From DNA’s dark corners: fresh clues about depression

In recent years, the stigma around mental health disorders and especially struggling with depression has been gradually decreasing, particularly in Western societies. We see Olympic champions such as Michael Phelps, leading artists such as Jim Carrey and Lady Gaga, and even royalty, British Prince Harry, describing in public their struggles with depression. As more people openly speak about their mental suffering and about seeking support, public opinion is gradually shifting from seeing depression as a personal weakness or failure to accepting it as part of the spectrum of being human. This has led to viewing mental health disorders and depression in the same lens as any other health condition, a blessed shift that brings hope for a future of better well-being to mankind.

Did you know that depression has been ranked as a leading cause of disability by the World Health Organization? While heart disease will kill you, depression can torment you and lead to disability and reduced life quality. Depression is a highly prevalent disorder that strikes more than a quarter billion people worldwide yearly and is estimated to affect at least 5% of adults. Depression has been reported throughout mankind’s history, with a similar prevalence around the world, with some fluctuation of its rates by culture and major historical events. For example, in the first year of the COVID-19 pandemic, there was an increase of 25% in depression and its frequent companion, anxiety. This immense personal suffering extends to a large toll on society, estimated at around 250 billion dollars annually in the USA alone, both from medical services costs and loss of workplace productivity.

People suffering from depression report devastating psychological, physiological, and cognitive symptoms. Sadness and lack of ability to feel pleasure for more than 2 weeks are the core symptoms required for a diagnosis, according to the Psychiatric Diagnostic and Statistical Manual of Mental Disorders. These are often accompanied by an excessive sense of guilt, loneliness, hopelessness, and thoughts about death and suicide. Physiological symptoms may include fatigue, irritability, disturbed sleep, and appetite, with either excessive sleep and eating or insomnia and lack of appetite. Cognition is also affected by depression, with features like attention and decision-making hampered (Figure 1). While depression tends to have an episodic nature, hence striking for several months followed by a gradual recovery, in many cases, the symptoms will later return and manifest in a recurrent episode. Despite these crushing sets of symptoms, about a third of depression cases never seek out treatment.

Modern psychiatry has brought a lot of hope to people suffering from depression. In addition to a variety of psychological therapy approaches, there are several options for antidepressant medications. The first line of treatments includes famous drugs like Zoloft, Lexapro, or Prozac, which all regulate the levels of serotonin in the brain. These drugs are among the most prescribed medications in the USA and bring a lot of relief, but they have major limitations. One needs to take such medications for several weeks before seeing any effect, and they often require a long process of trial and error to find the appropriate drug and dose for a certain individual. Overall, antidepressants have low rates of response (feeling better) and remission (not being depressed anymore). Particularly challenging are individuals suffering from depression who do not respond to medication, then treated with more forceful drugs, like ketamine, and potentially psychedelics in the future, or brain stimulation approaches. There are two important points to highlight regarding antidepressants: First, they were discovered by chance as effective in reducing depression and are not based on research on the neuroscience or molecular mechanism of depression. Second, we do not have an objective biological biomarker to predict which intervention will work for a specific individual or to diagnose depression.

Depression researchers believe that if we better understand the neuroscience and molecular biology causing this disorder, we can then develop tools to prevent, diagnose, and treat it better. Many years of research suggest that the risk of developing depression has a genetic component of about 30%. This is a relatively limited heritable contribution compared to other mental health conditions like schizophrenia or autism. The other trigger for depression is life events, mainly exposure to chronic stress, for example, getting fired, divorced, or locked down due to a pandemic. This means that depression is caused by an interaction between genetic factors that set some individuals at higher risk, and environmental factors, like chronic stress, that trigger the onset of an episode. What is mediating this Gene X Environment interaction at the molecular level? This is where epigenetics comes into play.

While our DNA is pretty much the same across the different cell types in our body organs, the expression levels of specific genes are dramatically different between nerve cells and heart cells, for example. Epigenetics is a term for some key molecular processes that mediate changes in gene expression that are not determined by DNA sequence. These processes are part of the normal function of our body, turning on and off specific genes across body development, but they are also affected by environmental factors, including chronic stress. There are several types of epigenetic processes, and scientists keep discovering new ones. One important process is changes in the methylation of DNA, which can affect the expression levels of nearby genes. Another is modifications on histones, the proteins that DNA is wrapped around in the nucleus, which can open and close specific genetic segments to regulate their expression levels. The latest class of epigenetic regulators to be discovered is the kingdom of noncoding RNAs (Figure 2). In this short feature, the focus is on examples from microRNAs and long noncoding RNAs.

