Cancer 2.0 – Travis Christofferson

6.8.16 | YouTube

The view from 30,000 feet

  • What is cancer?
  • Cancer is unique among diseases
  • Over 3 million PubMed papers under the search term “cancer” (circa 2016)
  • Cancer Genome Atlas (TCGA)
  • Emerging Theories of Cancer
  • Cancer 2.0 cancer as an orderly epigenetic disease
  • The importance of hexokinase 2 (HK2) in the cancer’s metabolic phenotype

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The somatic mutation theory has dominated cancer biology for almost 50 years

“Cancer, we now know, is a disease caused by the uncontrolled growth of a single cell. This growth is unleashed by mutations changes in DNA that specifically affect genes that incite unlimited cell growth (Mukherjee, The Emperor of All Maladies, 2010).”

“The Scientists say that bad luck plays a stronger role in some cancers than in others. In two-thirds of the cancers 22 cancer types random mutations in genes that drive cancer could explain why the disease occurred (The Guardian, January, 2015 CKTK).”

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The somatic mutation theory of cancer

  • Simple initiating mutator mutation
  • Sequential, multi-step mutagenesis and selection
  • Wind up with a tumor

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The Cancer Genome Atlas

The Cancer Genome Atlas  Breast cancer example:

  • Sequenced the tumors of 100 women with breast cancer
  • These are the genes they determined to be the driving genes
  • If they can’t determine through functional data, it’s the frequency of the mutation
  • These are point mutations, copy mutations, but the important part — what caught everyone off-guard — was the huge degree of intertumoral heterogeneity from one patient’s tumor to the next
  • There are very few commonly mutated genes
  • The other thing that caught people off-guard was that there were many samples with single driving mutations, two driving mutations, or ZERO driving mutations
  • So it’s impossible to reconcile a genetic origin with this data.
  • How can there be zero driver mutations in cancer?

There is a strikingly high degree of intertumoral heterogeneity (i.e., the degree of mutational difference that exists from person to person) and intratumoral heterogeneity (i.e., the degree of mutational difference that exists within the same tumor, from cell to cell)

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Cancer Genome Landscapes

Paper by Vogelstein’s group (Vogelstein et al., 2013 CKTK)

  • Bert Vogelstein wrote a review asking this question: Where are the missing mutations?
  • He goes on to describe what he calls dark matter
  • There’s some presumptive force that we’ve yet to identify that’s driving the disease

Problems with the somatic mutation theory

  • Missing mutations  Impossible to reconcile neoplasms with few to no driver mutations
  • Ad hoc addition of mutator mutation (like Tom said: bank teller analogy) when you measure the mutation rate within human cells, it’s very low
  • >> It’s impossible to reconcile the rates of cancer with the known rates of mutation
  • >> They modified and said that the first mutation must be in the gene that controls DNA repair
  • >> This allows for the probability fo other mutations to occur
  • >> Impossible to explain tremendous “gain of function” by rendering biological system dysfunctional
  • >> Systematically wiping out biological systems
  • >> Dramatically illustrated in TCGA ancillary study looking for genes that correlate to metastasis
  • >> The most important feature of cancer
  • >> They found zero
  • >> They couldn’t correlate a single mutation to metastasis
  • >> And that’s what the Hanahan and Weinberg model presupposes: every hallmark of cancer is driven by oncogenes
  • >> But they can’t find them

New theories have emerged explaining cancer

The metabolic theory

  • Explains the genetic heterogeneity observed in most solid tumors
  • Explains the consistent reversion to fermentation (the Warburg effect)
  • Explains how neoplasms can exist with two or fewer drivers
  • Casts cancer as an epigenetic disease
  • Explains the tremendous gain of function observed in cancer
  • Agrees with the series of nuclear transfer experiments

The Tissue Organization Field Theory (TOFT)

TOFT:

  • Explains confusing sequencing data
  • Agrees with series of experimental data testing stroma/epithelial interaction after exposure to a carcinogen
  • Explains “gain of function”
  • Casts cancer as an epigenetic disease

TOFT:

