lecture 11: epigenetics and cancer stem cells Flashcards
Cancer epigenetics – focus on DNA methylation 1. tumour suppressor hypermethylation and silencing – single genes as biomarkers – sets of genes, such as "bivalent" genes from embryonic/adult stem cells 2. genome-wide hypomethylation – genomic instability 3. contribution of DNA methylation changes to cancer 4. alterations to epigenetic modifiers and epigenetic therapy Cancer stem cells and cancer stem cell epigenetics 5. cancer stem cell hypothesis and clonal evolution
<p>What is important to note about the hallmarks?</p>
<ul>
<li>aberrant epigenetic control </li>
<li>this and its consequences influences all of the hallmarks of cancer </li>
<li>cancer (simple): uncontrolled cell growth
<ul>
<li>activation of oncogenes </li>
<li>inactivation of tumour suppressors </li>
</ul>
</li>
<li>this is achieved both genetically and epigenetically </li>
</ul>
<p>In what ways are epigenetic and genetic changes similar and different?</p>
<ul>
<li>both are heritable </li>
<li>epigenetic changes are also reversible </li>
<li>DNA methylation is mitotically heritable because:
<ul>
<li>DNMT1 recognises hemi-methylated DNA and restores methylation on both strands </li>
<li>TET proteins involved in active demethylation are only expressed at very restricted times in development </li>
</ul>
</li>
<li>DNA methylation is reversible actively (TET proteins) or passively via DNA replication int he absence of DNMT1</li>
<li>In general DNA methylation is maintained and therefore heritable through presence of DNMT1 and rare expression of TET proteins </li>
<li>Important in therapy for cancer because of genetic mistakes and epigenetic mistakes, the epigenetic ones can be undone </li>
</ul>
<p>What are epigenetic aberrations in cancer?</p>
<ul>
<li>DNA methylation</li>
<li>histone modifications </li>
<li>chromatin remodelling </li>
<li>histone variants </li>
<li>piRNAs and long noncoding RNAs</li>
<li>nuclear architecture </li>
<li>lead to: global and gene-specific changes in all aspects of epigenetic control in cancer </li>
</ul>
<p>What are DNA methylation aberrations in cancer?</p>
<ul>
<li>CpG island hypermethylation: CpG islands and imprint control regions
<ul>
<li>often occurs at the tumour suppressor genes </li>
</ul>
</li>
<li>Genome-wide hypomethylation: repeats, CpG poor promoters, intergenic regions and imprint control regions
<ul>
<li>has it's own set of consequences, in particular genomic instability</li>
</ul>
</li>
</ul>
<p>What is CpG island hypermethylation?</p>
<ul>
<li>DNA methylation is an alternative to genetic mutation, to silence tumour suppressor genes in cancer
<ul>
<li>can identify origin of a tumour by its hypermethylation pattern</li>
</ul>
</li>
<li>occurs frequently in tumours (250-700 islands/tumour c.f. <200 non-synonymous mutations)</li>
<li>can also occur at imprint control regions, leading to loss of imprinting and overexpression og imprinted genes that control growth</li>
<li>identity of hypermethylated CGIs varies by tumour type (different tumour suppressors relevant in different tissues)</li>
<li>CGI methylation progress with time, but confounded by DNA methylation alterations increasing with age</li>
</ul>
<p>What are single gene examples of CpG island hypermethylation in cancer?</p>
<ul>
<li>RB in retinoblastoma </li>
<li>MLH1 in colorectal cancer </li>
<li>BRCA1 in breast cancer </li>
<li>MGMT in gliomas and colorectal tumours </li>
<li>hypermethylated genes can be used as biomarkers as CGI are usually unmethylated
<ul>
<li>discriminate tumour from normal/benign tissue for diagnosis </li>
<li>sometimes informs prognosis </li>
<li>monitor tumour burden during treatment </li>
<li>may alter treatment strategy </li>
</ul>
</li>
</ul>
<p>What about sets of genes being hypermethylated?</p>
<ul>
<li>sets of genes allow more precise diagnosis, prognosis, monitorin g</li>
