prepare for next week’s unit)

7. Bonus videos

=====================================

(1) Vocabulary

Centromere

Chromosome

Chromatid

mRNA

Promoter

Protein

(At the www.genome.gov site find the word and its definition.  Click on “Illustration” as well as the brief comments by scientists while reading the definition. mRNA is not on that site, so head for Google.  The Wikipedia entry is good. )

===================================

(2)  The Central Dogma

The central dogma of molecular biology is DNA (deoxyribonucleic acid) directs the synthesis of proteins through the intermediary of RNA (ribonucleic acid) and RNA directs the synthesis of proteins..   While DNA stores the code for protein synthesis, it is RNA that carries out the instructions in order to produce proteins. The order of bases (Adenine, Guanine, Cytosine, and Uracil) in DNA  spell out the order in which the amino acid sequence of a specific protein is assembled. Messenber RNA molecules (mRNA) are synthesized from DNA templates (transcription) and proteins are synthesized from mRNA templates (translation).

===============================

(3)  Visual aid: You can see this process in the video: http://www.youtube.com/watch?v=NJxobgkPEAo

and this short section from the PBS special “Cracking the Genetic Code” (Chapter 9m “Finding Cures is Hard,” from Genes to Proteins. http://www.pbs.org/wgbh/nova/genome/program.html

=============================

(4)  Reading Genes and Genomes, by Eric S. Lander, Ph.D  Howard Hughes Lecture Series, Human Genetics,

http://www.hhmi.org/biointeractive/genomics/lectures.html  (58:35)

And here’s the webcast version of the same lecture that gives you the option to click on subjects within the talk

http://www.hhmi.org/lectures/webcast/ondemand/02webcast1/index.html

(Don’t miss the section illustratingsize of the human genome compared to Fifth Avenue in New York City.)

===============================

(5) Pop Quiz..test yourself:   Describe the role of DNA in the manufacture of individual proteins.  What role is played by mRNA? By chromosomes?  By histones? Ribosomes?  (This is a collaborative seminar.  E-mail any questions or insights  you might have to share with the others to zhenyasenyak@gmail.com)

==================================

(6)   Homework

Next week we consider the application of genetics and molecular biology to our myeloproliferative neoplasms.  Unit Three is devoted to the BCR-ABL oncogene, the Philadephia chromosome, and Gleevec.  Here’s the background:

http://www.dnai.org/d/index.html

This link takes you to the DNA Applications page of the  Cold Spring Harbor Lab  DNAI site,  At the bottom of the page, click on GENES and MEDICINE. At the top of the resulting page you’ll have four options. Click on  DRUG DESIGN

That will take you to the Gleevec and Philadelphia Chromosome page with several options. Play around as much as you like but at some point click on the PHILADELPHIA CHROMOSOME icon and follow the animation, the creation of the BCR-ABL oncogene.

==================================

(7) Bonus

(A) MIT Open Courseware, offers free classes in many areas and includes this lecture on experimental use of genetics by Eric Lander complete with a transcript. http://ocw.mit.edu/OcwWeb/Biology/7-012Fall-2004/VideoLectures/detail/embed08.htm

(B) How does that long 6 feet long strand of DNA fit into the nuclei of every cell in our body? How do chromosomes form from DNA?. (This is another look at the role of histones, from the Howard Hughes Medical Institute

http://www.hhmi.org/biointeractive/dna/DNAi_packaging_vo2.html

(C) The MPD Foundation is a valuable source of information on clinical trials and breaking scientific  developments

http://mpdfoundation.org/

Unit Two:  Genetics for MPNs….From genes to proteins

 

Introduction…As patients or caregivers, we lack the narrative necessary to bring the names, acronyms, formulas and processes of genetics and gene therapy into focus.  Stories can be life changing and the story written in the multiple billion year strand of our DNA is filled with the letters and codes that tell those stories.  In the process of duplication, of translation and transcription of that code into proteins, mutations arise, sometimes for the good, sometimes not. Perhaps no one can tell this part of the story better than Professor Eric Lander, an MIT mathematician, scientists and geneticist, a teacher,  story teller and pioneer in sequencing the human genome. In this unit we are in Dr. Lander’s freshman genetics class at MIT.

    Starting with Unit Three, next week,  we explore some likely genetic causes and potential cures of our myeloproliferative diseases. The object is to convert some of the vital reports coming out of  labs and clinical trials from incomprehensible scientific abstracts into narratives we can understand and apply.  

