viruses
How Double-Stranded RNA Protects the Brain Against Infection While Making Damaging Neuroinflammation More Likely
Posted on by Lawrence Tabak, D.D.S., Ph.D.
When you get a run-of-the-mill viral infection, after a few days of symptoms your immune system typically fends off the bug, and you’ll make a full recovery. In rare cases, a virus can infect the brain. This can lead to much bigger problems, including cognitive impairments known as “brain fog,” other neuropsychiatric symptoms, potentially irreversible brain damage, or even death. For this reason, the brain, more than other parts of the body, relies heavily on immune responses that can control viral infections immediately.
Now some intriguing findings from an NIH-funded team reported in Science Immunology help to explain how the brain is protected against infections.1 However, the findings also highlight a serious downside: these same mechanisms that protect the brain also leave it especially vulnerable to damaging levels of neuroinflammation.
The new findings may help to explain what goes on in the brains of people with a wide range of neurodegenerative conditions, including amyotrophic lateral sclerosis (ALS) and Alzheimer’s disease. They also point to promising targets for developing treatments that might turn inflammatory immune responses in the brain up or down, as desired, to treat these and other serious conditions.
How does it work? The key is double-stranded RNA (dsRNA).
RNA molecules are readouts of genetic information in DNA that carry instructions for building the proteins that carry out various cell functions. RNA molecules in our cells are most often in single-stranded or short dsRNA form. In contrast, lengthy dsRNAs are a hallmark of viruses. When a virus invades our cells, our immune system’s first line of defense can sense those long viral dsRNAs and trigger a response.
But it turns out that dsRNAs aren’t unique to viruses, as the new study highlights. The researchers, led by Tyler Dorrity and Heegwon Shin, both members of Hachung Chung’s lab at Columbia University Irving Medical Center, New York, found that human neurons—even when they’re normal and healthy—also have exceptionally high levels of long dsRNAs.
Their lab studies in cells and tissues show that these dsRNAs in neurons can trigger an inflammatory immune response just as they do in viruses. By manipulating neurons in a way that cut back on the number of dsRNAs, they found they could lower the innate immune response. However, cells with fewer dsRNAs also showed greater susceptibility to infection with Zika viruses and herpes simplex virus, which can produce a form of viral encephalitis.
The researchers also knew from earlier studies that people with a rare, inherited condition called Aicardi-Goutières syndrome (AGS), which primarily affects the brain and immune system, carry a mutation that causes their cells to lack an enzyme needed to edit dsRNAs. As a result, neurons carrying this mutation have so many dsRNAs that it is toxic.
They went on to show that they could shift this dynamic by altering levels of two other proteins that bind RNA. The proteins normally encourage dsRNA formation in the brain. When the researchers deleted these RNA-binding proteins from the AGS neurons, those neurons made fewer long dsRNAs, which in turn protected them from the inflammatory immune responses and allowed them to survive longer. As expected, however, those cells also were more susceptible to viral infection.
The findings show how this tricky balance between susceptibility to infection and inflammation in the brain works in both health and disease. It also leads to the tantalizing suggestion that treatments targeting these various players or others in the same pathways may offer new ways of treating brain infections or neuroinflammatory conditions, by boosting or dampening dsRNA levels and the associated immune responses. As a next step, the researchers report that they’re pursuing studies to explore the role of dsRNA-triggered immune responses in ALS and Alzheimer’s, as well as in neuropsychiatric symptoms sometimes seen in people with lupus.
References:
[1] TJ Dorrity TJ, et al. Long 3’UTRs predispose neurons to inflammation by promoting immunostimulatory double-stranded RNA formation. Science Immunology DOI: 10.1126/sciimmunol.adg2979 (2023).
NIH Support: National Institute of Neurological Disorders and Stroke, National Institute of Allergy and Infectious Diseases, National Institute of General Medical Sciences
Unraveling the Role of the Skin Microbiome in Health and Disease
Posted on by Lindsey A. Criswell, M.D., M.P.H., D.Sc., National Institute of Arthritis and Musculoskeletal and Skin Diseases
Human skin is home to diverse ecosystems including bacteria, viruses, and fungi. These microbial communities comprise hundreds of species and are collectively known as the skin microbiome. The skin microbiome is thought to play a vital role in fending off disease-causing microorganisms (pathogens), boosting barrier protection, and aiding immune defenses.
