One gene one .... what? The problem with the 'Centra Dogma'...or any dogmas in science

One thing that has been found in recent years, and about which knowledge has been rapidly expanding is that the grand old 'Central Dogma of Biology', that one gene codes for one protein is, well, substantially wrong (to be kind to it).

Gene transcription, from The Mermaid's Tale, Weiss & Buchanan, 2009

The Central Dogma held that DNA is a string of codes that specifies messenger RNA (mRNA) that is translated in the cell into protein.  One gene, one protein.  That was how it looked when the nature of DNA was first being discovered.  But it's been decades since we knew that was not accurate.

A few of the reasons are

1. genes are interrupted coding sequences (they have non-coding 'introns'),  
2. introns are spliced out of mRNA by particular DNA sequence motifs,  
3. genomes evolve by duplication of whole segments, 
4. much more DNA is transcribed into RNA than was thought; 
5. some of this RNA has complimentary sequences to protein codes and there is an elaborate mechanism for this, which is never translated into protein, to inhibit 'real' genes (this known as microRNA);  
6. some non-protein RNA--copied from genes without the usual gene processing sequence elements, is nonetheless found attached to ribosomes in the cell as if it were being translated anyway; 
7. gene usage is determined in part by the way DNA in the gene's part of a chromosome is packaged and chemically modified ('epigenetics'); 
8. important aspects of variation are due to mutations that happen during the lifetime of the organism; 
9. each cell uses only some of its genes, and sometimes only one of its two copies of a gene that it is using; 
10. genes can be assembled via effects of genes from other chromosomes or even make mRNA that is a composite of pieces from two different chromosomes ; and (so we don't have to keep on and on), 
11. some mRNA is 'edited' after being transcribed, in replicable ways sometimes conserved among distantly related species, in which one nucleotide copied from the DNA template is replaced by a specific other nucleotide, thus changing the function, including the protein code, of the mRNA.

These are among many other things that we now know to be parts of DNA function.  They don't change the basic idea that DNA specifies protein structure, but there are so many details, of so many sorts, that it is clear that the idea of the Central Dogma is essentially wrong.  Yet, why do we still have 'exome' sequencing in so many expensive studies, or gene 'for' this or that trait, in so many expensive studies, when we know how simplistic this is?

There are many answers, and we regularly harp on them.  Here, the main point is that these discoveries are real, their importance highly variable and mainly unknown, and that they always add to, but rarely if ever reduce, the complexity between DNA and the traits that it affects.  Promises of simple prediction have been aided and abetted by the addictive discoveries that really work like the genes Mendel studied in peas.  We do a lot of hand-waving to dismiss complexity, but we cling like drowning sailors to life-rafts to the simple, Central Dogma, in the fervent hope that we'll find the Big Gene Story.   Yet those who are thinking about science itself, rather than about what they have to do to maintain their careers, know very well that we know very little about the nature of genetic function.

Dogma should not be part of science.  But historians and philosophers of science have shown that it certainly is.  A new book, for example, shows how this has affected immunology for decades, as  investigators clung to a 'fictive' theory, the idiotype network theory, even though it never had much basis (the book, The network collective: Rise and fall of a scientific paradigm, edited by Klaus Eichmann, is reviewed in the July issue of Bioessays). There's no place for dogma in science, nor for the tribalism that accompanies it.  But, well, we're only human so purging the motivations that drive dogma, and the careers that are made on its basis, may not be in the cards.

RAiN gutter, or RNAi down the tubes?

Here's a story that may not seem so but is actually about the kind of extensive cooperation that characterizes life, and is a major theme in our book.

"Drug giants turn their backs on RNAi," reports Nature this week.  The headline writer must have had a hard time resisting the urge to end that sentence with an exclamation point, because RNA interference has been seen for the last decade or so as the latest greatest drug technique on the horizon, and if that's no longer true, that's news.

Not long ago, a technique called RNA interference (RNAi) seemed to be on the fast track to commercial success. Its discovery in 1998 revealed a new way to halt the production of specific proteins using specially designed RNA molecules, and it quickly became a favourite tool of basic research. In 2006, the scientists who made the discovery were awarded the Nobel prize for medicine, and the New Jersey-based pharmaceutical giant Merck paid more than US$1 billion to snatch up Sirna Therapeutics in San Francisco, California — one of the first biotechnology companies aiming to harness RNAi to create new drugs.

As one company, Alnylam Pharmaceuticals, one of the best endowed RNAi start-ups in the world, describes it:

RNAi is a revolution in biology, representing a breakthrough in understanding how genes are turned on and off in cells, and a completely new approach to drug discovery and development. RNAi offers the opportunity to harness a natural mechanism to develop specific and potent medicines, and has the potential to become the foundation for a whole new class of therapeutic products.

The discovery of RNAi has been heralded as a major scientific breakthrough that happens only once every decade or so, and represents one of the most promising and rapidly advancing frontiers in biology and drug discovery today. 

Well, according to the story in Nature, Alnylam has just laid off 50 workers, more than a fifth of its work force, because the Big Pharma company, Novartis, declined to extend its partnership with them.  Of course Alnylam says they still believe wholeheartedly in the promise of RNAi, but they would have to say that, wouldn't they?  Is protecting your stock prices and nervous investors an excuse for shading honesty, one of our recent themes?