====================================

Scope of Unit Two

In this second unit we complete the overview of the genetics portion of our seminar by considering how DNA moves from genes carrying the code of the genome to creation of the proteins needed for cell structure, function, and repair.

=====================================

This Unit has seven sections:

1. Vocabulary

2. The Central Dogma

3. Visual Aid: From RNA to Protein Synthesis

4 The Eric Lander MIT lectures

5. Test yourself

6. The BCR-ABL video (homework to prepare for next week’s unit)

7. Bonus videos

=====================================

(1) Vocabulary

Centromere

Chromosome

Chromatid

mRNA

Promoter

Protein

(At the www.genome.gov site find the word and its definition.  Click on “Illustration” as well as the brief comments by scientists while reading the definition. mRNA is not on that site, so head for Google.  The Wikipedia entry is good. )

===================================

(2)  The Central Dogma

The central dogma of molecular biology is DNA (deoxyribonucleic acid) directs the synthesis of proteins through the intermediary of RNA (ribonucleic acid) and RNA directs the synthesis of proteins..   While DNA stores the code for protein synthesis, it is RNA that carries out the instructions in order to produce proteins. The order of bases (Adenine, Guanine, Cytosine, and Uracil) in DNA  spell out the order in which the amino acid sequence of a specific protein is assembled. Messenger RNA molecules (mRNA) are synthesized from DNA templates (transcription) and proteins are synthesized from mRNA templates (translation).

===============================

(3)  Visual aid: You can see this process in the video: http://www.youtube.com/watch?v=NJxobgkPEAo

and this short section from the PBS special “Cracking the Genetic Code” (Chapter 9m “Finding Cures is Hard,” from Genes to Proteins. http://www.pbs.org/wgbh/nova/genome/program.html

=============================

(4)  Reading Genes and Genomes, by Eric S. Lander, Ph.D  Howard Hughes Lecture Series, Human Genetics,

http://www.hhmi.org/biointeractive/genomics/lectures.html  (58:35)

And here’s the webcast version of the same lecture that gives you the option to click on subjects within the talk

http://www.hhmi.org/lectures/webcast/ondemand/02webcast1/index.html

(Don’t miss the section illustratingsize of the human genome compared to Fifth Avenue in New York City.)

===============================

(5) Pop Quiz..test yourself:   Describe the role of DNA in the manufacture of individual proteins.  What role is played by mRNA? By chromosomes?  By histones? Ribosomes?  (This is a collaborative seminar.  E-mail any questions or insights  you might have to share with the others to zhenyasenyak@gmail.com)

==================================

(6)   Homework

Next week we consider the application of genetics and molecular biology to our myeloproliferative neoplasms.  Unit Three is devoted to the BCR-ABL oncogene, the Philadephia chromosome, and Gleevec.  Here’s the background:

http://www.dnai.org/d/index.html

This link takes you to the DNA Applications page of the  Cold Spring Harbor Lab  DNAI site,  At the bottom of the page, click on GENES and MEDICINE. At the top of the resulting page you’ll have four options. Click on  DRUG DESIGN

That will take you to the Gleevec and Philadelphia Chromosome page with several options. Play around as much as you like but at some point click on the PHILADELPHIA CHROMOSOME icon and follow the animation, the creation of the BCR-ABL oncogene.

==================================

(7) Bonus

(A) MIT Open Courseware, offers free classes in many areas and includes this lecture on experimental use of genetics by Eric Lander complete with a transcript. http://ocw.mit.edu/OcwWeb/Biology/7-012Fall-2004/VideoLectures/detail/embed08.htm

(B) How does that long 6 feet long strand of DNA fit into the nuclei of every cell in our body? How do chromosomes form from DNA?. (This is another look at the role of histones, from the Howard Hughes Medical Institute

http://www.hhmi.org/biointeractive/dna/DNAi_packaging_vo2.html

(C) The MPD Foundation is a valuable source of information on clinical trials and breaking scientific  developments

http://mpdfoundation.org/

 

 

 

About

Originally called Molecular Biology for English Majors the current seminar series is now called Genetics for MPNs,  thus addressing both the subject and the object of the enterprise.   The first title, however, conveyed the intent of these seminars, i.e., interpret the flood of highly relevant findings emerging from scientific journals for the subjects of all this work:  Patients with myeloproliferative disorders..  The idea is to empower patients with materials to share with their primary care physicians and hematologists in order to help secure the most effective therapeutic outcome.

