Posted on by Dr. Francis Collins
In the language of Morse code, the letter “S” is three short sounds and the letter “O” is three longer sounds. Put them together in the right order and you have a cry for help: S.O.S. Now an NIH-funded team of researchers has cracked a comparable code that specialized immune cells called macrophages use to signal and respond to a threat.
In fact, by “listening in” on thousands of macrophages over time, one by one, the researchers have identified not just a lone distress signal, or “word,” but a vocabulary of six words. Their studies show that macrophages use these six words at different times to launch an appropriate response. What’s more, they have evidence that autoimmune conditions can arise when immune cells misuse certain words in this vocabulary. This bad communication can cause them incorrectly to attack substances produced by the immune system itself as if they were a foreign invaders.
The findings, published recently in the journal Immunity, come from a University of California, Los Angeles (UCLA) team led by Alexander Hoffmann and Adewunmi Adelaja. As an example of this language of immunity, the video above shows in both frames many immune macrophages (blue and red). You may need to watch the video four times to see what’s happening (I did). Each time you run the video, focus on one of the highlighted cells (outlined in white or green), and note how its nuclear signal intensity varies over time. That signal intensity is plotted in the rectangular box at the bottom.
The macrophages come from a mouse engineered in such a way that cells throughout its body light up to reveal the internal dynamics of an important immune signaling protein called nuclear NFκB. With the cells illuminated, the researchers could watch, or “listen in,” on this important immune signal within hundreds of individual macrophages over time to attempt to recognize and begin to interpret potentially meaningful patterns.
On the left side, macrophages are responding to an immune activating molecule called TNF. On the right, they’re responding to a bacterial toxin called LPS. While the researchers could listen to hundreds of cells at once, in the video they’ve randomly selected two cells (outlined in white or green) on each side to focus on in this example.
As shown in the box in the lower portion of each frame, the cells didn’t respond in precisely the same way to the same threat, just like two people might pronounce the same word slightly differently. But their responses nevertheless show distinct and recognizable patterns. Each of those distinct patterns could be decomposed into six code words. Together these six code words serve as a previously unrecognized immune language!
Overall, the researchers analyzed how more than 12,000 macrophage cells communicated in response to 27 different immune threats. Based on the possible arrangement of temporal nuclear NFκB dynamics, they then generated a list of more than 900 pattern features that could be potential “code words.”
Using an algorithm developed decades ago for the telecommunications industry, they then monitored which of the potential words showed up reliably when macrophages responded to a particular threatening stimulus, such as a bacterial or viral toxin. This narrowed their list to six specific features, or “words,” that correlated with a particular response.
To confirm that these pattern features contained meaning, the team turned to machine learning. If they taught a computer just those six words, they asked, could it distinguish the external threats to which the computerized cells were responding? The answer was yes.
But what if the computer had five words available, instead of six? The researchers found that the computer made more mistakes in recognizing the stimulus, leading the team to conclude that all six words are indeed needed for reliable cellular communication.
To begin to explore the implications of their findings for understanding autoimmune diseases, the researchers conducted similar studies in macrophages from a mouse model of Sjögren’s syndrome, a systemic condition in which the immune system often misguidedly attacks cells that produce saliva and tears. When they listened in on these cells, they found that they used two of the six words incorrectly. As a result, they activated the wrong responses, causing the body to mistakenly perceive a serious threat and attack itself.
While previous studies have proposed that immune cells employ a language, this is the first to identify words in that language, and to show what can happen when those words are misused. Now that researchers have a list of words, the next step is to figure out their precise definitions and interpretations  and, ultimately, how their misuse may be corrected to treat immunological diseases.
 Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses. Adelaja A, Taylor B, Sheu KM, Liu Y, Luecke S, Hoffmann A. Immunity. 2021 May 11;54(5):916-930.e7.
 NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages. Cheng QJ, Ohta S, Sheu KM, Spreafico R, Adelaja A, Taylor B, Hoffmann A. Science. 2021 Jun 18;372(6548):1349-1353.
Overview of the Immune System (National Institute of Allergy and Infectious Diseases/NIH)
Sjögren’s Syndrome (National Institute of Dental and Craniofacial Research/NIH)
Alexander Hoffmann (UCLA)
NIH Support: National Institute of General Medical Sciences; National Institute of Allergy and Infectious Diseases
Posted on by Dr. Francis Collins
Spiders spin webs to catch insects for dinner. It turns out certain human immune cells, called neutrophils, do something similar to trap bacteria in people who develop sepsis, an uncontrolled, systemic infection that poses a major challenge in hospitals.
