Sam Rhine - Genetic Update Conferences - www.samrhine.com
Genetics of Common Human Traits and Diseases…..
and Stem Cells…..New Medical Applications
Basic Genetic Stuff Review:
I. CHROMOSOMES - CYTOGENETICS:
A. Metaphase Spread - first observation was in 1956 - confirmed chromosome number = 46
B. Karyotype - chromosomes cut out and arranged by size - from tallest to shortest
1. Autosomes - #1 thru #22
2. Sex Chromosomes - XX - Female; XY - Male
3. Chromosome Anatomy - Chromosome #5
a. Centromere - constriction
b. p-arm - short arm - placed up in the karyotype
c. q-arm - long arm - placed down in the karyotype
d. Telomeres - top and bottom of every chromosome
e. Chromatids - duplicated arms of the chromosome - fuse with banding
f. Has #5 - Homo sapiens chromosome #5
4. Chromosome Identification - How do you tell them apart?
a. Chromosome Banding - unique sets of stripes on all the chromosomes
b. Permits individual chromosome identification = 'Bar Code"
c. International System of stripes and numbers
d. Ideogram - Idealized Diagram of banded chromosomes
e. Pinpoint Break Points…..1q23
f. Pinpoint Gene Locus (Loci) = address…..Rh - 1p34; UDGP - 1q21
h. High Resolution Banding - see more bands - Cystic Fibrosis - 7q31.2
C. Syndrome: a recognizable pattern of anomalies, a group of signs or symptoms,
that occur together and characterize a particular abnormality
D. Chromosome Syndromes: 1 in 160 live births / 50% of a miscarriages
MCA babies (Multiple Congenital Anomalies
1. Trisomy 16 - most common chromosome syndrome - always miscarries
2. Trisomy 21 - most common chromosome syndrome in live born babies
a. Down Syndrome - 1/800 - Dr John Langdon Haydon Down - 1866
b. Most common GENETIC cause of Mental Disability
c. Principle Features - Syndrome Diagnostic Criteria
d. Best of the whole chromosome syndrome children
e. Karyotype - Trisomy 21
f. Cause - Non-Disjunction of pair 21 on egg or sperm formation
g. Monosomy 21 - other possibility with NDJ of #21
h. Parents are usually fine - error in formation of egg or sperm
i. 90% Maternal NDJ / Increase of DS with increasing Maternal age
j. DSCR - Down Syndrome Critical Region at 21q22.1 = tripled for DS
3.
4.
5.
6.
Trisomy 18
Trisomy 13
Monosomy X
XXY Syndrome
-
Edwards Syndrome
Patau Syndrome
Turner-Ulrich Syndrome
Klinefelter Syndrome
-
NDJ pair 18
NDJ pair 13
NDJ of XXs or XY
NDJ of XXs or XY
E. Why does a baby with an extra chromosome have a diability?
1.
2.
3.
4.
Why MCA?
Why is Trisomy 21 best?
Principle of Duplicate Balance - Biallelic - Genes come in pairs
Trisomy 21 - 231 genes on chromosome #21 are in triplicate
a. Triple dose of all the proteins from the genes on chromosome #21
b. Leukemia increase
c. Fewer solid tumors
d. APP Inherited Alzheimer gene 21q21 - Down Syndrome all develop Alzheimer
e. DSCR-1 Gene tripled - deficient number of dendritic spines = MR
II MONOGENIC INHERITANCE - SINGLE GENE PAIR - MENDEL'S RULES of INHERITANCE
19th Century - Inheritance thought to be BLENDING - even mixture from both parents
A. Johann Gregor Mendel
1. Monk - Church of the Assumption - St. Thomas Monastery in Brno, Czech Republic
2. born: July 20, 1822 - died January 6, 1884
3. published work on peas - 1866 / Forgotten / Rediscovered ~1900
4. "My time will come, people will see it one day, it doesn't matter that I will not be there"
5. Beginning of Particulate Inheritance - inheritance via particles called genes
Pairs of genes that…..1. Segregate and 2. Independently Assort
20th Century - Inheritance understood to be PARTICULATE
B. Monogenic Reference Sites:
1. OMIM - Online Mendelian Inheritance in Man - ~20,000 with code numbers
http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim
2. Genes and Disease - summaries of ~80 common monogenic conditions
http://www.ncbi.nlm.nih.gov/books/NBK22183/?depth=2
3. Code Numbers: 100000 = AD; 200000 = AR; 300000 = XL;
400000 = YL; 500000 = ML (mitochondrial)
C. AUTOSOMAL DOMINANT INHERITANCE - AD
One Parent Affected / One Parent OK / Passed to half the children / 50%
1. Brachydactly - first recognized AD in humans - OMIM = 112500 - multiple types
2. Huntington Disease - OMIM = 143100 - 4p16.3 - Late Onset - shows up in 40's or 50's
CAG Triplet Repeat Mutation - gene elongates every generation
Mutant HTT Huntingtin Protein - leads to loss of striatal neurons in brain
3. Neurofibromatosis - OMIM = 162200 - 17q11.2
Causes small benign tumors - neurofibromas - may be mild to very severe
4. Marfan Syndrome - OMIM = 154700 - 15q1.5
Tall; slender; long arms, legs and fingers; prone to aortic aneurysm
5. Alzheimer Disease - ~1% of cases inherited - APP = Amyloid Precursor Protein
APP gene > APP Protein > cleaved to become Amyloid Beta > accumulates
D. AUTOSOMAL RECESSIVE INHERITANCE - AR
Both Parents OK / Both Parents are Heterozygous Carriers / 1 in 4 / 25%
What does 1 in 4 mean - shuffle the four Aces - draw a card - Ace of hearts = aa
1. Cystic Fibrosis - OMIM = 219700 - 7131
Abnormal CFTR membrane protein - leads to abnormal cell secretions
Respiratory complications and infections - more common in Caucasians
2. Sickle Cell Anemia - OMIM = 141900 - 11p15.5 - Beta Globin Gene
Causes sickling of RBCs in situations of low oxygen tension
More common in individuals of African and Mediterrsnesn ancestry
3. Tay-Sachs Disease - OMIM = 272750 - 15q23 - Hexosaminidase A deficiency
Causes slow down hill deterioration from ~4 months to ~48 months
More frequent in Ashkenazi Jewish populations
E. X LINKED RECESSIVE INHERITANCE - XLR
Mother is fine but Carrier if a harmful recessive gene / Father is fine
Half the sons will be affected / half of the daughters will be carriers
1. Hemophilia Type A and Type B - OMIM = A - #306700 - Xq28 - Factor VII
B - #306900 - Xq26.3 - Factor IX
Blood clotting Factors deficient - sometimes called the 'Bleeders Disease'
2. Duschenne Muscular Dystrophy - OMIM = 310200 - Xp21.1
Most common type of Muscular Dystrophy
3. Fragile X Syndrome - OMIM = 309550 - Xq27.3 - bottom of long arm of X