  • The default state of epithelial cells is cell division
  • The epithelium is kept in check by the tissue architecture field
  • Exerts negative controls to keep the epithelium from dividing
  • Once that relationship breaks down, the epithelium begins neoplastic growth
  • Explains the confounding data from the Atlas project
  • Agrees with a series of convincing experimental data testing stroma/epithelium interaction after exposure to a carcinogen
    • When you apply a carcinogen to the stroma and disrupt this architecture and then recombine epithelial cells that haven’t been exposed to a carcinogen, you get cancerous growth
    • When you flip it: hit epithelial cells with a carcinogen, put them back into intact architecture, and neoplasm is suppressed
  • Casts cancer as an epigenetic disease

Paradigm shift — “cancer 2.0” — epigenetics

  • Combined in the notion that cancer is driven by a predetermined subroutine
  • Shifting the perception that cancer is a disease of order rather than a disease of disorder
  • Process driven by epigenetic changes

Raises a big question: why would all life have a “cancer subroutine” preloaded in its DNA?

Why would all life have a cancer “subroutine” preloaded in its DNA?

The Atavistic Model of cancer

It’s deterministic, systematic, unfolding some preprogrammed response: what gives?

  • Recent answer: the atavistic model by Paul Davies and Charlie Lineweaver
  • An evolutionary throwback: we all have it within us, but it’s suppressed

How life populated the planet

  • Formed 4.6 billion years ago
  • Life began about 4 billion years ago
  • Begins as unicellular life: simple biological imperative is to replicate (replicative immortality)
  • About 1 billion years ago, cells begin living in clumps: multicellular life
  • They signed a contract with each other (Nick Lane line about
  • Repressed multicellular replicative immortality for the good of the collective
  • Speciation took off
  • Unicellular ==> Colonial ==> Multicellular
  • Species don’t reinvent themselves anew: they build on old programs

Each layer of capabilities is built on, and depends upon, the earlier layers

Davies calls the “bells and whistles of evolution” the newest capabilities to evolve big brains, etc but embedded in all of this, the earliest capabilities are still there, which is replicative immortality

Development of a whale

Begins with fertilization of an egg:

  • Cells trickle down Waddington’s epigenetic landscape towards terminal differentiation
  • An idea in developmental biology that ontogeny recapitulates phylogeny: embryogenesis reflects our evolutionary sweep across the planet
  • The earliest genes we express are the first genes to have evolved
  • The lates genes, the terminal differentiation genes, are the newest genes to have evolved
  • The whale undergoes the developmental program of legs
  • Because a whale evolved in an ocean, it suppresses that program
  • Occasionally that suppression system breaks down and you get an atavism: whales with rudimentary legs
  • We see atavisms in nature all the time
  • Snakes with legs
  • Humans with little tails or webbed feet

Development of cancer

We can look at cancer in this same context: an atavism

  • Life begins with a fertilized egg
  • Totipotent cells which trickle down towards terminal differentiation
  • Some cells get purged as stem cells along the way
  • According to the atavistic model: cancer begins with a stem-like cell
  • They’re already purged epigenetically closer to neoplasm
  • You can see this in the methylation patterns, etc.
  • Or they revert that pattern
  • There are triggers: it could be a nuclear gene mutation, it could be mitochondrial damage, the disruption of the tissue architecture
  • Then what happens is the cell reverts to the “safe mode”
  • But it begins running the arrow of evolution backward, away from the modern genes of multicellular living and cooperation, and towards earliest genes, of early embryogenesis, of replicative immortality
  • We’ve known this: cancer cells re-express fetal genes, they’re expressing these early genes of embryogenesis

Embryogenesis looks a lot like cancer:

  • Highly glycolytic
  • Undifferentiated
  • They exhibit replicative immortality

The re-expression of fetal genes is what’s defining cancer:

  • Within a multicellular context, we’ve divested our immortality to the germline
  • The methylation tags, epigenetic signals get wiped clean every time we go through embryogenesis, and that’s what’s happening with cancer
  • Global hypermethylation
  • Hypermethylation of the promoter regions of tumor suppressor genes

Human embryonic genes re-expressed in cancer cells

Human preimplantation embryonic cells are similar in phenotype to cancer cells. Both types of cell undergo deprogramming to a proliferative stem cell state and become potentially immortal and invasive (Monk and Holding, 2001).

