Figure 18.3 SmallRNAs induced by alcohol can bind to messenger RNAs that don’t create alcohol tolerance. The smallRNAs don’t bind to the messenger RNA molecules that promote alcohol tolerance. This leads to a relative preponderance of the messenger RNA molecules that code for protein versions associated with tolerance to alcohol.
Mis-expression of smallRNAs has been implicated in a number of diseases that have a major impact on global human health. These include cardiovascular diseases{381} and cancer.{382} The latter is perhaps unsurprising, given that cancer represents abnormalities in cell fate and cell development, and smallRNAs are very important in these processes. One very clear example of the importance of smallRNAs in cancer is in a type of tumour that is characterised by inappropriately expressing developmental rather than postnatal genes. It’s a subtype of a childhood brain tumour which usually presents before the age of two. Sadly, it’s a very aggressive form of cancer, and the prognosis is poor even with powerful therapy.[64] The cancer develops following an inappropriate rearrangement of genetic material in the brain cells. A promoter that normally drives strong expression of a protein-coding gene recombines with a particular smallRNA cluster. This whole rearranged region is then amplified, meaning multiple copies are produced in the genome. As a consequence, the smallRNAs downstream of the relocated promoter are expressed far too strongly. The levels of the smallRNAs are between 150 and 1,000 times higher than they should be.
The cluster codes for over 40 different smallRNAs, and is in fact the largest cluster in primates. It is usually only expressed early in human development, in the first eight weeks of foetal life. Switching it on strongly in the brain of an infant has a catastrophic effect on gene expression. One of the downstream effects of this is to drive expression of an epigenetic protein which adds modifications to DNA. This leads to global changes in DNA methylation patterns, resulting in abnormal expression of a whole range of genes, many of which should be expressed only when the immature brain cells are dividing during development. This generates a cancerous cell programme in the infant.{383}
This cross-talk between smallRNAs and the epigenetic machinery of the cell may be significant in other situations where cells become predisposed to cancer. This mechanism can amplify the impact of disrupted smallRNA expression, by altering epigenetic modifications, which can be passed on to daughter cells. This can start a hard-wiring in of potentially dangerous alterations in gene expression.
Not all the steps have been unravelled in how smallRNAs interact with epigenetic processes, but hints are emerging. For example, a particular class of smallRNAs which trigger increased aggressiveness in breast cancer targets the messenger RNAs for certain enzymes that remove key epigenetic modifications. This alters the pattern of epigenetic modifications in the cancer cell, and further disrupts gene expression.{384}
Many cancers are surprisingly difficult to monitor in a patient. They may be inaccessible, so that they are hard to sample. This can make it difficult for clinicians to monitor how a cancer is changing, and exactly how it is responding to therapies. They may have to rely on indirect measures, such as imaging the tumour on a scan. Some researchers have suggested that smallRNA molecules may provide a new technique for following the natural history of a tumour. When cancer cells die, this often results in the smallRNAs leaving the cell as it breaks down. These little junk molecules are often complexed with cellular proteins, or wrapped in fragments of the cell’s membranes. This makes them very stable in body fluids, so they can be isolated and analysed. Because the amounts are low, researchers need to use very sensitive analytical techniques. This isn’t impossible though, because nucleic acid sequencing sensitivity is improving all the time.{385} Data in support of this approach have been published for breast{386} and ovarian cancer,{387} among others. In the case of lung cancer, circulating smallRNAs have been analysed and shown to be useful at discriminating between patients with a solitary lung nodule that is benign (doesn’t require therapy) from patients where the nodule is a tumour (and needs treatment).{388}
SmallRNAS are turning up in all sorts of unexpected situations. There is a really horrible viral infection called North American eastern equine encephalitis virus. It’s transmitted by mosquito bites. When this virus infects horses, the animals die. The situation isn’t much better in humans, where the fatality rate is between 30 and 70 per cent. The patients die because the virus gets into the central nervous system and causes severe inflammation of the membranes around the brain.{389} The virus that causes the infection has a genome that is made of RNA, not DNA.
When this virus first enters the human bloodstream following a mosquito bite, it is taken up by white blood cells. These are the front line in surveillance against invaders. But then something very odd happens. A smallRNA naturally produced by the white blood cells binds to the end of the virus’s RNA genome, and stops it from coding for protein.
This might seem like a good thing but it’s quite the opposite. Our white blood cells normally recognise if they have been infected by a virus. The cells will initiate a set of reactions including raising body temperature, and producing various anti-viral chemicals. Together, these repel the tiny invaders.
But when the smallRNA in the white blood cells binds to the equine encephalitis virus genome, the virus goes quiet. Consequently, the immune system doesn’t notice that the body has been infiltrated. This leaves other viral particles free to drift through the body. If some of them reach the central nervous system, they can then trigger the lethal responses in the brain tissues.{390}
The researchers described this in terms of the virus hijacking the smallRNA system, and it doesn’t seem to be the only example of this happening. The hepatitis C virus also has an RNA genome. When this virus infects liver cells, the viral RNA binds to a small-RNA naturally expressed by these cells. In this case, the binding stabilises the viral genome, making it harder to break down. As a consequence, more viral proteins are produced, and the infection becomes more damaging and more aggressive.{391}
It’s pretty clear that smallRNAs are involved in a whole range of human pathologies from infection to cancer, and from development to neurodegeneration. This of course raises an interesting question: if junk DNA can cause or contribute to disease, is it also possible to use junk to fight common human illnesses?
19. The Drugs Do Work (Sometimes)
Billions of dollars are spent every year by companies trying to create new drugs to treat human diseases. They hope to find ways to tackle unmet medical needs, a situation that is becoming ever more urgent with the increasing age profile of the global population. The breakthroughs in the understanding of the impact of junk DNA on gene expression and disease progression are triggering a slew of new companies seeking to exploit this field. Specifically, most of the new efforts are in using non-protein-coding RNAs as drugs in themselves. The basic premise is that junk RNA — long non-coding, smallRNAs or another form called antisense — will be given to patients, to influence gene expression and control or cure disease.