Past Stories
Millions of Single-Cell Analyses Yield Most Comprehensive Human Cell Atlas Yet
Posted on by Lawrence Tabak, D.D.S., Ph.D.
There are 37 trillion or so cells in our bodies that work together to give us life. But it may surprise you that we still haven’t put a good number on how many distinct cell types there are within those trillions of cells.
That’s why in 2016, a team of researchers from around the globe launched a historic project called the Human Cell Atlas (HCA) consortium to identify and define the hundreds of presumed distinct cell types in our bodies. Knowing where each cell type resides in the body, and which genes each one turns on or off to create its own unique molecular identity, will revolutionize our studies of human biology and medicine across the board.
Since its launch, the HCA has progressed rapidly. In fact, it has already reached an important milestone with the recent publication in the journal Science of four studies that, together, comprise the first multi-tissue drafts of the human cell atlas. This draft, based on analyses of millions of cells, defines more than 500 different cell types in more than 30 human tissues. A second draft, with even finer definition, is already in the works.
Making the HCA possible are recent technological advances in RNA sequencing. RNA sequencing is a topic that’s been mentioned frequently on this blog in a range of research areas, from neuroscience to skin rashes. Researchers use it to detect and analyze all the messenger RNA (mRNA) molecules in a biological sample, in this case individual human cells from a wide range of tissues, organs, and individuals who voluntarily donated their tissues.
By quantifying these RNA messages, researchers can capture the thousands of genes that any given cell actively expresses at any one time. These precise gene expression profiles can be used to catalogue cells from throughout the body and understand the important similarities and differences among them.
In one of the published studies, funded in part by the NIH, a team co-led by Aviv Regev, a founding co-chair of the consortium at the Broad Institute of MIT and Harvard, Cambridge, MA, established a framework for multi-tissue human cell atlases [1]. (Regev is now on leave from the Broad Institute and MIT and has recently moved to Genentech Research and Early Development, South San Francisco, CA.)
Among its many advances, Regev’s team optimized single-cell RNA sequencing for use on cell nuclei isolated from frozen tissue. This technological advance paved the way for single-cell analyses of the vast numbers of samples that are stored in research collections and freezers all around the world.
Using their new pipeline, Regev and team built an atlas including more than 200,000 single-cell RNA sequence profiles from eight tissue types collected from 16 individuals. These samples were archived earlier by NIH’s Genotype-Tissue Expression (GTEx) project. The team’s data revealed unexpected differences among cell types but surprising similarities, too.
For example, they found that genetic profiles seen in muscle cells were also present in connective tissue cells in the lungs. Using novel machine learning approaches to help make sense of their data, they’ve linked the cells in their atlases with thousands of genetic diseases and traits to identify cell types and genetic profiles that may contribute to a wide range of human conditions.
By cross-referencing 6,000 genes previously implicated in causing specific genetic disorders with their single-cell genetic profiles, they identified new cell types that may play unexpected roles. For instance, they found some non-muscle cells that may play a role in muscular dystrophy, a group of conditions in which muscles progressively weaken. More research will be needed to make sense of these fascinating, but vital, discoveries.
The team also compared genes that are more active in specific cell types to genes with previously identified links to more complex conditions. Again, their data surprised them. They identified new cell types that may play a role in conditions such as heart disease and inflammatory bowel disease.
Two of the other papers, one of which was funded in part by NIH, explored the immune system, especially the similarities and differences among immune cells that reside in specific tissues, such as scavenging macrophages [2,3] This is a critical area of study. Most of our understanding of the immune system comes from immune cells that circulate in the bloodstream, not these resident macrophages and other immune cells.
These immune cell atlases, which are still first drafts, already provide an invaluable resource toward designing new treatments to bolster immune responses, such as vaccines and anti-cancer treatments. They also may have implications for understanding what goes wrong in various autoimmune conditions.
Scientists have been working for more than 150 years to characterize the trillions of cells in our bodies. Thanks to this timely effort and its advances in describing and cataloguing cell types, we now have a much better foundation for understanding these fundamental units of the human body.
But the latest data are just the tip of the iceberg, with vast flows of biological information from throughout the human body surely to be released in the years ahead. And while consortium members continue making history, their hard work to date is freely available to the scientific community to explore critical biological questions with far-reaching implications for human health and disease.
References:
[1] Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. Eraslan G, Drokhlyansky E, Anand S, Fiskin E, Subramanian A, Segrè AV, Aguet F, Rozenblatt-Rosen O, Ardlie KG, Regev A, et al. Science. 2022 May 13;376(6594):eabl4290.
[2] Cross-tissue immune cell analysis reveals tissue-specific features in humans. Domínguez Conde C, Xu C, Jarvis LB, Rainbow DB, Farber DL, Saeb-Parsy K, Jones JL,Teichmann SA, et al. Science. 2022 May 13;376(6594):eabl5197.