When activated to catch sepsis-causing bacteria or other pathogens, neutrophils rupture and spew sticky, spider-like webs made of DNA and antibacterial proteins. Here in red you see one of these so-called neutrophil extracellular traps (NETs) that’s ensnared Staphylococcus aureus (green), a type of bacteria known for causing a range of illnesses from skin infections to pneumonia.
Yet this image, which comes from Kandace Gollomp and Mortimer Poncz at The Children’s Hospital of Philadelphia, is much more than a fascinating picture. It demonstrates a potentially promising new way to treat sepsis.
The researchers’ strategy involves adding a protein called platelet factor 4 (PF4), which is released by clot-forming blood platelets, to the NETs. PF4 readily binds to NETs and enhances their capture of bacteria. A modified antibody (white), which is a little hard to see, coats the PF4-bound NET above. This antibody makes the NETs even better at catching and holding onto bacteria. Other immune cells then come in to engulf and clean up the mess.
Until recently, most discussions about NETs assumed they were causing trouble, and therefore revolved around how to prevent or get rid of them while treating sepsis. But such strategies faced a major obstacle. By the time most people are diagnosed with sepsis, large swaths of these NETs have already been spun. In fact, destroying them might do more harm than good by releasing entrapped bacteria and other toxins into the bloodstream.
In a recent study published in the journal Blood, Gollomp’s team proposed flipping the script . Rather than prevent or destroy NETs, why not modify them to work even better to fight sepsis? Their idea: Make NETs even stickier to catch more bacteria. This would lower the number of bacteria and help people recover from sepsis.
Gollomp recalled something lab member Anna Kowalska had noted earlier in unrelated mouse studies. She’d observed that high levels of PF4 were protective in mice with sepsis. Gollomp and her colleagues wondered if the PF4 might also be used to reinforce NETs. Sure enough, Gollomp’s studies showed that PF4 will bind to NETs, causing them to condense and resist break down.
Subsequent studies in mice and with human NETs cast in a synthetic blood vessel suggest that this approach might work. Treatment with PF4 greatly increased the number of bacteria captured by NETs. It also kept NETs intact and holding tightly onto their toxic contents. As a result, mice with sepsis fared better.
Of course, mice are not humans. More study is needed to see if the same strategy can help people with sepsis. For example, it will be important to determine if modified NETs are difficult for the human body to clear. Also, Gollomp thinks this approach might be explored for treating other types of bacterial infections.
Still, the group’s initial findings come as encouraging news for hospital staff and administrators. If all goes well, a future treatment based on this intriguing strategy may one day help to reduce the 270,000 sepsis-related deaths in the U.S. and its estimated more than $24 billion annual price tag for our nation’s hospitals [2, 3].
 Fc-modified HIT-like monoclonal antibody as a novel treatment for sepsis. Gollomp K, Sarkar A, Harikumar S, Seeholzer SH, Arepally GM, Hudock K, Rauova L, Kowalska MA, Poncz M. Blood. 2020 Mar 5;135(10):743-754.
 Sepsis, Data & Reports, Centers for Disease Control and Prevention, Feb. 14, 2020.
 National inpatient hospital costs: The most expensive conditions by payer, 2013: Statistical Brief #204. Torio CM, Moore BJ. Healthcare Cost and Utilization Project (HCUP) Statistical Briefs. Agency for Healthcare Research and Quality (US); 2016 May.
Sepsis (National Institute of General Medical Sciences/NIH)
Kandace Gollomp (The Children’s Hospital of Philadelphia, PA)
Mortimer Poncz (The Children’s Hospital of Philadelphia, PA)
NIH Support: National Heart, Lung, and Blood Institute
Posted on by Dr. Francis Collins
Many people who contract COVID-19 have only a mild illness, or sometimes no symptoms at all. But others develop respiratory failure that requires oxygen support or even a ventilator to help them recover . It’s clear that this happens more often in men than in women, as well as in people who are older or who have chronic health conditions. But why does respiratory failure also sometimes occur in people who are young and seemingly healthy?
A new study suggests that part of the answer to this question may be found in the genes that each one of us carries . While more research is needed to pinpoint the precise underlying genes and mechanisms responsible, a recent genome-wide association (GWAS) study, just published in the New England Journal of Medicine, finds that gene variants in two regions of the human genome are associated with severe COVID-19 and correspondingly carry a greater risk of COVID-19-related death.