With the completion of the human genome project at the beginning of the 21st century, it was clear that as little as 2% of it is coding for proteins, considered at the time the main effectors in the cell. At first, the rest of the DNA was termed “junk,” but this large amount of junk compared to treasure raised some eyebrows. The fact that proteins are almost identical between humans, mice, and other mammals is unsettling. This suggests that the “dark side” of the genome that does not make proteins may have a functional role after all. Later developments in our ability to profile RNA in an unbiased manner and to make sense of expression screens with bioinformatic tools revealed that about 80% of human DNA turns into RNA. These RNA molecules give rise to tens of thousands of noncoding RNAs, defined negatively by the fact that they do not serve as a template for protein. These noncoding RNAs come in many flavors and are typically categorized by size, distinguishing shorter forms from longer ones (Figure 3). This year’s Nobel Prize in Physiology and Medicine for discovering a type of short noncoding RNA called microRNA is an additional validation of the importance of noncoding RNAs in biology.

One unique feature of noncoding RNAs is that their proportion in the genome of different animals increases along evolution. We can find the various classes of noncoding RNAs in simple creatures like worms, where microRNAs were discovered. However, DNA has more noncoding genes as the organisms' complexity scales. There is a big jump in mammals for some of the short RNAs and an even bigger increase in the number of long noncoding RNAs in our immediate ancestors’ primates. If that is not enough, many noncoding RNAs are enriched or exclusively expressed in the brain. One may wonder if these noncoding RNA are what makes our human brain this magnificent and powerful computer? Maybe the additional layer of noncoding RNA regulation supports our higher brain functions? Are noncoding RNAs what makes us human at the molecular level? If this is the case, when noncoding RNAs are out of control, we can experience brain disorders like, for example, depression.

Researchers have found roles in the brain for many members of the noncoding RNA kingdom. Here, I want to mention some of my recent findings on the robust regulation of long noncoding RNAs in depression because they focus on a unique aspect—sex differences. We have known for decades that depression strikes women twice as often as men, but the question of why has remained open. It turns out that long noncoding RNAs play a very important role in women’s risk for depression but can also protect them from chronic stress. In postmortem brain samples, we found that depression has an entirely different signature between the sexes, and this is particularly true when it comes to long noncoding RNAs. Our analysis suggested that hundreds of long noncoding RNAs are regulated in depression compared to healthy brains and in a sex-specific way. This is exciting because many of these RNAs are unique to the human brain and completely uncharacterized. We have systematically studied two examples of long noncoding RNAs—one called LINC00473 and the other that we named FEDORA. We focused our research on frontal brain regions that are expanded in human evolution and critical for higher brain functions. To make a long story short, we found that FEDORA is more abundant in the frontal brain regions only of women with depression compared to healthy controls. On the contrary, LINC00473 has lower levels in the frontal brain in depression. When we introduced their RNAs into mice’s respective brain sites, to our amazement, we found that FEDORA promoted features that resemble depression, while LINC00473 protected from chronic stress—only in females. These studies are just the tip of the iceberg, and there is much more to discover on the role of long noncoding RNAs and other RNAs in depression and its sex differences.

Noncoding RNAs are found in unexpected places, including body fluids, from blood, urine, saliva, cerebrospinal fluid, breast milk, and seminal fluid. In blood, microRNAs have emerged as promizing biomarkers for multiple conditions, including depression. Several approaches have been used to identify candidate microRNA biomarkers for depression, including studying animal models, examining postmortem brain tissue, and directly analyzing microRNAs in blood samples from patients. Some key microRNAs that have shown promize as diagnostic (telling if someone is depressed) or prognostic (telling which treatment may work) include miR-16 and miR-135a, which are involved in regulating the serotonin system, miR-1202, which was identified in postmortem brain studies, and Let-7, which is downregulated in the blood of depression patients. Few studies have explored changes in long noncoding RNAs in the blood in depression, including reports on global patterns of alternation in expression levels and changes in DNA methylation of noncoding cases compared to controls. Overall, this is an emerging area of study that may provide new insights into the biology of depression and possible ways to diagnose and monitor this condition.