Moderate to Severe MR / Autism in ~50% / long face / large ears / large jaw
CGG Triplet Repeat of Mutation in FMR1 gene - at Fragile Site on X chromosome
Most common Inherited Cause of Mental Retardation and Autism
Diminished number of Dendritic spines - Therapy CTEP inhibition of mGluR5
4. Happiness Gene - sex limited - only in females - low MAOA levels
X linked recessive deficiency that Lyonizes in females
Genome and Genes Review:
I. INTRODUCTION: Genome and Genes…..September 1, 2012
A. Genome: the sum total of all the genetic information for any biologic organism
1. DNA - double strand
2. RNA - single strand
3. Expressed as the total number of nucleotides
a. Human Genome: ~3,000,000,000 nucleotides pairs, ~20,000 genes
b. HIV Genome
9,749 nucleotides
9 genes
4. Human Genome:
~1.5% - 'Coding' DNA………carries DNA Code of 21,000 protein producing genes
~98.5% - 'Non Coding' DNA…'Junk' DNA
B. Gene:
1. 'Coding' DNA Genes - carry the genetic code to make a protein
a. sequence of DNA responsible for the production of a specific protein molecule
b. DNA double strand with promoter (on/off) region in nucleus
b. DNA transcribed into mRNA (transcript) in nucleus
transcript with genetic code, plus 5' and 3' UTRs - UnTranslated Regions
c. Transcript translated into protein at the ribosome - at endoplasmic reticulum
d. both Coding and Non Coding DNA segments within almost all Coding Genes
Coding Segments
- Exons - part of the 1.5% Coding DNA
Non Coding Segments - Introns - part of the 98.5% Non Coding DNA
e. RNA Processing - occurs in the nucleus - at the Spliceosome
Remove the Introns / Splice the Exons together
2. 'Non Coding' Genes - carry a code to make RNA only
a. sequence of DNA responsible for the production of a specific RNA molecule
b. produce ~500 small non coding RNAs - microRNAs - negative gene control
3. Coding and Non Coding DNA in Coding Genes:
a.
b.
c.
d.
e.
EXOME
- sum total of all the Coding DNA in all the Exons
- 1.5%
INTROME - sum total of all the Non Coding DNA in all the Introns - 98.5%
Exome plus Introme = ~30% of the genome, therefore ~70% 'Junk'
500 Non Coding microRNA genes in the 70%
Most of the microRNA genes are in the 'Junk' - but some are in the introns
microRNA gene in an intron - 'Gene within a Gene' - mirTRON
f. mirTRON - Non Coding DNA gene exists with an Intron of a Coding DNA gene
g. Total Number of Human Genes: ~21,500…..21,000 Coding + 500 Non Coding
h. Summary - Coding DNA Genes contain both:
Coding DNA (exons) and
Non Coding DNA (introns)
Non Coding DNA Genes contain:
Non Coding DNA only
C. GENE CONTROL = GENE REGULATION - ON / OFF MECHASNISMS
1. Transcription Factors - turn transcription ON and OFF
a. attaches to the Promoter
b. promoter acts as 'Docking Site'
c. TF Activators - bind to promoter and turns genes ON
d. TF Repressors - bind to promoter and turns gene OFF
e. Enhancers - can also bind to DNA and enhance protein output
2. microRNA = miRNA - negative regulators - turn genes OFF
a. microRNA, ~22 nts, complementary to and binds to 3' UTR of transcript
b. helps usher RISC (RNA Induced Silencing Complex) to the 3' UTR
c. RISC blocks the ribosome > blocks translation > turns gene off
d. referred to as miRNA 'Gene Silencing'
e. microDNA - newly discovered type of normal human cellular DNA
small circles of non-repepitive DNA, 200-400 bp in length
widespread in all human somatic cells
produced by chromosomal microdeletions
3. Epigenetics - 'Epi' means upon / on top of / above and beyond the DNA
a. Chromatin - epigenetic control mechanism acts on chromatin
DNA (Genome) interacting with Histone Proteins
DNA / Histone Complex
b. Histone Proteins: H1, H2A, H2B, H3, H4
NCP - Nucleosome Core Particle - octomer: 2-H2A, 2-H2B, 2-H3, 2-H4
Nucleosome - DNA wrapped around the NCP
Nucleosome Fiber - strand of multiple nucleosomes
DNA…..'Never Acts Alone'
c. Gene Contol: the Degree of Chromatin Compaction
i. Methylation of Cytosine in the DNA of Chromatin at CpG Islands
add methyl groups - compact = 'Closed' chromatin = OFF
lose methyl groups - loose
= 'Open' chromatin = ON
ii. Acetylation of Histone Proteins = 'Open' chromatin = ON
d. Methylation and Acetylation
Epigenetic Marks on the Chromatin
Remodels the Chromatin Architecture
e. Enzyme Controlled Mechanism:
Methylation Enzymes: DNMT - DNA Methyl Transferase
de novo
DNMT-3
maintainence - DNMT-1
Acetylation Enzymes:
HAT Histone Acetylase
HDAC Histone DeAcetylase
f. Epigenome
Chromatin modified - DNA sequence does not change - 'above & beyond'
Genome
- 3,000,000,000 nucleotides of DNA
Epigenome - Chromatin modifications - determines all of our phenotypes
Modification is an ongoing, life-long process, affected by the environment
Identical twins - two persons who are genetically identical
but may not be epigenetically identical > different phenotypes
GENOME
- stable - does not change
EPIGENOME - fluid - changes all the time
Epigenetic modifications can be passed through the gem line!!
D. ENCODE - ENCyclopedia Of Dna Elements - new information as of September 5, 2012
1. International Consortium
2. 32 Research Institutions
3. 442 Consortium members
4. 10 Year Genome Annotation Research Project
5. 30 Coordinated Research Papers released Sept 5, 2012
6. 4 Major Journals: Nature, Science, Genome Research and Genome Biology
7. New Genome Findings:
a. many non coding DNA parts of the genome…..the 'Junk'
contain 'Docking Sites' where control proteins effect gene
expression of both nearby and distant genes…..How Many?
2,890,000 - newly discovered Docking Sites…..in the 'Junk' DNA
~200,000 active in any given cell at any one time
8. Gene Switches do not turn genes ON /OFF - they are 'Dimmer Switches'
9. Also in the 'Junk':
a. sncRNAs - small non coding RNAs:
20 to 200 nucleotides - microRNA,, rRNA, tRNA -
~500
b. lncRNAs - long non coding RNAs:
200 to 1000s of nucleotides - control Coding genes 10. 80% of the genome nucleotides now have a biochemical function!
80%.....going to be 100% soon!