<li>relevant to stem cell epigenetics: hypermethylated genes are enriched for genes silenced by polycomb repressive complex 2 (PRC2) in embryonic and adult stem cells </li>
</ul>
<p>What are "bivalent genes" in stem cells?</p>
<ul>
<li>PRC2 mediated H3K27me3</li>
<li>MLL mediated H3K4me3</li>
<li>paused RNA Pol II at the promoter </li>
<li>no DNA methylation </li>
<li>these genes are inactive, but poised for rapid ativation </li>
<li>upon differentiation, bivalent marks allow rapid activation or repression </li>
<li>these genes are developmental regulators such as lineage specific transcruption factors in ES cells and adult stem cells </li>
<li>in cancer: genes no longer poised for activation, more stably repressed </li>
</ul>
<p>What is genome-wide hypomethylation?</p>
<ul>
<li>historically, earliest epigenetic abnormality found</li>
<li>occurs in all tumour types tested, progresses with tumourigenicity</li>
<li>consequence of hypomethylation depends on location
<ul>
<li>*repeats/intergenic regions: genomic instability </li>
<li>CpG poor promoters: oncogene activation </li>
<li>imprint control regions: loss of imprinting </li>
</ul>
</li>
</ul>
<p>What is the result of hypomethylation of repeats/intergenic intervals?</p>
<ul>
<li>Genomic instability
<ul>
<li>illegitimate recombination between repeats, as recombination requires open chromatin</li>
<li>transcriptional activation of repeats and transposition</li>
</ul>
</li>
</ul>
<p>What is the contribution of DNA methylation to cancer?</p>
<ul>
<li>some places have too much, others too little... </li>
<li>role of DNA methylation is context dependent </li>
<li>different tumours have different dependencies
<ul>
<li>driven by tumour suppressor hypermethylation, then depletion of DNA methylation appears to <b>suppress</b> tumourigenesis </li>
<li>driven by chromosomal instability, then depletion of DNA methylation appears to enhance tumourigenesis</li>
</ul>
</li>
</ul>
<p>How do the alterations in epigenetic marks occur?</p>
<ul>
<li>stoachastic alterations then selective pressure?</li>
<li>influence of cellular stress?</li>
<li>chronic inflammation?</li>
<li>exposure to environmental insults?</li>
<li>mutations/expression changes in epigenetic modifiers themselves </li>
</ul>
<p>What are mutations in all types of epigenetic regulators?</p>
<ul>
<li>different genetic and epigenetic disruptions to epigenetic modifiers</li>
<li>observed in a wide range of cancers</li>
<li>epigenetic modifiers can be oncogenes or tumour suppressors, dependent on targets in each cell type e.g. EZH2</li>
<li>Histone methyltransferases:
<ul>
<li>DOT1L: targets H3K79, translocation, loss of function, AML</li>
<li>EZH2: H3K27, Amplification, gain of function, breast, prostate</li>
<li>EZH2: H3K27, mutation, gain, lymphoma</li>
<li>EZh2: H3K27, mutation, loss, MDS</li>
<li>MLL1: H3K4, translocation, loss, AML, ALL</li>
<li>MLL3: H3K4, deletion, loss, leukaemia</li>
<li>RIZ1: H3K9, CpG hypermethylation, loss, breast, liver</li>
</ul>
</li>
<li>Histone demethylases:
<ul>
<li>UTX: H3K27, mutation, loss, multiple types</li>
<li>LSD1: H3k4, H3K9, amplification, gain, prostate, bladder, lung, colon</li>
</ul>
</li>
</ul>
<p>What is the yin/yang of cell heading towards cancer?</p>
<ul>
<li>alteration to epigenetic modifiers (genetic change) leads to change in epigenetics leads to genomic leads to genomic instability leads to alteration in genetics (e.g. in epigenetic modifiers)</li>
</ul>
<p>What are drugs that target the epigenetic machinery?</p>
<ul>
<li>epigenetic alterations are reversible</li>
<li>wariness due to systemic use – critical role of epigenetic control in all other tissues, side effects</li>
<li>primary aim for cancer patients – survival</li>
<li>drugs targeting enzymatic epigenetic regulators, since enzymes are most readily targeted with small molecule inhibitors, but others now also being developed (BET inhibitors)</li>
<li>mechanism of action is still unclear, even with oldest drugs (DNMT inhibitors)</li>
<li>DNMTi
<ul>
<li>Myelodysplastic syndrome progressed to AML CSCs