RNAi is a naturally occurring process that interferes with gene expression when the antisense strand of an RNA molecule binds to the sense strand, thus inhibiting its translation into a protein.  The discovery of RNAi was a major discovery worthy of a Nobel prize because it revealed how cells naturally titer their level of gene expression.  They can start using a gene, but then quickly shut it down if brief or highly controlled timing is important, in forming organs in an embryo, for example, or cell differentiation or response to environmental changes.  It shows that nature is like the mushroom in Alice in Wonderland: nibble from one side to get taller, and the other to get shorter.

RNAi was quickly and widely heralded as a major breakthrough, and its potential in treatment of diseases like Huntington's or Parkinson's and so forth was obvious and exciting to researchers, pharma, and patients alike.

But, as with other forms of gene therapy, the realities of delivering the RNAi molecule to its target within cells is proving to be daunting.

The development of RNAi-based drugs has stalled as companies confront the challenge of delivering RNA molecules, which are notoriously fragile, to target cells in the human body, and then coaxing those cells to take up the RNA. "Getting these molecules exactly where we want them to go is a little more difficult than originally thought," says Michael French, chief executive of Marina Biotech, an RNAi company based in Bothell, Washington.

Of the dozen RNAi-based therapeutics in early clinical testing, most apply the RNA molecules directly to the target tissues, or aim to shut down the production of a protein in the liver, which takes up the RNA as it filters the blood. Several candidates also package the RNA within a lipid nanoparticle, a delivery vehicle that both protects the RNA and allows it to be shuttled across cell membranes. 

Alnylam claims to have a number of possible drugs in the proverbial (just-in-time-for-Christmas?) pipeline, and still enough money, even without Novartis, to do some testing, and other companies are still holding on as well.  So apparently we aren't hearing the actual death knell yet, but it's starting to look a lot like the sobering of the dance of enthusiasm for personalized genomic medicine by Big Pharma a decade or so ago because of the realities of complex disease.

There are several things here worthy of comment besides the discouraging news that a hopeful-sounding therapy might not work.  Differentiated organisms rely on internal integrity of their many cooperating parts -- organs, tissues within each organ, and complex interactions among components within each cell.  Stuff from the outside that is not brought in under controlled circumstances is not likely to be usefully incorporated into cellular machinery.  That's why immune systems of various kinds, often quite intricate, exist.  That's why cells highly control what crosses their membranes from the outside in, and get rid of what's no longer needed by kicking it out.

All this involves detection and cooperative action of large numbers of components that must be in the right place, on guard or ready for duty, at the right time.  It is no wonder that trying to sneak in something external, that is supposed to coopt the cell for its own purposes, is difficult!  Especially if this requires shanghaing many different parts of the cell to get this done.  Whether the problem can be solved is only for the future to tell, but the hyperbole by companies about how RNAi would quickly lead to a revolution in medicine was typically highly over-worked.

Years ago, David Stock, a very fine post-doc in our lab (now a prominent faculty member in beautiful Boulder, Colorado) spotted something strange in some work we were doing with embryonic mouse teeth.  We were interested in how teeth are patterned, and were working with a gene we had discovered called Dlx3.  David said he had sequenced some RNA -- purportedly messengerRNA coding for the Dlx3 gene -- but instead he had discovered the reverse sequence.  This was, at the time, 'impossible' and we dismissed it as a laboratory artifact.  RNAi had not yet been discovered, and since it was so unexpected we just never followed up on this finding (maybe we should have!).  That's how surprising RNAi seemed to be when it was shown to be real, widespread, ancient, and important in the biology of normal organisms.

But the idea, including the potential for practical application, was not new.  Even in our lab, we had tinkered with experimental uses of anti-sense RNA.  Various people had thought of using introduced anti-sense RNA in cells to experimentally alter gene expression.  The idea that this could have  application was also expressed by many, and we think some pharma explored this.  If genes are expressed via mRNA, which is translated into protein, then if you could inhibit that translation you could experimentally (or therapeutically) slow or stop the expression of the targeted gene.  AntisenseRNA would bind to the corresponding messengerRNA in the cell, so it couldn't be translated into protein.

Unfortunately, the method proved very difficult to use.....that is, it basically didn't work.  Even in cell or organ culture (such as, in our lab, growing embryonic mouse tooth germs in culture), the cells simply did not like incoming RNA, and RNA is quite unstable to begin with.  We and many others tried this approach, but gave up on it.

Thus it was that investigators thought of doing what nature had been doing, systematically and precisely and unbeknownst to science, for many many millions of years.  And unlike BigPharma, nature has made it work! 

The bottom line here (for science, citizens, and investors) is to keep the enthusiasm under control when making promises or pronouncements.  Stay closer to the truth.  And work harder before drawing conclusions.

Sooner or later technology and engineering often do succeed, and it's dangerous to bet against them.   But not everything works, and it's hard to know in advance what will.  Hopefully something as specifically targeted as RNAi will find useful biomedical or other application eventually, but without the hype.