11. Total number of genes in the Human Genome? ~31,000
21,000 Coding Genes + 10,000 Non Coding Genes = 31,000
~9,500
Genetics of Common Human Traits and Diseases…..
and their Multifactorial / Polygenic Origins
A. the GENETIC BOXES: Box 1 - Cytogenetics / Box 2 - Monogenic
Genetic Medicine - the use of knowledge about chromosomal syndromes and single gene
disorders to improve the diagnosis and treatment of our patients
B. CLASSIC GENETIC CLASSROOM: Genetic Medicine
1. Box 1 - Cytogenetics - Chromosomes:
a. Down Syndrome
Trisomy 21
(1/800)
b. Patau Syndrome
Trisomy 13
(1/10,000)
c. Edwards Syndrome
Trisomy 18
(1/6000)
d. Klinefelter Syndrome
XXY
(1/500 males)
e. Turner Syndrome
Monosomy X (1/5000 females)
EASY to Understand - via Karyotype - but most syndromes are very RARE
2. Box 2 - Mendelian - Monogenic Traits - AD, AR, XLR:
a. Sickle Cell Anemia / Cystic Fibrosis / Tay-Sachs Disease - AR
b. Huntington Disease / Neurofibromatosis / Marfan Syndrome - AD
c. Fragile X Syndrome / Hemophilia / Duchene Muscular Dystrophy - XLR
d. Retinitis Pigmentosa - AR or AD or XLR
EASY to Understand - via Punnett Square - but most conditions are very RARE
3. Why don't we study the genetics of…..Common Conditions:
a. Adult Type 2 Diabetes / Macular Degeneration / Hypertension
b. High Cholesterol / Heart Disease & Stroke / Cancer & Tumors
c. BiPolar Disorder (Manic/Depressive) / ADHD - Attention Deficit / Alzheimer
d. Alcohol Dependency / Autism Spectrum - ASD / Epilepsy / Asthma / etc.
…..COMMON DISEASES…..but COMPLEX GENETIC TRAITS
4. Why don't we study the genetics of …..Autoimmune Diseases:
1. Type 1 Diabetes (insulin dependent) / Rheumatoid Arthritis / Multiple Sclerosis
2. Lupus Erythematosis / Scleroderma / Crohn's Disease / Grave's / Psoriasis
…..COMMON DISEASES…..but COMPLEX GENETIC TRAITS
C. There has always been a THIRD BOX…..
BOX 3 - Multifactorial - Complex Genetic Traits - COMMON DISEASES
NEW: Genomic Medicine - the use of knowledge about the entire GENOME
1.
2.
3.
4.
5.
plus NONGENOMIC factors that effect health and disease;
new diagnostic and therapeutic approaches to help
understand COMMON MEDICAL conditions
by studying POPULATIONS of people
Genomic Medicine - there is no 'Normal'…..No Normal human genome
a. 'Variants' - millions of differences among individuals in a population
b. 'Mutation' - DNA variant that is pathologic / causes disease
"We are all Mutants"
6. Person to Person Genomic Sequence - 99.6% identical DNA Sequences
0.4% different DNA Sequences
a. 0.4% different = 24,000,000 nucleotides variants in the genome
b. 24,000,000 variants in DNA sequence between you and any other person
2. HYPOTHESIS that might Explain Complex Diseases:
a. 'COMMON DISEASES / COMMON VARIANTS HYPOTHESIS'
b. Persons with the same Common Disease…..
would have a unique set of DNA Variants in Common
c. Variant = DNA change found in 1% to 5% of the population
d. Quantitative Human Traits:
Continuous Distribution in a Population
Most Common Diseases are Part of a Quantitative Trait
3. Common Diseases - have a Genetic Component
a. runs through the family
b. twin study evidence - MZ v. DZ
c. but no Mendelian inheritance pattern - no AR, AD, or XLR - not Box 2
d. chromosomes and karyotype are fine - not Box 1
e. many genes involved - Polygenic - Polygenes (~700 polygenes for height)
d. Environmental Factors involved…..Multifactorial!
4. HERITABILITY: H - the proportion of Phenotype variation for a particular
trait that is strictly due to Genetic differences in a certain
population at a certain time
a. Height
H = 80%
E = 20%
b. Cystic Fibrosis
H = 90%
E = 10%
c. Adult II Diabetes H = 55%
E = 45%
d. HIV / AIDS
H = 5%
E = 95%
e. FASD / FAS
H = 5%
E = 95%
5. HUMAN QUANTATIVE TRAITS
a. easily measurable traits - easy to quantify
b. continuous distribution in a population
c. in a general population - normal distribution - bell shaped curve
Low / Mean / High
68% of population within one standard deviation of mean
Height
Finger Print Ridge Count
Blood Pressure
Blood Glucose Level
IQ
6. IF we could find one of the genes for a quantitative trait
a.
b.
c.
d.
locate it's QTL - Quantitative Trait Locus - e.g. 6p24.2
then check the genes at 6p24.2 from human genome map
relate the polygene to a function - what does that gene do?
how could that gene contribute to that quantitative trait
7. Flipping Pennies Model:
a. each penny represents one polygene for a quantitative trait - ten polygenes
i.e. height, blood pressure, blood glucose level
b. Height: H = 80% - Heads = Tall gene
Tails = Short gene
c. Polygenes - Additive or Cumulative - NOT Dominant & Recessive
d. Two average height parents usually have an average height children - most likely
BUT two average height parents can have a very tall child
AND two averge height parents can have a very short child
e. Medical Conditions - Threshold effect:
Blood Pressure:
Most people have average blood pressure
High Blood Pressure - cross threshold - Cardiac Risk
Low Blood Pressure cross opposite threshold - BP concerns
Blood Glucose Level:
Most people have average blood glucose levels
High Blood Glucose - cross the threshold - Diabetes
Low Blood Glucose - cross the opposite threshold Neuron Synapse Development:
Most people have the average number of synaptic connections
Fewer Synaptic Connections - cross threshold - Autism - ASD
Extra Synaptic Connections - cross opposite threshold - schizo
f. TWO perfectly NORMAL parents can have an AFFECTED child!!
POLYGENIC INHERITANCE…..is BLENDING!
BLENDING of POLYGENES!
g. MOST COMMON DISEASES are part of a QUANTITATIVE TRAIT
D. QUANTATIVE TRAITS and POLYGENES in COMMON DISEASES:
What we do NOT know…..
1. How many polygenes for a particular common disease or trait?
2. Where are the polygenes located - their QTLs = address
3. What do those genes do - the function of that one gene?
4. Can we one day prevent the medical problems?
5. One Day…..Modify the polygenes in such a way we could
…..Correct a Polygenic Disease
…..stop people from Crossing the Threshold!
E. What would it take to find the Polygenes for Common Diseases?
1. HGP - Human Genome Project - Director: Dr. Francis Collins
Largest ever Scientific Endeavor!