The two stretches of DNA implicated as harboring risks for severe COVID-19 are known to carry some intriguing genes, including one that determines blood type and others that play various roles in the immune system. In fact, the findings suggest that people with blood type A face a 50 percent greater risk of needing oxygen support or a ventilator should they become infected with the novel coronavirus. In contrast, people with blood type O appear to have about a 50 percent reduced risk of severe COVID-19.
These new findings—the first to identify statistically significant susceptibility genes for the severity of COVID-19—come from a large research effort led by Andre Franke, a scientist at Christian-Albrecht-University, Kiel, Germany, along with Tom Karlsen, Oslo University Hospital Rikshospitalet, Norway. Their study included 1,980 people undergoing treatment for severe COVID-19 and respiratory failure at seven medical centers in Italy and Spain.
In search of gene variants that might play a role in the severe illness, the team analyzed patient genome data for more than 8.5 million so-called single-nucleotide polymorphisms, or SNPs. The vast majority of these single “letter” nucleotide substitutions found all across the genome are of no health significance, but they can help to pinpoint the locations of gene variants that turn up more often in association with particular traits or conditions—in this case, COVID-19-related respiratory failure. To find them, the researchers compared SNPs in people with severe COVID-19 to those in more than 1,200 healthy blood donors from the same population groups.
The analysis identified two places that turned up significantly more often in the individuals with severe COVID-19 than in the healthy folks. One of them is found on chromosome 3 and covers a cluster of six genes with potentially relevant functions. For instance, this portion of the genome encodes a transporter protein known to interact with angiotensin converting enzyme 2 (ACE2), the surface receptor that allows the novel coronavirus that causes COVID-19, SARS-CoV-2, to bind to and infect human cells. It also encodes a collection of chemokine receptors, which play a role in the immune response in the airways of our lungs.
The other association signal popped up on chromosome 9, right over the area of the genome that determines blood type. Whether you are classified as an A, B, AB, or O blood type, depends on how your genes instruct your blood cells to produce (or not produce) a certain set of proteins. The researchers did find evidence suggesting a relationship between blood type and COVID-19 risk. They noted that this area also includes a genetic variant associated with increased levels of interleukin-6, which plays a role in inflammation and may have implications for COVID-19 as well.
These findings, completed in two months under very difficult clinical conditions, clearly warrant further study to understand the implications more fully. Indeed, Franke, Karlsen, and many of their colleagues are part of the COVID-19 Host Genetics Initiative, an ongoing international collaborative effort to learn the genetic determinants of COVID-19 susceptibility, severity, and outcomes. Some NIH research groups are taking part in the initiative, and they recently launched a study to look for informative gene variants in 5,000 COVID-19 patients in the United States and Canada.
The hope is that these and other findings yet to come will point the way to a more thorough understanding of the biology of COVID-19. They also suggest that a genetic test and a person’s blood type might provide useful tools for identifying those who may be at greater risk of serious illness.
 Characteristics of and important lessons from the Coronavirus Disease 2019 (COVID-19) outbreak in China: Summary of a report of 72 314 cases from the Chinese Center for Disease Control and Prevention. Wu Z, McGoogan JM, et. al. 2020 Feb 24. [published online ahead of print]
 Genomewide association study of severe Covid-19 with respiratory failure. Ellinghaus D, Degenhardt F, et. a. NEJM. June 17, 2020.
Andre Franke (Christian-Albrechts-University of Kiel, Germany)
Tom Karlsen (Oslo University Hospital Rikshospitalet, Norway)
Posted on by Dr. Francis Collins
If you’ve spent time with individuals affected with Alzheimer’s disease (AD), you might have noticed that some people lose their memory and other cognitive skills more slowly than others. Why is that? New findings indicate that at least part of the answer may lie in differences in their immune responses.
Researchers have now found that slower loss of cognitive skills in people with AD correlates with higher levels of a protein that helps immune cells clear plaque-like cellular debris from the brain . The efficiency of this clean-up process in the brain can be measured via fragments of the protein that shed into the cerebrospinal fluid (CSF). This suggests that the protein, called TREM2, and the immune system as a whole, may be promising targets to help fight Alzheimer’s disease.