[3] Mapping the developing human immune system across organs. Suo C, Dann E, Goh I, Jardine L, Marioni JC, Clatworthy MR, Haniffa M, Teichmann SA, et al. Science. 2022 May 12:eabo0510.
Links:
Ribonucleic acid (RNA) (National Human Genome Research Institute/NIH)
Studying Cells (National Institute of General Medical Sciences/NIH)
Regev Lab (Broad Institute of MIT and Harvard, Cambridge, MA)
NIH Support: Common Fund; National Cancer Institute; National Human Genome Research Institute; National Heart, Lung, and Blood Institute; National Institute on Drug Abuse; National Institute of Mental Health; National Institute on Aging; National Institute of Allergy and Infectious Diseases; National Institute of Neurological Disorders and Stroke; National Eye Institute
Welcome to Response Team Members
Posted on by Lawrence Tabak, D.D.S., Ph.D.
Artificial Pancreas Improves Blood Glucose Control in Young Kids with Type 1 Diabetes
Posted on by Lawrence Tabak, D.D.S., Ph.D.
Last week brought some great news for parents of small children with type 1 diabetes (T1D). It involved what’s called an “artificial pancreas,” a new type of device to monitor continuously a person’s blood glucose levels and release the hormone insulin at the right time and at the right dosage, much like the pancreas does in kids who don’t have T1D.
Researchers published last week in the New England Journal of Medicine [1] the results of the largest clinical trial yet of an artificial pancreas technology in small children, ages 2 to 6. The data showed that their Control-IQ technology was safe and effective over several weeks at controlling blood glucose levels in these children. In fact, the new device performed better than the current standard of care.
Two previous clinical trials of the Control-IQ technology had shown the same in older kids and adults, age 6 and up [2,3], and the latest clinical trial, one of the first in young kids, should provide the needed data for the U. S. Food and Drug Administration (FDA) to consider whether to extend the age range approved to use this artificial pancreas. The FDA earlier approved two other artificial pancreas devices—the MiniMed 770G and the Insulet Omnipod 5 systems—for use in children age 2 and older [4,5].
The Control-IQ clinical trial results are a culmination of more than a decade-long effort by the NIH’s National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) and many others to create technologies, such as an artificial pancreas, to improve blood glucose control. The reason is managing blood glucose levels remains critical for the long-term health of people with T1D.
What exactly is an artificial pancreas? It consists of three fully integrated components: a glucose monitor, an insulin pump, and a computer algorithm that allows the other two components to communicate. This automation frees people with T1D from checking their blood glucose levels multiple times a day and from many insulin dosing decisions, though they still interact with the system at mealtimes.
In this clinical trial, led by Marc D. Breton, University of Virginia School of Medicine, Charlottesville, researchers tested their Control-IQ technology (manufactured by Tandem Diabetes Care, San Diego, CA), also known as a hybrid closed-loop control system. Thanks to an algorithm developed at the University of Virginia Center for Diabetes Technology, insulin doses are administered automatically every few minutes based on readings from a continuous glucose monitor.
But treating younger children with T1D presents its own set of age-specific challenges. Younger kids generally require smaller doses of insulin more frequently. They also tend to have a more unpredictable schedule with lots of small snacks and random bursts of physical activity.
On top of all that, these young children have a tougher time than kids a few years older when it comes to understanding their own needs and letting the adults around them know when they need help. For all these reasons, young children with T1D tend to spend a greater proportion of time than older kids or adults do with blood glucose levels that are higher, or lower, than they should be. The hope was that the artificial pancreas might help to simplify things.
To find out, the trial enrolled 102 volunteers between ages 2 and 6. Sixty-eight were randomly assigned to receive the artificial pancreas, while the other 34 continued receiving insulin via either an insulin pump or multiple daily injections. The primary focus was on how long kids in each group spent in the target blood glucose range of 70 to 180 milligrams per deciliter, as measured using a continuous glucose monitor.
During the trial’s 13 weeks, participants in the artificial pancreas group spent approximately three more hours per day with their blood glucose in a healthy range compared to the standard care group. The greatest difference in blood glucose control was seen at night while the children should have been sleeping, from 10 p.m. to 6 a.m. During this important period, children with the artificial pancreas spent 18 percent more time in normal blood glucose range than the standard care group. That’s key because nighttime control is especially challenging to maintain in children with T1D.
Overall, the findings show benefits to young children similar to those seen previously in older kids. Those benefits also were observed in kids regardless of age, racial or ethnic group, parental education, or family income.
In the artificial pancreas group, there were two cases of severe hypoglycemia (low blood glucose) compared to one case in the other group. One child in the artificial pancreas group also developed diabetic ketoacidosis, a serious complication in which the body doesn’t have enough insulin. These incidents, while unfortunate, happened infrequently and at similar rates in the two groups.