15 Year International Cooperative effort - 20 Countries - Mainly US + UK
Began: October 1, 1990 projected completion date: Sept. 30, 2005
Actual Completion Date: April 25, 2003 - Watson / Crick Anniversary
How many human genes? 100,000 > 21,000 coding genes
Plus the addresses of all the gene loci
~3,000,000,000 nucleotide pairs
~1.5% Coding / ~98.5% Non-Coding
'Rough Draft' - June 26, 2000 - US / British joint announcement
1600 Pennsylvania Avenue in DC / 10 Downing Street in London
Human DNA - we are all 99.6% Identical DNA Sequence
Same among and between racial groups
No DNA basis for the term 'Race'
Published: Nature - February 15, 2001 / Science - February 16, 2001
"To determine our DNA Sequence is to achieve an historic step
forward in Human Knowledge"
2. SNPs and CNPs
a. SNPs - Single Nucleotide Polymorphisms = SNVs - Single Nucleotide Variant
"snips" - found in >1% of the population - common
How many SNPs in me or you? ~3,750,000
b. CNPs - Copy Number Polymorphisms = CNVs - Copy Number Variants
"cnips" - found in >1% of the population - common
c. If we are all 99.6% identical in our DNA sequences
d. Differences that cause common diseases - must be in 0.4% where we are different
SNPs = SNVs - Small Scale variants - ~80% of the 0.4%
CNPs = CNVs - Large Scale variants - ~20% of the 0.4%
Mutation - Rare change - associated with pathology / disease
SNPs
- Common
- normal variant in the population
e. How do we find the SNPs? Search for groups of SNPs - Haplotypes
Haplotype - Sets of nearby SNPs - located close together on a chromosome
HAPMAP - Haplotype Map - find the addresses of the SNP loci
Hapmap I
2005 - 1,000,000 most common SNPs
Hapmap II 2006 - 10,000,000 SNPs
Hapmap III 2010 - 1,440,616 SNPs for detailed studies
Average Person: 1 SNP every ~800 bp = ~3,750,000
f. HYPOTHESIS: COMMON DISEASES / COMMON VARIANTS
COMMON DISEASES / COMMON SNPs
F. GWAS - GenomeWide Association Studies - New England Journal Med July 8, 2010
1. Evaluate the entire genome of thousands of people
2. See if any SNPs might be Associated with a particular Common Disease
3. GWAS Example: T2D - Type 2 Diabetes - usually adult onset
a. Experimental Group: 2500 people - medically confirmed DO have T2D
b. Control Group: 2500 persons - medically confirmed - DO NOT not have T2D
c. Scan their 5,000 genomes and check to see which SNPs are present
d. Question? Do the 2500 persons with T2D have a unique set of SNPs
in Common that persons without T2D DO NOT HAVE? YES
e. AND…..we know the QTLs of those unique SNPS…..
one unique T2D SNP is located at 10p12.3
one of the polygenes for T2D must be located at 10p12.3 - Candidate Gene
f. go to Human Genome Map - to 10p12.3 - see which genes are there
g. attempt to link that SNP to a known gene Function
4. We have TESTED the HYPOTHESIS:
COMMON DISEASE / COMMON VARIANTS HYPOTHESIS
5. All GWAS results available - One Web Site: www.genome.gov/gwastudies/
a.
b.
c.
d.
Over 1700 hundred entries - as of June 1, 2012
> 1700 GenomeWide Association Studies
> 250 Distinct Human Traits and Diseases
> 7291 SNP - Trait Associations - as of September 12, 2012
G. How do the GWAS tests work? Using CHIPS to find the SNPs
1. CGH Technology - Comparative Genomic Hybridization
a. Microarray Chip = SNP Chip = DNA Chip
b. Glass chip with array of DNA fragments synthesized in a laboratory
c. Fragments on chip - one side of the DNA molecule - 5' to 3' side = PROBE
d. Location and sequence of all PROBE fragments on array is known
e. Each PROBE fragment on the Chip carries a known SNP sequence
Unknown DNA to be tested is chopped into fragments - 3' to 5' side
Unknown fragments are tagged with a fluorescent colored label
Unknown DNA fragments - 3' to 5' - placed on the chip with the PROBES
Unknown fragments hybridize (form double helix) with known fragment
f. Laser Scanner 'reads' the fluorescent colored spots on the Chip
g. Presence & Intensity of colored spots identifies the SNPs in unknown DNA
2. Affymetrix 'Gene Chip' - >1.8 million probes = genetic markers
906,600 probes for SNPs + 946,000 probes for CNPs
3. GENOMICS of COMMMON DISEASES - MIT & Harvard - Sept 6 - 9, 2008
'The Beginning of the New Genetics'
H. GWAS STUDIES:
1. T2D - Adult Onset Type 2 Diabetes
a. 18 SNPs = 18 Polygenes - 18 QTLs / today = 53
b. QTLs connected to glucose metabolism pathway genes
2. T1D - Juvenile Onset Type 1 Diabetes - autoimmune disease
a. 18 previous SNPs + 14 new SNPs = 32 Polygenes / QTLs / today = 45
b. QTLs connected to HLA - immune system genes
3. Inflammatory Bowel Disease - Crohn's and Ulcerative Colitis
a. Crohn's Disease - 32 SNPs - 32 QTLs / today = 71
b. QTLS connect to autophagy pathways
c. Ulcerative Colitis - 10 SNPs - 10 QTLs / today = 47
4. GIANT Studies - Genomic Investigation of ANthropormorphic Traits
GWAS for BMI, Obesity, Height, Weight, Adiposity
a. Obesity - 6 SNPs = 6QTLs - BMI and Risk of Obesity Genes / today = 34
9 SNPs = 15 QTLs - Hypothalmic Weight Control
Obesity is a polarizing polygenic trait with thin habitus
b. Height - H = 80% - 180 SNPs = 180 QTLs - only 20% of H - 700 total?
Single Gene Mutation - override polygene effects - achondroplasia
5. Malaria Resistance Medication SNPs
6. Blood Lipids - major indicator of heart disease
100,000 persons tested - 95 distinct SNP and CNP variants
59 new - never found before
7. SNPs and I.Q. - g = general cognitive ability - Scientific American - Oct 2008
8. SNPs and Human Personality Traits:
Neuroticism / Extraversion / Openness /
Agreeableness / Conscientiousness / Music Ability
All human behaviors polygenic??
