Environmental Factor – May 2022: Science Moonshot: Now is the time to sequence RNA, expert says

Rick Woychik, Ph.D., NIEHS Director's Corner Rick Woychik, Ph.D., directs the NIEHS and the National Toxicology Program. (Image courtesy of NIEHS)

Almost two decades have passed since the publication of the first sequence of a complete set of DNA under the Human Genome Project. This initiative has broadened the understanding of certain cancers, enhanced the effectiveness of certain pharmaceuticals, and spurred the discovery of how genetic variation can influence disease, among other breakthroughs. Yet scientists are now learning that genomics is necessary but not sufficient to advance precision medicine and a deeper understanding of how our genes interact with the environment. This is where RNA comes in.

“RNA determines cellular identity and mediates responses to cellular needs,” the NIEHS grantee wrote. Vivian Cheung, MDfrom the University of Michigan, and colleagues in a commentary published last year in Natural genetics. “Such diverse cellular functions derive from the vast chemical composition of RNA comprising four [major] ribonucleotides…and over 140 modified ribonucleotides,” they explained.

Vivian Cheung, MD Cheung is a professor of pediatrics and genetics at the University of Michigan. (Photo courtesy of Vivian Cheung)

“Many years of RNA research have laid the foundation for the development of RNA-based therapies as diverse as antisense oligonucleotide therapy for spinal muscular atrophy and mRNA [messenger RNA] vaccines,” the authors continued. “[Such] achievements have been made possible by modified ribonucleotides, but the ‘true’ RNA sequence, i.e. the ‘RNome’, remains unknown. This key knowledge gap in understanding the building blocks of RNA needs to be filled.

I recently spoke with Cheung, a National Academy of Medicine researcher and pediatric neurologist, to find out why she thinks an effort similar to the Human Genome Project — but focused on RNA — would dramatically improve biomedical research. . Cheung explained why RNA changes, some of which are influenced by environmental exposures, represent a missing link in our understanding of genetic variation and the origins of disease.

She explained how Rnome sequencing will lead to new therapies, strengthen the scientific response to COVID-19 and even strengthen food safety. We talked about the promise of relevant technologies like nanopore sequencing, and I asked Cheung what inspired her to pursue a career as a medical researcher (see lateral bar).

Building knowledge to advance therapeutics

Rick Woychik: Can you explain why a better understanding of RNA is important for the advancement of biomedical research?

Viviane Cheung: Sure. Although your DNA sequence is different from mine, inside both of us our cells have the same DNA even though they have different functions. A lymphocyte, which is a type of immune cell, helps our body fight viruses, whereas a motor neuron has a totally different shape and biological role. But the lymphocyte and the motor neuron have the same DNA. What allows them to have different functions? Much of this information is in RNA.

Although we have a basic understanding that RNA is the regulatory code for our cells, we don’t yet know the exact details of this code. It is difficult to study the function of RNA and how it regulates cellular processes because we do not have complete knowledge of its sequence. If RNA were a book, I would say that we read it with only a small part of the alphabet available. We can piece together the gist of the book, but we don’t know all the intricacies.

Many years ago, researchers believed that there was a one-to-one relationship between DNA and RNA – that RNA is just an exact copy of DNA. But it turns out to be much more complicated than that. While it is true that RNA is an exact copy of DNA when it is made, it changes very quickly. Today we know that there are more than 140 different modifications on RNA.

We also know that exposures to heavy metals, endocrine disruptors and arsenite can affect RNA changes. But is this a good biological response or what leads to cellular toxicity? We do not know yet. Until we know the complete RNA sequence – what I call the RNome – it will be very difficult to comprehensively assess the biological processes affected by exposures, and we will not understand how our cells and our genes are regulated. This lack of knowledge will limit the efforts of the biomedical community to develop effective therapies.

Genetic basis of Alzheimer’s disease

RW: Among other topics, your lab at the University of Michigan studies RNA processing and genetic variation caused by environmental stress. Can you tell us about some of your latest work?

resume: We recently discovered a non-coding RNA [ncRNA] which regulates the gene APOE, identified 30 years ago as the highest risk factor for Alzheimer’s disease. Today, we still have no APOE– targeted therapy for this disease. And until recently, when we discovered this lncRNA, it was not known how the gene is regulated. It’s important because we can’t target a gene for therapy if we don’t know how it’s controlled.