The findings come from an international research team led by Michael Ewers, Institute for Stroke and Dementia Research, Ludwig-Maximilians-Universität München, Germany, and Christian Haass, Ludwig-Maximilians-Universität München, Germany and German Center for Neurodegenerative Diseases. The researchers got interested in TREM2 following the discovery several years ago that people carrying rare genetic variants for the protein were two to three times more likely to develop AD late in life.
Not much was previously known about TREM2, so this finding from a genome wide association study (GWAS) was a surprise. In the brain, it turns out that TREM2 proteins are primarily made by microglia. These scavenging immune cells help to keep the brain healthy, acting as a clean-up crew that clears cellular debris, including the plaque-like amyloid-beta that is a hallmark of AD.
In subsequent studies, Haass and colleagues showed in mouse models of AD that TREM2 helps to shift microglia into high gear for clearing amyloid plaques . This animal work and that of others helped to strengthen the case that TREM2 may play an important role in AD. But what did these data mean for people with this devastating condition?
There had been some hints of a connection between TREM2 and the progression of AD in humans. In the study published in Science Translational Medicine, the researchers took a deeper look by taking advantage of the NIH-funded Alzheimer’s Disease Neuroimaging Initiative (ADNI).
ADNI began more than a decade ago to develop methods for early AD detection, intervention, and treatment. The initiative makes all its data freely available to AD researchers all around the world. That allowed Ewers, Haass, and colleagues to focus their attention on 385 older ADNI participants, both with and without AD, who had been followed for an average of four years.
Their primary hypothesis was that individuals with AD and evidence of higher TREM2 levels at the outset of the study would show over the years less change in their cognitive abilities and in the volume of their hippocampus, a portion of the brain important for learning and memory. And, indeed, that’s exactly what they found.
In individuals with comparable AD, whether mild cognitive impairment or dementia, those having higher levels of a TREM2 fragment in their CSF showed a slower decline in memory. Those with evidence of a higher ratio of TREM2 relative to the tau protein in their CSF also progressed more slowly from normal cognition to early signs of AD or from mild cognitive impairment to full-blown dementia.
While it’s important to note that correlation isn’t causation, the findings suggest that treatments designed to boost TREM2 and the activation of microglia in the brain might hold promise for slowing the progression of AD in people. The challenge will be to determine when and how to target TREM2, and a great deal of research is now underway to make these discoveries.
Since its launch more than a decade ago, ADNI has made many important contributions to AD research. This new study is yet another fine example that should come as encouraging news to people with AD and their families.
 Increased soluble TREM2 in cerebrospinal fluid is associated with reduced cognitive and clinical decline in Alzheimer’s disease. Ewers M, Franzmeier N, Suárez-Calvet M, Morenas-Rodriguez E, Caballero MAA, Kleinberger G, Piccio L, Cruchaga C, Deming Y, Dichgans M, Trojanowski JQ, Shaw LM, Weiner MW, Haass C; Alzheimer’s Disease Neuroimaging Initiative. Sci Transl Med. 2019 Aug 28;11(507).
 Loss of TREM2 function increases amyloid seeding but reduces plaque-associated ApoE. Parhizkar S, Arzberger T, Brendel M, Kleinberger G, Deussing M, Focke C, Nuscher B, Xiong M, Ghasemigharagoz A, Katzmarski N, Krasemann S, Lichtenthaler SF, Müller SA, Colombo A, Monasor LS, Tahirovic S, Herms J, Willem M, Pettkus N, Butovsky O, Bartenstein P, Edbauer D, Rominger A, Ertürk A, Grathwohl SA, Neher JJ, Holtzman DM, Meyer-Luehmann M, Haass C. Nat Neurosci. 2019 Feb;22(2):191-204.
Alzheimer’s Disease and Related Dementias (National Institute on Aging/NIH)
Alzheimer’s Disease Neuroimaging Initiative (University of Southern California, Los Angeles)
Ewers Lab (University Hospital Munich, Germany)
Haass Lab (Ludwig-Maximilians-Universität München, Germany)
Institute for Stroke and Dementia Research (Munich, Germany)
NIH Support: National Institute on Aging
Posted on by Dr. Francis Collins
A big challenge in unlocking the mysteries of aging is how long you need to study humans, or even human cells, to get answers. But, in partnership with NASA, NIH is hoping that space will help facilitate this important area of research.
It’s already known, from what’s been seen in astronauts, that the weightless conditions found in space can speed various processes associated with aging. So, might it be possible to use the space station as a lab to conduct aging experiments?