9. SNPs and Human Facial Appearance - VisiGen - International Visible Trait Genetics
a. 5 polygenes found that affect human facial shape
b. 24 polygenes for eye and hair color - Forensic - facial ID from blood
c. Hope to identify victims / perps face from DNA in blood samples at crime scenes
10. Pet Project - Neuropsychiatric Disorders: Nature - August 26, 2010
a. Doberman Pinscher - narcolepsy / obsessive compulsive
b. Golden Retriever - aggression / dominance / seizures
c. English Cocker Spaniel - epilepsy / sudden onset aggression
d. Dalmation - deafness / kidney stones / aggression
11. GWAS - Big Questions…..
a. ONLY ~12% of GWAS SNPs are located in coding gene regions
b. ~40% of GWAS SNPs are in non-coding introns
c. ~49% of GWAS SNPs are in intergenic regions
d. may indicate intronic or intergenic gene control elements
Now we know e. "Missing Heritability"
T2D: 18 SNPS - 18 Polygenes - H = 55% - only ~6% of H - ~94% missing
Height: 180 SNPs - only 20% of H - 80% missing
Look Deeper - 500,000 persons with SNP evaluations?
f. 'Revolution Postponed' - Scientific American - October 2010
I. CNVs / CNPs - Copy Number Variants = Copy Number Polymorphisms
1. Normal - 2 copies / CNP = 1 copy, 3 copies, etc.
2. Large Scale Variation - ~20% of the 0.4%
3. INDELS: INsertions / DELetions or Rearrangements
a. MAY be INHERITED…..passed from parents or
b. MAY arise DE NOVO - mistake in meiosis - not passed from parents
c. Copy Number Variant - five instead of two
d. Most Common Example - Down Syndrome - all genes on chromosome #21 - x3
4. Epilepsy / HIV / Heart / Schizophrenia / Tourette's / Obesity / Autism
J. AUTISM - Autism Spectrum Disorders - National Autism Assn http://nationalautismassociation.org
Spectrum – from very mild to very severe
May be Autism only - Simplex Family or Multiplex Family
May be part of a Syndrome: Fargile X, Rett, Tuberous Sclerosis
Many forms of Autism = Many different causes
1 in 88 children.....1 in 54 males.....Males : Females = 4 : 1
Neurodevelopmental disorder characterized by:
1. Social Impairments
2. Cognitive Impairments
3. Communications Difficulties
4. Repetitive Behaviors
Can range from very mild to very severe.
Can occur in any ethnic, socioeconomic and age groups.
Some children with autism appear normal before age 1 or 2 then suddenly 'regress' and lose language
skills they had previously gained. This is the regressive type of autism.
SIGNS of AUTISM:
1. No big smiles or other warm, joyful expressions by six months or thereafter.
2. No back and forth sharing of sounds, smiles or other facial expressions by nine months or thereafter.
3. No babbling by 12 months.
4. No gesturing (pointing, waving bye-bye) by twelve months.
5. No words by 16 months.
6. No two-word meaningful phrases (without imitation or repeating) by 24 months.
7. Any loss of speech or babbling or social skills at any age.
EARLY SIGNS OF AUTISM:
1. Doesn't make eye contact (e.g. look at you when being fed).
2. Doesn't smile when smiled at.
3. Doesn't respond to his or her name or to the sound of a familiar voice.
4. Doesn't follow objects visually.
5. Doesn't point or wave goodbye or use other gestures to communicate.
6. Doesn't follow the gesture when you point things out.
7. Doesn't make noises to get your attention.
8. Doesn't initiate or respond to cuddling.
9. Doesn't imitate your movements and facial expressions
10. Doesn't reach out to be picked up.
11. Doesn't play with other people or share interest and enjoyment.
12. Doesn't ask for help or make other basic requests.
1.
2.
3.
4.
5.
Children with autism carry a higher load of rare CNPs
Some inherited from parents as polygenes - others having arisen de novo
de novo CNVs account for 5-8% of simplex cases - paternal age effect
also in Mental Retardation – numerous de novo mutations with Exome Trios
Obesity & Underweight / Macrocephaly & Microcephaly / Autism & Schizophrenia
Examples of CNVs and Reciprocal Variants - Phenotypic Opposites
K. SNPs and CNPs associated with:
Migraines / Fatty Liver Disease / Glaucoma / Narcolepsy / Alzheimer Disease
Scleroderma / Intracranial Anyeurisms / Essential Tremor / Epilepsy
Osteoarthritis / Osteoporosis / Restless Leg Syndrome / Tobacco Dependency
Cerebral Palsy / Attention Deficit Hyperactivity Disorder / Psoriasis
Asthma / Voter Turnout / Criminal Behavior? - one family…..50 convictions!
DNA Analysis of Adam Lanza’s DNA?
L. All GWAS results available - One Web Site: www.genome.gov/gwastudies/
M. Early Genetics…..1800's-1900's - BLENDING Inheritance
Blending of Characters of Father & Mother
Beginning in 1900's - PARTICULATE Inheritance - particles called genes - Mendelian
Today - BLENDING of POLYGENES from MOTHER and FATHER
N. SAGE - Study of Addiction Genetics and Environment
1. COGA
- Collaborative Study of Genetics of Alcoholism
2. FSCD
- Family Study of Cocaine Dependence
3. COGEND - Collaborative Genetic Study of Nicotine Dependence
O. TCGA - The CANCER GENOME ATLAS
1.
2.
3.
4.
Prostate Cancer - CaP - Prostate Cancer - 45 SNPs - predisposition SNPs
Breast Cancer - 25 predisposition SNPs - Monthly self evaluations!
Colorectal Cancer - 20 predisposing SNPs
Lung Cancer - Tumor cells contain up to 50,000 SNPs…..Cancer Causing Mutations!
P. HUMAN MICROBIOME PROJECT
1. 800,000,000,000,000 - cells in the human body
a. 80,000,000,000,000 - human cells
b. 720,000,000,000,000 - Microbes: Bacteria, Fungi, Protozoa
c. Major Environmental Factors - Multifactorial
Q. YOUR PERSONAL TOTAL GENOME EVALUATION
1. 'The Language of Life' - book by Dr. Francis Collins - Director of NIH
2. Construct Your Own Detailed Family History / Pedigree Online via HHS
www.familyhistory.hhs.gov/
3. Today - Check you Total Genome - 3,000,000,000 bp - $25,000
4. Partial Genome & Common SNPs - $1,000
5. Faster and Cheaper Sequencing in the Future…..Whole Genome - 2014 - $1000
2020 - $100
6. 23andMe / Navigenics / DeCODEme / National Geographic - trace origins
R. THE '1000 GENOME PROJECT'
1.
2.
3.
4.
5.
6.
7.
- began in January 2008
Collaboration among US, UK, China, Germany
Produce an extensive catalogue of human genetic variation - SNPs & CNPs
Goal is to provide a resource of almost all human variants
Will allow more extensive GWAS studies / Hapmap III is a part of it
Over 1000 genomes of unidentified individuals from around the world
Form the basis for ethnic group comparisons and tracking people groups
Three Pilot Studies…..
a. Deep sequencing of Mother-Father-Adult child trios
b. Light sequencing to see how data can be combined across samples
c. Cataloguing Coding DNA Exome regions of the 1000 genome
Web Site: http://www.1000genomes.org/page.php
8. We each receive ~60 new mutations in our genome from our parents
S. YOUR PERSONAL DNA CHIP
1. 'Genomic Era of Medicine' - 'Personalized Medicine'
2. Pharmacogenetics - Personalized Prescriptions - Personalized Cancer Therapy
3. GPP - your personal Genetic Predisposition Profile - your Medical Future
a. Do you want to know?
b. Who else should know?
c. Who pays? Insurance?
d. Who else should have access?
e. Where will you keep the information?
f. Who will explain it?