Maintaining a balanced skin microbiome involves a complex and dynamic interplay among microorganisms, immune cells, skin cells, and other factors. In general, bacteria far outnumber viral, fungal, or other microbial species on the skin. Bacterial communities, which are strongly influenced by conditions such as skin moisture, temperature, and pH, vary widely across the body. For example, facial cheek skin hosts mostly Cutibacterium along with a bit of the skin fungus Malassezia. The heel is colonized by different types of bacteria including Staphylococcus and Corynebacteria.
In some diseases, such as acne and eczema, the skin microbiome is altered. Typically, this means an increase in pathogenic microorganisms and a decrease in beneficial ones. An altered skin microbiome can also be associated with inflammation, severe disease symptoms, and changes in the human immune system.
Heidi H. Kong is working to understand the role of the skin microbiome in health and disease. She is a senior investigator in the Intramural Research Program at NIH’s National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) and an adjunct investigator at NIH’s National Cancer Institute (NCI).
More than a decade ago, Kong and Julie A. Segre, an intramural researcher at NIH’s National Human Genome Research Institute, analyzed the microbial makeup of healthy individuals. Kong swabbed the skin of these healthy volunteers in 20 different sites, from the forehead to the toenail. The study revealed that the surface of the human body provides various environmental niches, depending on whether the skin is moist, dry, or sebaceous (oily). Different bacterial species predominate in each niche. Kong and Segre were particularly interested in body areas that have predilections for disease. For example, psoriasis is often found on the outside of elbows and knees, and the back of the scalp.
Earlier this year, Kong and Segre published another broad analysis of the human skin microbiome [1] in collaboration with scientists at the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), United Kingdom. This new catalog, called the Skin Microbial Genome Collection, is thought to identify about 85 percent of the microorganisms present on healthy skin from 19 body sites. It documents more than 600 bacterial species—including 174 that were discovered during the study—as well as more than 6,900 viruses and some fungi, including three newly discovered species.
Kong’s work has provided compelling evidence that the human immune system plays a role in shaping the skin microbiome. In 2018, she, Segre, and colleagues from the intramural programs of NCI and NIH’s National Institute of Allergy and Infectious Diseases analyzed skin from eight different sites on 27 people with a rare primary immunodeficiency disease known as DOCK8 deficiency [2].
People with the condition have recurrent infections in the skin, sinuses, and airways, and are susceptible to different cancers. Kong and colleagues found that the skin of people with DOCK8 deficiency contains significantly more DNA viruses (90 percent of the skin microbiome on average) than people without the condition (6 or 7 percent of the skin microbiome).
Other researchers are hoping to leverage features of the microbiome to develop targeted therapies for skin diseases. Richard L. Gallo, a NIAMS grantee at the University of California, San Diego, is currently focused on acne and eczema (also called atopic dermatitis). Acne is associated with certain strains of Cutibacterium acnes (C. acnes, formerly called Propionibacterium acnes or P. acnes). Eczema is often associated with Staphylococcus aureus (S. aureus).
Severe cases of acne and eczema are commonly treated with broad-spectrum antibiotics, which wipe out most of the bacteria, including beneficial species. The goal of microbiome-targeted therapy is to kill only the disease-associated bacteria and avoid increasing the risk that some strains will develop antibiotic resistance.
In 2020, Gallo and colleagues identified a strain of Staphylococcus capitis from healthy human skin (S. capitis E12) that selectively inhibits the growth of C. acnes without negatively impacting other bacteria or human skin cells [3]. S. capitis E12 produces four different toxins that act together to target C. acnes. The research team created an extract of the four toxins and tested it using animal models. In most cases, the extract was more potent at killing C. acnes—including acne-associated strains—than several commonly prescribed antibiotics (erythromycin, tetracycline, and clindamycin). And, unlike antibiotics, the extract does not appear to promote drug-resistance, at least for the 20 generations observed by the researchers.
Eczema is a chronic, relapsing disease characterized by skin that is dry, itchy, inflamed, and prone to infection, including by pathogens such as S. aureus and herpes virus. Although the cause of eczema is unknown, the condition is associated with human genetic mutations, disruption of the skin’s barrier, inflammation-triggering allergens, and imbalances in the skin microbiome.