<ul>
<li>Decitabine - FDA approved</li>
<li>Vidaza - FDA approved</li>
<li>more in clinical trial</li>
</ul>
</li>
</ul>
</li>
<li>HDACi
<ul>
<li>cutaneous T cell lymphoma
<ul>
<li>vorinostat - FDA approved</li>
<li>Romidepsin - FDA approved</li>
</ul>
</li>
<li>panobinostat - ph III</li>
<li>Valproic acid - ph III</li>
<li>belinostat - ph II pivotal</li>
<li>many more early trials and preclinical</li>
</ul>
</li>
<li>HMTi
<ul>
<li>EPZ5676 - DOT1Li, clinical trial</li>
<li>GSK126- EZH2i, preclinical</li>
<li>Many more in development against G9a, CARM1 etc</li>
</ul>
</li>
<li>HATi
<ul>
<li>CBP/EP300i - preclinical tests</li>
<li>more in development</li>
</ul>
</li>
<li>HMTi
<ul>
<li>LSD1i - 2 compounds in preclinical tests</li>
<li>more in development</li>
</ul>
</li>
</ul>
<p>What is the cancer stem cell theory?</p>
<ul>
<li>tumours are heterogeneous</li>
<li>CSC population: self-renew to regenerate the tumour, but also differentiate to form other cells within the tumour (like normal stem cells)</li>
<li>CSCs tend to be resistant to therapy</li>
<li>If target CSCs, then will have effective remission
<ul>
</ul>
</li>
</ul>
<p>What drives tumour heterogeneity?</p>
<ul>
<li>driven by epigenetic changes as well as genetic changes</li>
</ul>
<p>What are important notes on cancer stem cell theory?</p>
<ul>
<li>CSCs may not feature in all cancers</li>
<li>CSC theory isn't mutually exclusive with genetic heterogeneity and clonal evolution; both co-exist
<ul>
<li>even within the cancer stem cell population they are not necessarily genetically identical</li>
</ul>
</li>
<li>CSC proportion and features change over time, like the rest of the cancer
<ul>
<li>more rounds of chemotherapy generate bigger proportions of CSCs that are also more resistant to treatment</li>
</ul>
</li>
</ul>
<p>Is self-renewal of CSCs a feature of the founder cell? Is self-renewal imparted on a more differentiated cell, as part of the tumourigenesis?</p>
<ul>
<li>In AML it is the haematopoeitic stem cell that is the cell of origin for the cancer</li>
<li>this doesn't have to be the case</li>
<li>differentiation is an epigenetic process</li>
<li>differentiation can be reversed as epigenetic changes are reversible</li>
<li>genetic and/or epigenetic changes could arise in stem, progenitor or differentiated cells to impart self-renewal</li>
<li>when differentiation capacity is retained, more likely to be an epigenetic change</li>
<li>stem cell doesn't have to be the cell of origin</li>
</ul>
<p>What is the epigenetics in cancer stem cells?</p>
<ul>
<li>Epigenetic changes may impart self-renewal capacity</li>
<li>faithfully transmitted epigenetic changes may allow maintenance of the stem cell state at the expense of differentiation in cancer</li>
<li>e.g. "bivalent" genes from ES and adult stem cells that become DNA hypermethylated</li>
<li>"Bivalent" genes are developmental factors important in commitment to specific lineages</li>
<li>DNA methylated in cancer, rather than poised for activation/repression</li>
<li>DNA methylation more stable due to restricted expression of DNA demethylation (TET) enzymes</li>
<li>developmental genes are more difficult to activate, CSCs less likely to differentiate, more likely to self-renew</li>
<li>epigenetic changes can enforce self-renewal at the expense of differentiation (as could genetic changes)</li>
<li>epigenetic changes are reversible</li>
<li>as they stay in the self-renewal state they will be relatively quiescent, won't divide as commonly, therefore resistant to chemotherapy</li>
</ul>
<p>What are the clinical implications of cancer stem cells?</p>
<ul>
<li>CSCs resistant to chemotherapy, perhaps partly due to their different epigenetic makeup e.g. at "bivalent" genes</li>
<li>prime CSCs for response using epigenetic drugs to remodel the CSC epigenome e.g. DNA methyltransferase inhibition to deplete DNA methylation at "bivalent" genes</li>
<li>CSCs susceptible to chemotherapy</li>
</ul>
