Week 4 - Non-coding RNA & Hallmarks of Cancer

Coding genes percentage and info

1% of genome, 20,000 code for DNA and most are the same in other species.

What does noncoding DNA do?

Goes against central DOGMA (DNA → transcription → mRNA → translation → protein)

• transcribe into noncoding RNA

• The fine-tuning gene expression in uniquely human

(noncoding RNA = regulatory)

Regulatory RNAs

RNA can encode without being translated into protein

Natural forms:

1. microRNAs

2. long Noncoding RNAs

• Long double stranded RNA (pathological)

• Short interfering RNA (synthetic)

microRNAs

small non-protein coding RNAs

21-22 nucleotides long

double stranded

Where are genes for microRNAs found?

Found throughout genome, often in introns or intergenic

microRNA function (2 functions)

1. Degradation: miRNA matches sequence of target mRNA perfectly = target is degraded = no protein

2. Block translation: miRNA matches sequence of target mRNA imperfectly = inhibited from translation = less protein

[number 2 is more common]

miRNA can have how many targets?

Many

• can have multiple functions and regulate various pathways.

Mir7

tumour suppressor miRNA

function = prevents invasion and migration in melanoma

downregulated in cancer

Mir200

miRNA family inhibit epithelial characteristics and promote mesenchymal traits.

function = suppresses ZEB1 and ZEB2 → which are in high conc. in mesenchymal cells and repress e-cadherin.

• therefore Mir200 family help sustain high e-cadherin conc.

ZEB1/2 (related to Mir200)

Transcriptional repressors of e-cadherin = leads to low e-cadherin = promotes epithelial to mesenchymal transition

• Mir200 suppresses it therefore maintaining e-cadherin levels.

Long noncoding RNAs

greater than 200 nucleotides

does no contain obvious protein coding potential

(a type of regulatory RNA)

• each as a unique DNA, RNA & protein recognition motif

• most never lease nucleus

Where are long noncoding RNAs found?

many locations:

- intergenic

- splice forms

- intronic

- antisense

LncRNA expression

lowly expressed

• Specific to a tissue or development stage

The function of most are unknown

LncRNA mechanism of action (name the 4 types)

1. signals

2. decoys

3. guides

4. scaffolds

LncRNA are regulating genes are the transcriptional level

Archetype 1: Signal LncRNA

They mimic the combinatorial actions of transcriptions factors (or signalling pathways)

• to form a response faster than making a new protein

LncRNA signal example → XIST

Role: X-inactivation

17kilobase lncRNA gene

• found in X chromosome in placental mammals

In order for X-chromosomes in women to be expressed at the same rate as men, one must be silenced.

XIST function

Signal = showing which X is silenced

Guide = recruites epigenetic machinery to one X chromosome, to silence it

(essential for X-inactivation)

Archetype 2: Decoy LncRNA

1. sequester transcription factors away from chromatin

2. sequester protein factors into nuclear domains

can also be decoys for miRNA

Archetype 3: Guide LncRNA

recruit chromatin modifying enzymes to target genes either in

• cis: near the site of the lncRNA production

  or

• trans: distant target genes

LncRNA guide example: HOTAIR

Found in HOX gene cluster

• HOX genes are vital for patterning in the embryo

• HOTAIR represses this by:

  1. changing epigenetic state

  2. Then inducing heterochromatin

Upregulated in many cancers (associated with metastasis)

Archetype 4: Scaffold LncRNA

Can bring together multiple proteins to form ribonucleoprotein complexes

• complexes can alter gene expression

• e.g. epigentic modification

Can also be structural to stabilise structures or signalling complexes

Scaffold LncRNA example: NEAT1

(decoy and scaffold)

23kb gene in mammals

Scaffold = structural scaffold for paraspeckles

Decoy = alters gene regulation by sequestering proteins and RNA

6 Hallmarks of cancer

1. Evade apoptosis

2. Self sufficient growth signals

3. Insensitive to anti-growth signals

4. Sustains angiogenesis

5. limitless replicative potential

6. tissue invasion and metastasis

Hallmark 1: Evading apoptosis (cancer)

mutations that:

- inactivate apoptotic sensors

- inactivate apoptotic effectors

Apoptotic Sensors

1. Cell surface receptors that bind survival/death factors

2. Intracellular sensors that monitor DNA damage

^ Signals tell mitochondria to release cytochrome C which is responsible for triggering apoptosis

• Mutation in cancer cells needs to inactivate these sensors

Apoptotic Effectors

Capsases = enzymes that break down cell organelles

• Inactivated by mutations in cancer cells

Apoptosis involves many effectors/capsases (drugs can kill the tumour by increasing levels of a different effector/s)

Hallmark 2: Self sufficiency in growth signals (3 ways cancer cells do it)

Tumour cells:

1. generate own growth signal

2. overexpress receptor for growth signals in a permanently activated forms

3. mutate downstream signalling molecules = permanent activation

Hallmark 3: Anti-growth signals in normal cells (overview)

in G1 phase:

- cells monitor environment

- can decide to put cell back to quiesccent or differentiated states

Anti-growth signals normal vs Cancer

Embryonic Myc-Max = keeps cells pluripotent

Mature cells Mad-Max = triggers differentiation

• cancer reactivates Myc = keeps cells pluripotent

pRB/E2F pathway (relation to cancer)

directs G1 to S

Cancer:

- TGFbeta blocks phosphorylation of pRB, cancer cells must prevent TGFbeta from doing this

freeing up of E2F:

• takes cell out of G1 phase into S phase

Hallmark 4: Sustained angiogenesis (cancer)

Early to mid stage step required by tumours

• formation of macroscopic tumours

cells must be 100microns from blood vessel:

• tumour redirects blood vessel growth towards it

Hallmark 5: Limitless Replicative Potential (cancer)

Normal cells = enter senescence after a number of doublings

Cancer = continues replicating by maintaining Telomeres

How do cancer cells continue replicating?

Maintain Telomeres by:

- upregulate telomerase (80-90%)

- the ALT mechanism that uses homologous recombination based process (10-20%)

Hallmark 6: Metastasis and Tumour invasion (cancer) - Requires what 2 things?

1. changes to physical coupling of tumour cells to stroma (supporting tissue)

2. activation of extracellular proteases

These allow for the transition from epithelial to mesenchymal cells

E-cadherin in cancer

is lost in invasive epithelial cancers:

- tumours change the integrins they produce

- which effects what the cells contact with

microRNA200 family reduce in concentration.

Cancer and cell jucntions

Adherens junctions and focal adhesions must be dismantled to successful form mesenchymal cells

Enabling characteristics of Cancer (2)

1. Genome instability

2. Inflammation

Genome instability in cancer

Cancer = increase sensitivity to mutagenic agents → decreases efficiency of DNA repair

(cancer enabling characteristic)

Inflammation

Innate immune cells supply:

• growth factors

• ECM modifying enzymes

• proangiogenic factors

• Survival factors

• release ROS

to help mutate nearby cells

Emerging hallmarks of Cancer (2)

1. Cellular energetics/metabolism

2. Avoiding immune system

Cellular Energetics/metabolism (in cancer)

Warburg effect:

- most cancer cells produce energy via glycolysis

- even in presence of oxygen → bypass need for ATP from mitochondria

- therefore cancer cells like glucose

Avoiding immune system

Not a universally recognised hallmark

• sick people aren’t MORE prone to cancer

• some cancers evade immune cells better than others

Multi Hit model of Carcinogenesis

Cancers develop over time as mutations accumulate

Cancers need all 6 of the hallmarks (acquires them through accumulating several mutations)

p53 tumour suppressor

Suppresses tumours

(if cancer cells are successful they evade it)

• mutating P53 achieves insensitivity to anti-growth and evading apoptosis

  • hitting two hallmarks in one

Why do cancer drugs fail?

targetting one hallmark = may activate others

therefore combination therapies are needed

Limitation of Cancer Hallmark Model (2)

1. Some cancers rely heavily on one hallmark (each hallmark isnt equal)

2. First 5 hallmarks dont focus on Metastasis, which is the real problem with cancer