4. GINA - Genetic Information Nondiscrimination Act
5. Prenatal Diagnosis and SNP evaluation of the unborn?
Your unborn baby is:
a. XY - boy
b. height SNPS - he will be about 6'1"
c. T2D SNPs - ~4.1% chance for adult onset Type 2 Diabetes
d. ~1.9% chance of developing rheumatoid arthritis
e. ~2.6% chance of developing osteoporosis
f. ~8.1% chance of attention deficit hyperactivity disorder
g. ~4.9% chance of developing hypertension
h. ~0.6% chance of becoming alcohol dependent
i. ~16.2% chance of developing prostate cancer as an adult
j. ~57.7% chance of being gifted musically
k. ~5.9% chance of having an agreeable personality
l. ~39.4% chance of being very conscientious
What if there was ~75% chance of migraines?
What if there was ~80% chance of being autistic?
First Human Prenatal Genome Evaluation reported in July 2012
‘Want to Know My Future’ - Time Magazine, December 24, 2012
…..its not coming - it is here!
T. SNP WHOLE GENOME EVALUATIONS - will be routine soon:
…..the 'Greatest Tidal Wave' of new medical information in world history
Cloning and Stem Cells…..New Medical Applications
I. INTRODUCTION
A.
B.
C.
D.
Public perception of cloning
What is your personal stance on…..Cloning? …..Stem Cells?
Scientific Literacy…..Be Well Informed…..Make Informed Decisions
Cloning: two procedures - 1. Reproductive Cloning
2. Therapeutic Cloning
3. How does it work? How are they similar? different? end point?
E. Four Main Types of Stem Cells: 1. Embryonic Stem Cells (ESCs) - first grown in lab - 1998
2. Adult Stem Cells (ASCs) - first recognized - 1961
3. induced Pluripotent Stem Cells (iPSCs) - man-made - 2007
4. Cancer Stem Cells (CSCs) - first recognized - 1997
F. Controversial - Bioethical Issues: ethical, moral, religious, political issues
II. BIOLOGIC BASIS of CLONING and STEM CELL TECHNOLOGIES:
A. Human Embryology - formation of the fetus = Applied Embryology
B. Review of Early Human Embryology
1. Fetus at 49 days - size of a quarter
2. Fetus at 56 days - size of a silver dollar - 220 somatic cell types
3. HOW?
C. Differentiation:
1. amazing process where all 220 fetal somatic cells become 'Specialized'…..220 Ways
2. "Other than making everything…..differentiation doesn't do anything!"
3. 220 One Way Streets = 220 Sets of Signals
4. Terminal Differentiation - end of the 220 Streets - 220 Specialized Somatic Cells
5. One Way Street - Basic Tenet of Human Embryology
6. What are the signals? Molecular Signal Proteins = Transcription Factors
Activate or Repress dozens to hundreds of genes at one time
Differentiation Pathway for Pancreatic Beta (insulin producing) cells: 10 signals
7. Human Embryome Project - International effort to find all 220 sets of signals
D. Fertilization to Stem Cells…..
1. Fertilization or Conception - egg and sperm unite
2. Zygote = fertilized egg - size = point of a straight pin
3. 2 cell embryo at ~36 hours
4. 4 cell embryo at ~42 hours
5. 8 cell embryo at ~48 hours > 16 cells > 32 cells > 64 cells
can mix and match blastomeres to make chimeric monkeys - 6 embryos > 12 parents
6. Blastocyst at ~ 6 days
a. 'basketball' - size of the point of a pin = implantation stage
b. inside blastocyst - fluid filled - one small cluster of cells = ICM
c. ICM - Inner Cell Mass = Embryonic Stem Cells - ESCs - becomes fetus/amnion
d. 'Ten Day Rule' - ESCs only exist for 10 days under natural conditions
e. ESCs first grown successfully in a lab - James Thomson - U. Wisconsin -1998
E. Embryonic Stem Cells…..
1. Why are they 'stem' - term borrowed from the plants - gives rise to all the branches
2. from the ESC stem immediately come four major branches
a. HSCs - Hematopoetic SCs > forms all blood cells
b. MSCs - Mesenchymal SCs > muscle, bone, cartilage, tendon, heart, vessels
c. ESCs - Endodermal SCs > liver, stomach, lungs, pancreas
d. NSCs - Neural SCs
> neurons, brain, spinal cord. Epidermis
3. these four major branches: beginnings of Adult Stem Cells
a. 220 branches
b. 220 one way streets
c. 220 sets of signals
d. 220 unique sets of epigenetic remodeling marks
4. Stem Cells do not come from the Brain Stem! Common politician misunderstanding!
F. Adult Stem Cells:
\
1. initial function - differentiate into 220 somatic cells in the developing fetus
2. continued function - produce replacement cells the rest of your life
3. Where are they today?
a. HSCs - in bone marrow (and in umbilical cord)
i. producing replacement blood cells
ii. i.e. produce ~15,000,000 RBC per second to replace those lost
b. MSCs - in bone marrow, adipose, amniotic fluid derived from pericytes
i. produce new muscle, bone, cartilage, tendon, heart, vessels
ii. produce paracrine signals for tissue repair, act as cellular pharmacy
c. ESCs - in lining of stomach and lining of intestine - making replacement cells
d. NSCs - in hippocampus and sub-ventricular zones of the brain
e. HSCs and MSCs are easily obtained from bone marrow or adipose
used therapeutically for over 50 years - 1st BM transplant was 1959
f. Differentiation begins at around 10 days…..continues forever
g. Adult Stem Cells - term might be misleading
i. ESCs - only in the early blastocyst embryo - gone by 10 days
ii. ASCs - in early embryo, fetus, newborn, toddler, child, teen, adult
h. Ectoderm = NSCs, Endoderm = ESCs, Mesoderm = MSC sans HSCs
G. ESCs - Embryonic Stem Cells
1. Self Renewal 2. Differentiate 3. Migrate
4. DNA Repair -
- unique characteristics:
Biologic Immortality / Telomerase
produce any of 220 specialized cells
throughout the developing embryo as the fetus forms
fix potentially lethal DNA damage from radiation or chemotherapy
H. Important 'Potent' Terms that describe stem cells
1. Totipotent - cell with the Total Potential to form a fetus, placenta and membranes
a. zygote
b. blastomeres up through the 8 cell embryo
2. Pluripotent - stem cell with the ability to differentiate into all 220 cell types
a. ESCs
b. iPSCs
3. Multipotent - stem cells that can form many, but not all, of the 220 cells - limited
a. HSCs, b. MSCs, c. ESCs, d. NSCs
III. REPRODUCTIVE CLONING
A. Clone - a genetically identically copy of…..anything you choose
B. Robert Briggs - first to clone an animal - frogs in 1952 - 'Father of Cloning' - IU
C. Definition - reproduce an individual…..create a genetically identical copy
of a particular individual…..they will be born as a new baby
D. Epigenetics - mechanism whereby chromatin…..our DNA and histones are modified
in such a way that two individuals with identical DNA, might have
different phenotypes
E. First Mammalian Clone: Animal - Sheep / Name - Megan & Morag - from embryo nucleus
F. DOLLY - first clone from an adult somatic donor nucleus
G. Reproductive Cloning Procedure: Somatic Cell Nuclear Transfer - SNCT
1. Oocyte Retrieval - obtain egg from the sheep ovary
2. Enucleation - remove the nucleus from the egg - surgery on the egg to remove nucleus
3. SCNT - transfer donor somatic nucleus into the egg - new set of instructions
the DONOR will be CLONED
4. Artificial Activation of the egg > 2cell, 4 cell, 8 cell…..
5. ET - Embryo Transfer from the petri dish into the uterus of a surrogate mother
H. Dolly born July 5, 1996 / dies February 14, 2003 - death from virus infection - not cloning
1. Ian Wilmut's lab in Roslin, Scotland
2. Dolly today: Royal Museum in Edinburgh
I. End Point for Reproductive Cloning - BABY born to surrogate mother - too risky for humans
J. Mammalian clones: Sheep, Mouse, Cattle, Pig, Goat, Gaur & Mouflon (endangered),
Rabbit, Cat, Mule, Rat, African Wildcat, Dog, Water Buffalo,
Horse, Ferret, Wolf, Banteng, Camel, 'Miracle' Pig in China,
Wooly Mammoth?
K. Prometea - first cloned horse - donor was also the surrogate - .12% success rate
Dolly
- success rate - .36% - very inefficient process - why…..Imprints/Epigenetics
L. Most important lesson from Dolly:
1. a highly specialized, terminally differentiated, somatic donor nucleus, when
placed in an enucleated egg, is reprogrammed back to a pluripotent state
2. What is it in the oocyte that reprograms the nucleus back to pluripotency?
3. Must be a cytoplasmic factor - because the egg nucleus in gone
4. Guess…..SIGNALS in the cytoplasm
5. How long would it take to find those signals?
6. How many signals would it take to reprogram nucleus back to pluripotency?
IV. THERAPEUTIC CLONING
A. Therapeutic Cloning Procedure: SCNT
1. Human Oocyte Retrieval - very difficult procedure
2. Enucleation of the egg - surgery on the human egg to remove nucleus
3. SCNT - transfer donor somatic nucleus to the egg - new set of instructions
4. Artificial Activation of the egg > 2 cell, 4 cell, 8 cell…..
5. Embryo continues to grow in lab for 6 days - clone in the petri dish
Clone of my friends embryo
Remove ECSs from the embryo and grow the cells in the lab
Establish a cell line from ESCs, let them grow until you have 10,000,000,000 ESCs
Directed Differentiation:
a. give those cells the signals for Spinal Motor Neurons (SMNs)
b. result: > 10,000,000,000 SMNs - genetically identical to my friend
c. the 'DREAM' - use those cells to repair his spinal cord - he walks again!
Definition: Therapeutic Cloning = Research Cloning
Create a Genetic Clone (copy) of an individual's embryo;
grow ECSs from the embryo; use the appropriate signals;
produce any of 22 human somatic cells to use for medical therapy
END POINT: a CELL that can be used for medical therapy
B. Applications:
1. Cell Replacement Therapy - autologous - no rejection
a. Spinal Motor Neurons - spinal cord injury
b. Pancreatic Beta Cells to produce insulin - Type I Diabetes
c. Dopamine producing neurons - Parkinson Disease
d. Red Blood Cells - Sickle Cell Anemia
e. 216 other possibilities
2. Human Disease Modeling
a. Lou Gerhig's Disease (ALS) donor > neurons
b. Huntington Disease donor > neurons
c. Type I Diabetes donor > Beta cells
d. Down Syndrome donor > neurons
3. Drug Therapy Screening - Test multiple small molecules / drugs for therapeutic effect
4. Regenerative Medicine / Tissue Engineering
5. Complications:
a. Oocyte Retrieval Procedure / Oocyte Shortage
b. Tedious / Costly
c. Tumors / Teratomas - ESCs form Teratoma Tumors in vivo and in vitro
d. Bioethical Issues - Ethical, Moral, Religious, Political
Therapeutic Cloning - obtain Pluripotent Stem Cells - Destroys Embryo
Blastocyst under the microscope - 'Clump of Cells' or 'Unborn Baby'
Who has the Theological / Philosophical wisdom make that determination?
White House Policy from 2001-08 - No Federal Taxpayer dollars may be
used for any research that involves the destruction of a Human Embryo
Only ~21 ESC lines available for study
6. Alternatives to Therapeutic Cloning for producing Pluripotent Stem Cells
"Ethical" Pluripotent Stem Cells
a. Biopsy 8-cell embryo
b. ANT - Altered Nuclear Transfer,
c. Living cells from 'Dead Embryo'
d. Parthenogenesis
e. Reprogramming
f. REPROGRAMMING
V. REPROGRAMMING = DeDifferentiation - make differentiation go backwards
1. Convert somatic cells backwards to pluripotent state
2. How? The lesson learned from Dolly!! Signals in the oocyte cytoplasm - 4 signals
3. Shinya Yamanaka - Kyoto University in Japan - Mouse iPSC - July 7, 2006
Hu iPSC - November 20, 2007
* Yamanaka – Nobel Prize in Physiology or Medicine - 2012 *
4. iPS - induced Pluripotent Stems - 4 signals: Japan - OCT 3/4, SOX2, c-MYC, KLF4
'Yamanaka Factors'
Wisconsin - OCT4, SOX2, NANOG, LIN28
'Thomson Factors'
5. Skin Biopsy > Reprogram Skin cells to iPS
Directed Differentiation of iPS > spinal motor neurons
> pancreatic beta cells
> dopamine producing neurons
No Rejection - No Embryos are needed
6. Tests for Pluripotency:
a. Cell Morphology under the microscope
b. Cell Biomarkers for pluripotency
c. Cell induces teratoma in SCID mouse
d. Cell with GFP followed in chimera embryos > egg and sperm
e. Cells form an embryo in 'Tetraploid Complementation' Test
the Definitive Test - Nature, September 3, 2009
7. Ian Wilmut - lead team that produced Dolly - full time iPS in November 2007
Special New "iPS Facilites" labs at Harvard, Toronto, Kyoto, et.al.