So this ncRNA is normally folded and part of the sequence is changed to prevent it from doing APOE, a gene that is normally made only in the liver and certain types of nervous system cells. But under stress, and it could be environmental stress, that RNA is unfolded to allow APOE to transcribe to respond to stress. By identifying this ncRNA and how it folds and changes, we begin to better understand the genetic basis of Alzheimer’s disease.

RNA Changes, COVID-19 and Food Safety

RW: This is fascinating, and it raises an important point, that a significant part of the genome is transcribed and produces RNA that does not make protein but still has a critically important biological function. In my opinion, better understanding these RNAs is a critical aspect of the RNome, and the ncRNA identified by your team is an excellent example of how this knowledge will advance biomedical research.

The other key components of the RNome involve identifying all the different types of mRNA present in each cell type and all the different RNA modifications. Can you explain why these are important aspects of the RNome?

resume: There are more than 140 different types of RNA modifications, and these are important in several ways, exemplified most recently by the mRNA vaccines developed during the COVID-19 pandemic. Vaccines in which the mRNA was not modified were found to be at least 48% less effective than those which were modified. The modification is necessary to ensure that the immune system responds properly to the COVID vaccine.

Another example involves the modification of m6A RNA. It has been linked to autoimmune diseases and cancer. There is now good evidence that heavy metals, endocrine disruptors, and arsenite decrease m6A in RNA in human cells, and I suspect that’s bad for the cells. A decrease in m6A may be one mechanism by which these toxins affect human health.

Interestingly, recent research has shown that m6A can affect barley’s propensity to absorb cadmium, a heavy metal, from soil. Thus, understanding m6A and other modifications could shed light not only on human diseases, but also on agricultural challenges and food security issues.

Coming back to the topic of COVID, I think we need a way for the scientific community to better respond to the pandemic, and RNA sequencing is one way to do that. After all, the disease is caused by an RNA virus, and there are 30 to 40 RNA bases in SARS-CoV-2 that are changed. Much remains to be learned about the implications of the virus. We can all just say, “Well, we have the mRNA vaccine, look what we’ve done. Or we can use the RNome project as a way to strengthen our scientific response, engage the public, and build trust in our research.

Innovation on the horizon

RW: In your opinion, which technologies are promising to advance the RNome?

resume: In the market today, we have nanopore technology, which is very promising. It involves tiny pores through which electrical currents pass. If you put the RNA through the pores, the RNA disrupts the current in different ways depending on its sequence, allowing direct RNA sequencing. However, the machine doesn’t know how to read all the RNA modifications, so the critical step at this point is to teach it to read them.

Vivian Cheung, MD “Our lab studies RNA processing in human cells,” Cheung’s website states. “We are interested in the basic mechanisms that contribute to variation in gene expression under normal physiological conditions and in response to stress. We use molecular and computational methods to study cellular processes in normal and diseased cells. (Photo courtesy of Vivian Cheung)

There is also mass spectrometry, which is a very precise way of identifying RNA. But to date, mass spectrometry cannot sequence long RNA. We can probably sequence 20 nucleotides. Given that our human DNA is made up of 3 billion nucleotides and RNA is much more complex than that, we are nowhere near where we need to be. Nevertheless, I am confident that in 10 years we will be able to easily sequence RNA.

I was just beginning my career when the human genome project was at its height, and I think most people at the time thought there was no way to sequence DNA, especially given the technological challenges at the time. Yet the researchers overcame these challenges. This is one of the reasons why I hope a large-scale initiative to sequence RNA will lead to innovation – perhaps even breakthrough technology that we cannot imagine today.

Quote: Alfonzo JD, Brown JA, Byers PH, Cheung VG, Maraia RJ, Ross RL. 2021. A call for direct full-length RNA sequencing to identify all changes. Nat Genet 53(8):1113–1116.

(Rick Woychik, Ph.D., directs the NIEHS and the National Toxicology Program.)

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