Hexokinase 2

The most important effector of cancer’s metabolic phenotype is the transition from hexokinase 1 to hexokinase 2

Hexokinase 2 is required for tumor initiation and maintenance and its systemic deletion is therapeutic in mouse models of cancer (Cancer Cell;24,2,213-228,2013TK)

  • The first enzyme of glycolysis is HK1
    • A little in skeletal muscle and heart
    • Cancer transitions to HK2, and then it wildly overexpresses it
  • HK2 is less subject to product inhibition to glucose-6-phosphate
    • Great for replicative immortality
    • Responsible for the Warburg effect
  • It binds to the VDAC channel
    • Associated with outer mitochondrial membrane
    • It induces a conformational change that closes the VDAC channel
    • The VDAC channel is the effector pore for apoptosis

This one transition to an isozyme that’s preprogrammed in us is responsible for two hallmark features of cancer

  1. Warburg effect
  2. Immortalization of the cell

Hexokinase 2 is responsible for the Warburg effect and immortalization of the cell

  • Most people attribute a PET scan to overconsumption of glucose (true)
  • More because HK2 phosphorylates glucose which is an irreversible reaction, which bloats the cancer cell
  • You wouldn’t have a PET scan without HK2

Developmental profile and regulation of the glycolytic enzyme hexokinase 2 in normal brain and glioblastoma multiforme

Paper in Neurobiol Dis (Wolf et al., 2011 CKTK)

“HK2 expression was highest in the early embryo, while HK1 expression increased with CNS maturation.”

  • Is there any other time that HK2 is overexpressed other than cancer?
  • Very early on during embryogenesis
  • A good theory has predictive power: this is exactly what you would expect

Cancer is “hop-scotching back in time to the Proterozoic ocean

  • The earth’s atmosphere had dramatically less oxygen, when unicellular life evolved
  • Glycolysis is the most ancient and conserved biochemical pathway
  • The degree of HK2 overexpression correlates to the degree of aggressiveness

The idea of an atavistic model:

  • If the foundation of embryogenesis is that built-in pattern of replicative immortality, you can’t rid of it
  • Evolution would get rid of cancer if it could, but it can’t because it’s the building block of embryogenesis
  • The cancer cell is reverting back to this: it’s hop-scotching back in time
  • During the great oxygenation of the planet is when multicellular life took over

“Geochemical data (1-6TK) suggest that oxygenation proceeded in two broad steps near the beginning and end of the Proterozoic eon (2,500 to 542 million years ago) (Tracing the stepwise oxygenation of the Proterozoic ocean, Nature, 452, 456-459, 2008 CKTK).”

You can see the exact methylation patterns that result in the overexpression of HK2:

Thus, bisulfite methylation footprint analysis revealed 18 methylated CpG sites within a CpG island (-350 to +781 bp) in the hepatocyte HK2 gene, but none in the hepatoma (Hexokinase II: Cancer’s double-edged sword acting as both facilitator and gatekeeper of malignancy when bound to mitochondria (Mathupala, Ko, and Pedersen, 2006 TK)

[pkm2?]

Therapeutic strategy of cancer 2.0

  • We have to know what cancer is in order to treat it
  • New theories guide cancer treatment strategy to epigenetic therapies: exploit differences in expression and/or engage the cancer cell in diplomacy experiments have shown this is possible
  • Direct and indirect epigenetic strategies

Direct strategies:

  1. DNMT inhibitors
  2. HDAC inhibitors
  3. Packaged microRNA (miRNA)

Indirect strategies:

  1. Decoupling from adaptive immune system
  2. Ketogenic diet and HBOT

Take-home messages:

  • Somatic mutations are not the whole picture
  • Cancer is a systematic, organized disease of altered protein expression (e.g., HKII)
  • This completely reconfigures therapeutic strategy away from the single cell hypotheses to diplomacy and the targeted killing of cancer cells