Stem Cells, Genomics and Cancer

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Stem Cells, Genomics and Cancer

• Scott A. Ness, Ph.D.
• Professor, Molecular Genetics Microbiology
• UNM School of Medicine
• UNM Cancer Center

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About Me
B.A. in Biology, UC San Diego (1980) PhD. in
Biochemistry, UCLA (1985) Post-doctoral
training Heidelberg Germany, European Molecular
Biology Laboratory (1986-1991) Faculty at
Northwestern University, Evanston, IL
(1991-1998) Faculty at UNM School of Medicine
and UNM Cancer Center (since 1998) Research
Area Leukemia, stem cells, oncogenes,
transcriptional regulation. Supported by NIH, NCI
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What APS Did For Me
Kelly Ness, Class of 2007 Currently a junior at
Washington Univ., St. Louis
Gregory Ness, Class of 2009 Starts at UNM next
week
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Goals for Today

• Highlight some topics related to stem cells,
  genomics and cancer biology
• Discuss why these topics are important to
  students and to the field of biology
• Show why much of what we know about biology and
  medicine is changing rapidly

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What is a Stem Cell?
A single cell that can
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Stem Cell Properties

• The ability to self-renew
• Make more stem cells
• The ability to differentiate into other cell
  types
• Stem cells have special properties
• Stem cells divide very slowly
• Stem cells reside in special protective niches
  in tissues

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Stem Cells The Promise
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The Controversy of Stem Cells

• Embryonic vs Tissue Stem Cells
• Embryonic Stem Cells are Totipotent
• Can give rise to all embryonic and
  extra-embryonic (e.g. placenta) tissues required
  for an organism
• Most of the controversy surrounds embryonic stem
  cells
• Tissue Stem Cells are Multipotent
• Can give rise to a subset of tissues (e.g. heart,
  neurons or blood cells)
• Most of the promise involves tissue stem cells

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Embryonic Stem Cells

• Derived from fertilized embryos
• Have the potential to form a whole person
• Embryonic Stem Cell Lines
• Grown in tissue culture in the laboratory
• Can be used for experiments
• Have many stem cell properties
• Cannot replace normal embryonic stem cells

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Tissue Stem Cells

• Derived from adult tissues
• e.g. Bone marrow for transplants
• Rare stem cells purified from organs, e.g. kidney
• Could be used for many experiments, perhaps for
  organ culture

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Example Bone Marrow Transplant

• Goal regenerate the bone marrow with new tissue
  stem cells
• Requires eliminating most of the old stem cells
  (e.g. whole body irradiation)
• Involves injecting bone marrow (hematopoietic
  stem cells) from a donor

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Hematopoiesis
Hematopoietic Stem Cell
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Example Kidney Dialysis

• 28 x 106 patients with diabetes in U.S.
• 1/3 will end up on dialysis in the next 10 years
• On average a patient on dialysis with diabetes
  lives 3 years-giving us 28 x 106 people dialysis
  years in next decade
• 1 year of dialysis treatment costs 70,000 per
  year
• Cost to deliver dialysis care 28 x 106 x
  70,000 (1.96 Trillion over 10 years)

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Need For Alternate Therapies

• 28 x 106 patients with diabetes
• By 2010 gt2 x106 million people with end stage
  renal failure (kidney disease)
• 58,000 in U.S. 300 in NM awaiting transplants
• Most patients wait years for transplant
• Need to explore new therapies, e.g. stem cell
  therapies

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How to Identify Kidney Stem Cells?