In 2017, Gallo’s research team discovered that, in healthy human skin, certain strains of Staphylococcus hominis and Staphylococcus epidermis produce potent antimicrobial molecules known as lantibiotics [4]. These beneficial strains are far less common on the skin of people with eczema. The lantibiotics work synergistically with LL-37, an antimicrobial molecule produced by the human immune system, to selectively kill S. aureus, including methicillin-resistant strains (MRSA).
Gallo and his colleagues then examined the safety and therapeutic potential of these beneficial strains isolated from the human skin microbiome. In animal tests, strains of S. hominis and S. epidermis that produce lantibiotics killed S. aureus and blocked production of its toxin.
Gallo’s group has now expanded their work to early studies in humans. In 2021, two independent phase 1 clinical trials [5,6] conducted by Gallo and his colleagues investigated the effects of these strains on people with eczema. These double-blind, placebo-controlled trials involved one-week of topical application of beneficial bacteria to the forearm of adults with S. aureus-positive eczema. The results demonstrated that the treatment was safe, showed a significant decrease in S. aureus, and improved eczema symptoms in most patients. This is encouraging news for those hoping to develop microbiome-targeted therapy for inflammatory skin diseases.
As research on the skin microbiome advances on different fronts, it will provide deeper insight into the multi-faceted microbial communities that are so critical to health and disease. One day, we may even be able to harness the microbiome as a source of therapeutics to alleviate inflammation, promote wound healing, or suppress certain skin cancers.
References:
[1] Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions. Saheb Kashaf S, Proctor DM, Deming C, Saary P, Hölzer M; NISC Comparative Sequencing Program, Taylor ME, Kong HH, Segre JA, Almeida A, Finn RD. Nat Microbiol. 2022 Jan;7(1):169-179.
[2] Expanded skin virome in DOCK8-deficient patients. Tirosh O, Conlan S, Deming C, Lee-Lin SQ, Huang X; NISC Comparative Sequencing Program, Su HC, Freeman AF, Segre JA, Kong HH. Nat Med. 2018 Dec;24(12):1815-1821.
[3] Identification of a human skin commensal bacterium that selectively kills Cutibacterium acnes. O’Neill AM, Nakatsuji T, Hayachi A, Williams MR, Mills RH, Gonzalez DJ, Gallo RL. J Invest Dermatol. 2020 Aug;140(8):1619-1628.e2.
[4] Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis. Nakatsuji T, Chen TH, Narala S, Chun KA, Two AM, Yun T, Shafiq F, Kotol PF, Bouslimani A, Melnik AV, Latif H, Kim JN, Lockhart A, Artis K, David G, Taylor P, Streib J, Dorrestein PC, Grier A, Gill SR, Zengler K, Hata TR, Leung DY, Gallo RL. Sci Transl Med. 2017 Feb 22;9(378):eaah4680.
[5] Development of a human skin commensal microbe for bacteriotherapy of atopic dermatitis and use in a phase 1 randomized clinical trial. Nakatsuji T, Hata TR, Tong Y, Cheng JY, Shafiq F, Butcher AM, Salem SS, Brinton SL, Rudman Spergel AK, Johnson K, Jepson B, Calatroni A, David G, Ramirez-Gama M, Taylor P, Leung DYM, Gallo RL. Nat Med. 2021 Apr;27(4):700-709.
[6] Use of autologous bacteriotherapy to treat Staphylococcus aureus in patients with atopic dermatitis: A randomized double-blind clinical trial. Nakatsuji T, Gallo RL, Shafiq F, Tong Y, Chun K, Butcher AM, Cheng JY, Hata TR. JAMA Dermatol. 2021 Jun 16;157(8):978-82.
Links:
Acne (National Institute of Arthritis and Musculoskeletal and Skin Diseases/NIH)
Atopic Dermatitis (NIAMS)
Cutaneous Microbiome and Inflammation Laboratory, Heidi Kong (NIAMS)
Julie Segre (National Human Genome Research Institute/NIH)
Gallo Lab (University of California, San Diego)
[Note: Acting NIH Director Lawrence Tabak has asked the heads of NIH’s Institutes and Centers (ICs) to contribute occasional guest posts to the blog to highlight some of the cool science that they support and conduct. This is the fifth in the series of NIH IC guest posts that will run until a new permanent NIH director is in place.]