Zhenya Senyak, a 15 year veteran of essential thrombocythemia, progressed to early stage myelofibrosis in 2009.  Based on his MF diagnosis and clear need to get up to speed on MPN clinical trials and the mechanisms of molecular biology  he created this program.

Genetics for MPNs is co-hosted by MPDchat.com and MPD-NET http://www.mpdinfo.org.  Units or links to full units, appear on both sites and advance units along with comments and discussion are e-mailed to seminar registrants.

Enjoy, watch the animated videos, and freely pass along to friends and relations. The cause and cure of our MPNs is in our genes.  Let’s have a look.

Genetics for MPNs 3.0: 

Unit Three:   Philadelphia Chromosome, BCR-ABL, Gleevec and Targeted Gene Therapy

Introduction: Chronic Myelogenous Leukemia is a rare disease and a myeloproliferative disorder.  In its chronic early stages, lasting about five years, there is a massive expansion of white blood cell production.  Its accelerated phase leads to a blast crisis in which survival is measured in just a few months.

Just a few years ago, we could only count on radiation, chemotherapy or the risky option of bone marrow transplant to extend our lives but death rates were high, life expectancy short, and treatment harsh.  With the debut of Imatinib (Gleevec) in 2001 all that has changed. Today CML is a manageable chronic disease with normal life expectancy. More than that, the discovery and deployment process of this drug has developed a new paradigm for the industry that will affect all of us with MPNs.

This is the Gleevec story.

==============================

April 5, 2001 – the NEJM

For those of us with myeloproliferative neoplasms, there can scarcely be a more significant event than the scientific paper published in the April 5, 2001 New England Journal of Medicine.  The findings made the cover of Time Magazine and the drug described was so effective it gained FDA approval the following month… in record time!   We need to file a copy of this paper with our medical records, hang a copy on our walls.  The breakthrough announced in this momentous article is the modern era equivalent of Andrew Fleming’s introduction of penicillin to a world without antibiotics in 1928.  And it applies directly to myeloproliferative disorders.

Gene therapy and all the sophisticated machinery of biotechnology created a magic bullet so precise that it pierced the heart of a myeloproliferative cancer, a genetically caused disease. .

The electrifying NEJM  headline that kicked off all the international attention is not catchy and it’s not easy to read but it’s life-changing:   Activity of a Specific Inhibitor of the BCR-ABL Tyrosine Kinase in the Blast Crisis of Chronic Myeloid Leukemia and Acute Lymphoblastic Leukemia with the Philadelphia Chromosome.” 

            Here’s the full abstract: http://nejm.highwire.org/cgi/content/full/344/14/1038#T4   (Do print this out!)  And http://nejm.highwire.org/cgi/reprint/344/14/1038.pdf

This is the payoff for your hard work in the course, a pathway into the highly technical headline of the abstract.  Let’s take it one step at a time in this seven question quiz:.

1 .Activity of specific inhibitor means : ­­­­­­­­­­­­­­­­________________________(Hint: what’s the opposite of gene expression?)

2. BCR-ABL …(Unless you already know the answer, put this aside for a minute, lots of description below.)

3. Tyrosine is    (a) an amino acid    (b) a gene  (c) a protein  (d) a City in the Ancient Middle East

4. Kinase means: _______________________ (Hint, this is one of our vocabulary words. Think “kinetic.:  The suffix “ –ase”  means enzyme. Kinase is shorthand for phosphotransferase.)

5. Blast crisis means: ____________________ (Blast is shorthand for myeloblast and is one of the elements pathologists  look for in bone marrow biopsies,)

6. Leukemia is ______________

7. The Philadelphia chromosome. (You’ve heard of it, you may even know if you’re positive or negative for it… but why on earth is it called the Philadelphia chromosome and what does I have to do with BCR-ABL, whatever that is?)

By the end of today’s unit you should be able to come back and answer all these questions.  Let’s start, however, by lightening up  with our video song of the day:

http://www.youtube.com/watch?v=fa7cj__4Em0

================================

BCR-ABL and the Philadelphia Chromosome

The beginning of the story takes place in Philadelphia in 1960 when two scientists, Peter Nowell from University of Pennsylvania School of Mediicnie and David Hungerford from Fox Chase Cancer Center discovered an abnormality on chromosome 22 associated with CML. They believed the chromosome  anomaly — taking its name from the city where it was discovered –  was not simply associated with CML but was causative.