Within body fluid, there is a unique pure fraction rich with noncoding RNAs, which has a lot of translational potential. These are extracellular vesicles, tiny membrane-wrapped structures released by cells. Once considered cellular waste, these vesicles are now seen as important messengers between cells and organs. Extracellular vesicles show promize as biomarkers for many diseases, including depression, because their contents, also called cargo, of proteins, noncoding RNAs (mostly short ones), and DNA, may reflect molecular processes of their source cells. Researchers have found differences in the size, number, and microRNA contents of extracellular vesicles between people with depression and healthy controls. Even more shocking are studies in mice, where transplanting extracellular vesicles between individuals changed mice’s behavior in stressful conditions depending on their noncoding RNA cargo. While much more work needs to be done, extracellular vesicles and their noncoding RNA cargo are potential avenues for RNA diagnostics and therapeutics in depression.

A peculiar outcome of the COVID-19 pandemic is that RNA is now a common-knowledge term. Billions of people worldwide were subjected to RNA diagnostics (with PCRs for viral RNA) and RNA therapeutics (with RNA-based vaccines). Together with the Nobel Prize in Physiology and Medicine for the discoveries at the foundation of the RNA vaccine for COVID-19, research on RNA-based clinical tools got boosted. This trend also brings hope to the mental health space and for depression (Figure 4). One can envision how we can use comprehensive profiling of noncoding RNAs in body fluids to diagnose depression, assign people to specific treatment groups, and assess if the treatment was effective. On the therapeutic side, manipulating expression levels of noncoding RNA using extracellular vesicles, antisense oligonucleotides, or gene therapy can open a whole new avenue for treatment.

Before the dream of noncoding RNAs and diagnostics and therapeutics for depression becomes a reality, much more research is needed. For the diagnostics, no single noncoding RNA has been shown to clearly distinguish depressed and control subjects at a clinically diagnostic level. For therapeutics, first, we need to identify specific and selective RNA targets that are unique to depression and not to other conditions. This is critical to ensure safety and minimize off-target effects. Second, delivery method progress is required to guide RNA molecules specifically to the target organ and cell type. This is especially challenging when targeting the brain, which requires penetrating the blood-brain barrier. The precedent of RNA therapy for neurological conditions has been made for spinal muscular atrophy. There, spinal delivery of antisense oligonucleotides corrects a genetic defect to modify an RNA. In turn, kids carrying such deadly genetic mutations now miraculously walk and live longer and better lives. I dream that in the future, we will have similar RNA-based clinical tools for depression and other mental health conditions.

• Depressive disorder (depression). The World Health Organization (WHO) https://www.who.int/news-room/fact-sheets/detail/depression

• RNA, the Epicenter of Genetic Information by John Mattick and Paulo https://www.taylorfrancis.com/books/oa-mono/10.1201/9781003109242/rna-epicenter-genetic-information-john-mattick-paulo-amaral

• Epigenetics, Development, and Psychopathology by Kieran J. O'Donnell, and Michael J. Meaney https://www.annualreviews.org/content/journals/10.1146/annurev-clinpsy-050718-095530

• Sex-Specific Role for the Long Non-coding RNA LINC00473 in Depression by Orna Issler, et al. https://www.cell.com/neuron/fulltext/S0896-6273(20)30230-0

• The rise of RNA therapeutics https://www.cshl.edu/the-rise-of-rna-therapeutics/

Perplexity was used to suggest grammar and spelling edits, search for synonyms and alternative phrasing, shorten the text, and to gather information in addition to PubMed and Google Scholar.

Figures 1 and 4 were made using BioRender and with the support of Apolline Savarit and Yentl van der Zee. Figure 2 was made by Jill Gregory, a medical illustrator at Icahn School of Medicine at Mount Sinai, NY.

Dr Orna Issler is an Assistant Professor at NYU Grosmann School of Medicine in New York City. She is a neuroscientist trained in Israel with a bachelor’s degree in both psychology and biology (Tel Aviv University), graduate work (Weizmann Institute of Science), and postdoctoral training in neuroscience (Icahn School of Medicine in Mount Sinai). Dr Issler’s research interests have been focused on how the mind and body meet, exploring the molecular mechanism of emotions in sickness and health. Specifically, Orna’s research focuses on the contribution of noncoding RNAs of different flavors to the response to chronic stress and depression. Email: [email protected]. Twitter: @IsslerOrna