• Stem cells divide slowly.
• Feed rats a dye that accumulates in dividing
  cells (BrdU)
• Wait two months for dye to leave the rapidly
  dividing cells
• Look to see which cells still have the dye

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Identify Kidney Stem Cells
BrdU is a synthetic analogue of thymidine
Oliver et al., 2004 J. Clin. Investig. 114795-804
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Kidney Stem Cells Produce a Kidney

• Isolate kidney stem cells
• Engineer an artificial kidney device
• Implant device in a recipient animal
• Wait to see what develops

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Future Tissue Engineering
Implanted kidney stem cells are able to grow into
a kidney-like structure. Engineered kidney
produces urine-like fluid.
Koh CJ, Atala A.J Am Soc Nephrol. 2004
May15(5)1113-25.
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Areas of Stem Cell Research

• How to identify and purify stem cells?
• What regulates the stemness of stem cells?
• Interactions with the special niches
• Special gene regulation mechanisms
• How can stem cells be generated from more
  differentiated cells?

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How Are Stem Cells Different?

• Self Renewal Capacity
• Slow Division Rate
• Capacity to Differentiate
• Epigenetic Differences
• Changes in DNA, but not mutations
• Epigenetic changes can be transmitted to daughter
  cells to make differentiation one way

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Epigenetics

• Epigenetic changes affect cell fate and control
  gene expression
• We are just beginning to understand the histone
  code of epigenetics
• Epigenetics will be critical for understanding
  how stem cells work

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Chromatin Organization
Multiple Levels of packing are required to fit
the DNA into the cell nucleus
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Histone Tails
The Histone tails are a critical determinant of
chromatin structure
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Histone Tails
Histone Tails are subject to a variety of
covalent modifications
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Histone Codes

• At least 25 different modifications possible on
  histone tails
• At least 225 different combinations of histone
  codes (33.5 million)
• This huge complexity helps explain the complexity
  of gene regulation

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Epigenetics DNA Methylation

• DNA methylation can shut down genes or
  chromosomes
• In females, one X chromosome is methylated and
  shut down
• During stem cell differentiation, genes required
  for stemness become methylated

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Hematopoiesis
Hematopoietic Stem Cell
Myeloid/Erythroid Stem Cell, CMP
CFU-E
CFU-Meg
CFU-Bas
Erythrocyte
Megakaryocyte
Basophil
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Effects of DNA Methylation

• DNA methylation blocks the expression of genes
  required for stemness
• DNA methylation prevents differentiation from
  going backwards
• DNA methylation locks differentiated cells into
  their mature phenotype

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How to Create Stem Cells?

• If stemness genes could be reactivated,
  differentiated cells could gain stem cell
  properties
• Treatments that reactivate silenced genes could
  induce stemness

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Induced Pluripotent Stem (IPS) Cells

• Produced in the laboratory from differentiated
  cells
• Were first induced by expressing multiple
  transcription factor oncogenes
• Shows the link between stem cells and cancer
• Can also be induced through special growth
  conditions
• Future induce with drugs?

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The Promise of IPS Cells

• IPS cells are pluripotent, like embryonic stem
  cells, but do not come from embryos
• Improvements in IPS cell technology could fulfill
  many of the promises of stem cells
• Currently, the IPS approach is inefficient and
  untested
• An improved IPS technology will produce
  customized stem cells in the future

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Uses for IPS Cells
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The Dark Side of Stem Cells

• Cancer Stem Cells
• Cancer cells, like stem cells, can self-renew
• Stem cells divide slowly, so they are resistant
  to cancer drugs
• Cancer stem cells may be responsible for drug
  resistance, relapse
• Cancer cells have epigenetic changes that make
  them stem cell-like

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Tumor Cells are Heterogeneous
Tumor Cells
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Two Models for Heterogeneity

• All tumor cells have the potential, but there is
  a low probability of forming colonies or tumors
  in animals
• Only a small subset of cancer stem cells have
  the ability to proliferate indefinitely

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Fighting Cancer Stem Cells
Tumor
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Stem Cells Summary

• Stem cells have special properties
• The stemness of stem cells is regulated by
  epigenetic changes in the DNA and chromatin,
  which can be reversed
• Understanding stem cell regulation has great
  potential for treating diseases and fighting
  cancer

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Genetics, Epigenetics and Genomics

• Genetic differences are inherited, or are caused
  by mutations
• Epigenetic differences in the DNA or chromatin
  are not permanent
• Genomics is the study of genes and gene
  expression at the whole genome level