Dr. Janet Rowley of the University of Chicago using the new techniques of chromosome banding and  visualization was able to confirm their view: Translocation of genetic material.  She discovered a crucial segment of chromosome 22, in patients with CML, had broken off and moved to chromosome 9. Simultaneously a piece of chromosome 9, including a chunk of the cancer-causing Abelson gene – moved to the breakpoint on chromosome 22.  This genetic translocation created an oncogene located on chromosome 22  that carries the code for the BCR-ABL protein.  (The protein’s name is taken from the two areas fused,  the “Breakpoint Cluster Region” of chromosome 22 coupled with the ABL gene from chromosome 9).  Beyond coding a protein, BCR-ABL incorporates the ability of the ABL gene to build complex molecules by adding phosphate groups to one of the basic amino acids, tyrosine.  That gave the BCR-ABL fusion gene/protein all the power of a kinase as well.

Along with signal transmission and control of processes within the cell, protein kinases catalyze molecular actions by adding phosphates to substrates. Since the substrate in this case is tyrosine, the BCR-ABL protein is known as a tyrosine kinase.

Continuously active, without the requirement for signalling from messaging proteins, BCR-ABL speeds up cell division and inhibits DNA repair.  The very capability that provides its lethal power  — its action as a tyrosine kinase  – opened the path to block its  depredations,   What was needed was something to disable BCR-ABL by inhibiting  its kinase component.

Enter Gleevec.

========================================

The Story of Gleevec the ultimate designer drug

This story is best told by the principal investigator responsible for driving thjis effort, Dr. Brian Druker. Here’s his 30 minute seminar, “Imatinib (Gleevec) a Targeted Cancer Therapy.”  It is essential viewing. http://www.youtube.com/watch?v=d6xU3bgBLIw&feature=channel

What follows are some notes to help place his comments in perspective.

=========================================

If we know the cause we can find the cure

 Consider the odds against producing an effective drug to combat chronic myelogenous leukemia.  The first problem is to find the cause.  Discovery of the Philadephia chromosome correlating with all cases of CML was a clue. Establishing the molecular process through which a piece of DNA carrying the genetic material for a cancer causing virus gets translocated and fused with another gene on a distant chromosome is another part of the process that would have been unthinkable not so long ago.  Once the cause of CML is established, the tyrosine kinase locked in the on position, next step is to turn it off.  Reach beyond the cellular level into the molecular processes governing interactions between genes and proteins and enzymes to short circuit this BCR-ABL kinase connection without affecting all other, nearly identical, biochemical activities or triggeirng a whole cascading series of undesirable biomolecular events?   And even if all this could be done in a test-tube or petri dish how could this technology be bio-engineered into a pill that would carry out this mission once swallowed and digested.   The miracle happened. A new era in drug design opened. And we have every good reason to expect new MPN drugs as the paradigm that created Imatanib is adopted in labs around the world.

=========================================

People behind Gleevec

Gleevec is the first in a new class of agents to selectively inhibit an enzyme responsible for the proliferation of cancer cells.  This inhibitor neutralizes the action of a specific oncogene responsible for chronic myeloid cancer. . While the development of Gleevec rests on the massive work done in the human genome project and the collaboration of teams of scientists and technicians, the contribution of three men is outstanding. For a capsule background here’s a New York Times Interview with  Brian Druker  http://www.nytimes.com/2009/11/03/science/03conv.html,. a close-up look at  Nicholas Lydon http://www.scienceheroes.com/index.php?option=com_content&view=article&id=379&Itemid=312 and Charles Sawyers http://www.mskcc.org/mskcc/html/72337.cfm

======================================

Review

(1) Work your way through the April 2001 NEJM article to test your knowledge of terms and processes used in genetics and molecular biology.  Share your questions and observations with others in the seminar.

(2) Re-visit last week’s introduction to BCR-ABL and Gleevec on the DNA Applications page of the Cold Spring Harbor Lab website.  Click on “Genes and Medicine” and then “Drug Design” and motor on over to the Philadelphia chromosome www.dnai.org/d/index.html

 ===========================

School’s out for vacation.  Back for summer school June 5, 2010  with  The Life Cycle of an RBC

 

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