VI. iPSCs Applications:
1. Correct Human sickle cell in mice w/ iPS + genetic engineering - Dec 2007
2. Fibroblast iPS for Parkinson's in rat model - GFP cell sorting to stop tumors
PNAS (OL) April 7, 2008
3. iPS from ALS patients (Lou Gerhig's) to study in vitro - July 31, 2008
Science OL
4. iPS for: Huntington Dx, Parkinson Dx, Muscular Dystrophies, Type 1 Diabetes,
ADA Deficient SCID, Gaucher Dx III, Shwachman-Bodian-Diamond Syn,
Lesch-Nyhan Carrier, Down Syndrome - study in vitro - August 6, 2008
5. 25,000,000 World Wide - visually impaired
AMD - Age Related Mauclar Dystrophies
Dry Form - Photoreceptor Loss / Wet Form - Neovascularization
Stargardt's - Photoreceptor loss - pediatric
a. huESCs from donated blastocysts for Dry MD and Stargardt's
risk of rejection but Retina is Immunopriveleged Site
ESC > Retina Pigment Epithelium - 99% pure
First Successful Human Trials - The Lancet - January 23, 2912
b. RP - Retinitis Pigmentosa - Most Common Inherited Vision Loss
AD, AR, XLR
iPS cells become Retinal Rod Cells Nature, May 3, 2012
c. Retinal Prosthesis with high resolution stimulator in sync
with the retina's neural code
d. Leber Congenital Amaurosis Type 2 - LCA2
one injection of 'RPE65' gene therapy via AAV vector
restored vision - Lancet, Nov 7, 2009
6. Hearing Loss - restore auditory spiral neurons
7. Huntington Disease - AD - CAG Triplet Repeat Mutation
a. Genetic Correction of HS Phenotypes in iPSCs
HD Patient Fibroblasts > HD iPSCs
HD iPSCs Genetically Corrected via Homologous Recombination
CAG72 > CAG21
Corrrected HD iPSCs > Striatum Neurons
b. patient specific, genetically corrected, HD patient iPSCs
critical step for the eventual use of these cells in Replacement therapy
CURE Huntington Disease?
c. turn off the mutant gene with ss-siRNA Gene Silencing delivered to ventricles
8. Mature Pulmonary Epithelium
a. Direct differentiation of iPSCs to mature airway epithelia with CFTR
b. Potential therapy for Cystic Fibrosis?
9. Also iPSCs for:
a. Alpha-1-Antitrypsin Deficiency - genetically corrected iPSCs > liver
b. Hutchison Guilford Progeria
c. Friedreich's Ataxia
d. Long Q T Syndrome - heart condition
e. Fragile X Syndrome
f. Rett Syndrome - Autism Spectrum Model
g. Parkinson Disease
h. Schizophrenia
10. Other Applications:
a.
b.
c.
d.
d.
huiPSCs > Neural Stem Cells > Rats with Parkinson - improvement
ALS iPSCs - Astrocytes destroying motor neurons
huHSCs > Red Blood Cells in vitro
hu DiPSCs
Spermatids from skin or ESCS
11. Direct Reprogramming: fibroblast directly to desired somatic cell - no iPSCs
a. Neurons
b. Dopamine Neurons
c. Intestinal Tissue
d. Alzheimer Neurons
e. Hepatocytes
f. Sperm
12. Man-Made Organs and Applications:
a. Teeth
b. Optic Cup Retina
c. Primitive Cerebral Cortex
d. Primitive Hypothalamus with hormone production
e. Primitive Cerebellum
f. MSCs on man-made scaffold - heart vein
e. Repair tracheal damage from tuberculosis with adult MSCs
f. Trachea made from scratch - MSCs plus man-made scaffold
g. Cartilage made from scratch - MSCs in seeded on polymer scaffold
h. Cardiac Fibroblasts make new Cardiomyocytes
i. Prenatal Diagnosis - heart valve anomaly - AF MSCs new valve
j. OI corrected before birth with maternal MSCs via cordocentesis
k. Finger Regeneration - cellular matrix powder from a pig bladder
l. Meat Lab - make burger and sausage from muscle stem cells
m. Made rat pancreas in a mouse embryo…..Human Pancreas??
o. Yamanaka - iPS Stock Cell Project in Japan
HLA screening ~64,000 umbilical cord blood samples
to find 75 Donors for >80% of Japanese population
will make iPS available for most of the Japanese population
Here are some College and Career 'Contribution' suggestions:
1. Go to you favorite Undergraduate college and obtain your Bachelor's degree.
Major in biology, biochemistry, molecular biology, bio-engineering etc.
Make sure you satisfy the Pre-Med requirements so you can apply to
medical school if you decide that is the best route for you.
2. Medical School is four years and the curriculum is very similar at all
medical schools in the US. The reason for that is that everyone must pass
the same national exam after finishing medical school - therefore the
schools must cover the subjects. If you pass that exam the summer after
finishing medical school then you can put M.D. behind your name.
3. Residency is then 4 - 8 years of specialty training to become a pediatrician,
obstetrician, orthopedic surgeon, oncologist, neurosurgeon or whatever
specialty you choose. If you want to pursue a career in Tissue Engineering
then you might want to get a residency with Dr. Anthony Atalla at Wake
Forest University. If you want to use antibodies to stop leukemia caused by
cancer stem cells you might want to do your residency in oncology at
Stanford University. Keep your ‘antennae out’ during the four years of
medical school - determine who is doing what you want to pursue for a
career - and go do your residency with that person - he or she.
_________________________________________________________________________
2. For those who are not interested in medical school - they might want to
pursue a career in research and they will go on after their undergrad work
and get their Masters and Ph.D. which may be 4 to 6 more years.
3. The Ph.D. is usually followed by Post Doctoral studies for 2 - 4 years to
gain special expertise for the research career you want to follow. Then
you will be ready to job on the faculty at a university to do research and
teach. Others will opt to get a job doing research in industry for biotech companies.
Also, some of these people are getting their Ph.D.s in biostatistics or computer science
where they will help with the planning and evaluation of research data being generated.
Many major Medical Schools offer a combined M.D. / Ph.D. for a person who may
one day be the chairperson of the Department of Molecular Medicine at
some medical college
Another option for some will be to get a Masters Degree in Genetic Counseling.
There are almost 30 places in the US where those programs are available.
For more information - check out this web site:
http://www.nsgc.org/iframepages/GeneticCounselingTrainingPrograms/tabid/336/Default.aspx
Also Remember…..many people who will make a major contribution to all these
careers in the future will do so by majoring in Education in college and
will be preparing young people in the future…..as your Teachers have been
preparing you!!
"Teachers Make All Other Professions Happen!"
UPDATED: December 8, 2012