Possible Explanation for Why Some People Get More Colds
Posted on by Dr. Francis Collins
Getty Images/yourstockbank
Colds are just an occasional nuisance for many folks, but some individuals seem to come down with them much more frequently. Now, NIH-funded researchers have uncovered some new clues as to why.
In their study, the researchers found that the cells that line our airways are quite adept at defending against cold-causing rhinoviruses. But there’s a tradeoff. When these cells are busy defending against tissue damage due to cigarette smoke, pollen, pollutants, and/or other airborne irritants, their ability to fend off such viruses is significantly reduced [1].
The new findings may open the door to better strategies for preventing the common cold, as well as other types of respiratory tract infections caused by non-flu viruses. Even small improvements in prevention could have big implications for our nation’s health and economy. Every year, Americans come down with more than 500 million colds and similar infections, leading to reduced work productivity, medical expenses, and other costs approaching $40 billion [2].
NIH Research Festival
Posted on by Dr. Francis Collins
We kicked off the 32nd NIH Research Festival on September 12, 2018. This annual three-day event showcases the incredible breadth of research conducted by NIH scientists. I offered some opening remarks, holding up this 3D model of the flu virus to highlight work underway on the NIH campus to better map viral structures. Credit: NIH
A Scientist Whose Music Gives Comfort
Posted on by Dr. Francis Collins
Over the past few years, my blog has highlighted a wide range of Creative Minds from across biomedical research. But creative minds come in many forms, and, for a change of pace, I’d like to kick back this August and highlight some talented scientists who are also doing amazing things in the arts, from abstract painting to salsa dancing to rock’n’roll.
My first post introduces you to Dr. Pardis Sabeti, a computational geneticist at the Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, and one of Time Magazine’s 2014 People of the Year for her work to contain the last major Ebola outbreak in West Africa. When she’s not in the lab studying viruses, Sabeti is the hard-driving voice of the indie rock band Thousand Days that has been rocking Boston for more than a decade.
Gene Expression Test Aims to Reduce Antibiotic Overuse
Posted on by Dr. Francis Collins
Caption: Duke physician-scientist Ephraim Tsalik assesses a patient for a respiratory infection.
Credit: Shawn Rocco/Duke Health
Without doubt, antibiotic drugs have saved hundreds of millions of lives from bacterial infections that would have otherwise been fatal. But their inappropriate use has led to the rise of antibiotic-resistant superbugs, which now infect at least 2 million Americans every year and are responsible for thousands of deaths [1]. I’ve just come from the World Economic Forum in Davos, Switzerland, where concerns about antibiotic resistance and overuse was a topic of conversation. In fact, some of the world’s biggest pharmaceutical companies issued a joint declaration at the forum, calling on governments and industry to work together to combat this growing public health threat [2].
Many people who go to the doctor suffering from respiratory symptoms expect to be given a prescription for antibiotics. Not only do such antibiotics often fail to help, they serve to fuel the development of antibiotic-resistant superbugs [3]. That’s because antibiotics are only useful in treating respiratory illnesses caused by bacteria, and have no impact on those caused by viruses (which are frequent in the wintertime). So, I’m pleased to report that a research team, partially supported by NIH, recently made progress toward a simple blood test that analyzes patterns of gene expression to determine if a patient’s respiratory symptoms likely stem from a bacterial infection, viral infection, or no infection at all.
In contrast to standard tests that look for signs of a specific infectious agent—respiratory syncytial virus (RSV) or the influenza virus, for instance—the new strategy casts a wide net that takes into account changes in the patterns of gene expression in the bloodstream, which differ depending on whether a person is fighting off a bacterial or a viral infection. As reported in Science Translational Medicine [4], Geoffrey Ginsburg, Christopher Woods, and Ephraim Tsalik of Duke University’s Center for Applied Genomics and Precision Medicine, Durham, NC, and their colleagues collected blood samples from 273 people who came to the emergency room (ER) with signs of acute respiratory illness. Standard diagnostic tests showed that 70 patients arrived in the ER with bacterial infections and 115 were battling viruses. Another 88 patients had no signs of infection, with symptoms traced instead to other health conditions.