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Genomics Definitions

• Known Genes
• Genes that encode known proteins or RNAs
• Hypothetical Genes
• Identified by analyzing the genome for exons
• Sometimes have homology to cDNAs or EST clones
• SNPs
• Single nucleotide polymorphisms

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Human Genome Project

• Humans have 25,000 to 42,000 genes
• Genes encode functional RNAs, proteins
• Many genes encode multiple products
• At least 100,000 different gene products
• Genetic Differences Diversity
• SNPs occur, on average, about every 1200
  nucleotides
• About 10,000,000 SNPs in combined human genome
• 300,000 to 600,000 SNPs needed to define an
  individual
• New Tools Provide Easy Access Genome Browsers
• Example Integrated Genome Browser (IGB)

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Genome Browsers

• Show positions of all known genes on the
  chromosomes
• Show the structures and directions of the genes
• Show the overall structure and complexity of the
  genome

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The detailed gene structure is visible after
zooming in on one gene
Vertebrate genes are discontinuous. The coding
regions are contained within the exons, which
are separated by intervening sequences or introns.
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Zooming in further gives more detail.
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Zooming out shows the complexity of the genome.
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Zooming all the way out shows all the genes on
this chromosome.
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Genes and Gene Products
e.g. p53, ras, myb
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Single Nucleotide Polymorphisms (SNPs)

• SNPs occur on average about 1 per 1200
  nucleotides in human genome
• Human genome 6x109 bp
• About 2x106 known SNPs in public databases
• About 4x106 more in private databases

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Single Nucleotide Polymorphisms (SNPs)

• ATGGTAAGCCTGAGCTGACTTAGCGT-AT
• ATGGTAAACCTGAGTTGACTTAGCGTCAT
• ? ? ?
• snp snp indel
• SNPs result from replication errors and DNA
  damage

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SNP Example Apolipoprotein E

• Apo E is a major apolipoprotein of the CNS
• Important regulator of cholesterol and lipid
  transport
• Risk factor for several neurodegenerative
  disorders
• Apo E has three protein polymorphisms e2 e3 e4

112 156 ...GTG TGC GGCAAG TGC CTG ...GTG
TGC GGCAAG CGC CTG ...GTG CGC GGCAAG CGC
CTG cysteine?arginine arginine?cysteine
ApoE e2 ApoE e3 ApoE e4
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Next Generation Genomics

• The human genome project cost Billions and took
  gt 10 years
• Each human genome 6 billion nucleotides
• New technologies can rapidly sequence entire
  genomes
• By next year cost per genome lt 1,000

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Genomes What Impact?

• Identify persons at risk for specific diseases
• Alzheimers, cancer, diabetes
• Characterize tumors and design specific therapies
• Customized therapies
• Designer drugs

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Genomics Challenges

• Huge amounts of information and data to analyze
  and interpret
• We are just at the beginning of understanding
  genomes and biology
• Much of what we know about genomes could change
  in the next few years

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Genomics Ethical Issues

• Genomic information could be used by insurance
  companies, employers
• Legal safeguards are needed to protect data and
  its uses

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Summary

• Stem cells have great potential
• Stem cells also have a dark side
• Understanding and controlling stem cells will be
  the key to new types of therapies and treatments
• Tissue engineering
• Cancer therapies

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What are the big lessons?

• Genes and Genomes are much more complicated than
  originally thought
• One gene can encode dozens of different proteins.
  Modifications (e.g. histone code) can produce
  millions of variants
• SNPs are the genetic diversity that defines each
  of us

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What are the big questions?

• What SNPs can be identified and used to help
  diagnose and treat diseases?
• How can stem cell technologies be used to treat
  diseases and fight cancer?
• How will low-cost genome sequencing affect
  biology, medicine, society?

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Where to contact me and get more info?

• Check my web page
• http//hsc.unm.edu/som/micro/stemcells.shtml
• Send me an e-mail ness_at_unm.edu
• Google ness unm