Interestingly, the trial took place during the COVID-19 pandemic. As a result, much of the training on use of the artificial pancreas system took place virtually. Breton notes that the success of the artificial pancreas under these circumstances is an important finding, especially considering that many kids with T1D live in areas that are farther from endocrinologists or other specialists.
Even with these clinical trials now completed and a few devices on the market, there’s still more work to be done. The NIDDK has plans to host a meeting in the coming months to discuss next steps, including outstanding research questions and other priorities. It’s all very good news for people with T1D, including young kids and their families.
References:
[1] Trial of hybrid closed-loop control in young children with type 1 diabetes. Wadwa RP, Reed ZW, Buckingham BA, DeBoer MD, Ekhlaspour L, Forlenza GP, Schoelwer M, Lum J, Kollman C, Beck RW, Breton MD; PEDAP Trial Study Group. N Engl J Med. 2023 Mar 16;388(11):991-1001.
[2] A randomized trial of closed-loop control in children with type 1 diabetes. Breton MD, Kanapka LG, Beck RW, Ekhlaspour L, Forlenza GP, Cengiz E, Schoelwer M, Ruedy KJ, Jost E, Carria L, Emory E, Hsu LJ, Oliveri M, Kollman CC, Dokken BB, Weinzimer SA, DeBoer MD, Buckingham BA, Cherñavvsky D, Wadwa RP; iDCL Trial Research Group. N Engl J Med. 2020 Aug 27;383(9):836-845.
[3] Six-month randomized, multicenter trial of closed-loop control in type 1 diabetes. Brown SA, Kovatchev BP, Raghinaru D, Lum JW, Buckingham BA, Kudva YC, Laffel LM, Levy CJ, Pinsker JE, Wadwa RP, Dassau E, Doyle FJ 3rd, Anderson SM, Church MM, Dadlani V, Ekhlaspour L, Forlenza GP, Isganaitis E, Lam DW, Kollman C, Beck RW; N Engl J Med. 2019 Oct 31;381(18):1707-1717.
[4] MiniMed 770G System-P160017/S076. U. S. Food and Drug Administration, December 23, 2020.
[5] FDA authorizes Omnipod 5 for ages 2+ in children with type 1 diabetes. Juvenile Diabetes Research Foundation news release, August 22, 2022
Links:
Type I Diabetes (National Institute of Diabetes and Digestive and Kidney Diseases/NIH)
Artificial Pancreas (NIDDK)
Marc Breton (University of Virginia, Charlottesville)
NIH Support: National Institute of Diabetes and Digestive and Kidney Diseases
Discussing Trust in Science
Posted on by Lawrence Tabak, D.D.S., Ph.D.
What an honor it was for me to receive the 2023 John C. Porter Legacy Award. The award, which honors the late U.S. Congressman from Illinois who was strong advocate for biomedical research, is presented annually to a person who shows an outstanding commitment to sustain the nation’s world-class leadership in medical and health research. I’m humbled to be the award’s fifth recipient.
While there, I took part in a panel discussion titled Trust in Science. It explored the public’s perception of research and efforts to bolster trust in science. In this photo, you can see (l – r) the panel moderator Donna Shalala, the esteemed American academic, politician, and government administrator; Noubar Afeyan, founder and CEO, Flagship Pioneering, Cambridge, MA; Pamela Davis, Center for Community Health Integration, Case Western Reserve University School of Medicine, Cleveland, OH; Michael Friedlander, vice president, Health Sciences and Technology, Virginia Tech and executive director, Fralin Biomedical Research Institute at VTC, Roanoke, VA.; Heywood Fralin, chairman, Retirement Unlimited, Inc., Richmond, VA; followed by me, Larry Tabak; Lori Rose Benson, executive director and CEO, Hip Hop Public Health, New York, NY; and Olajide Williams, founder, Hip Hop Public Health. Credit: Research! America
Childhood Cancer: Novel Nanoparticle Shows Early Promise for Brain Tumor
Posted on by Lawrence Tabak, D.D.S., Ph.D.
The human brain is profoundly complex, consisting of tens of billions of neurons that form trillions of interconnections. This complex neural wiring that allows us to think, feel, move, and act is surrounded by what’s called the blood-brain barrier (BBB), a dense sheet of cells and blood vessels. The BBB blocks dangerous toxins and infectious agents from entering the brain, while allowing nutrients and other essential small molecules to pass right through.
This gatekeeping function helps to keep the brain healthy, but not when the barrier prevents potentially life-saving drugs from reaching aggressive, inoperable brain tumors. Now, an NIH-funded team reporting in the journal Nature Materials describes a promising new way to ferry cancer drugs across the BBB and reach the sites of disease [1]. While the researchers have not yet tried this new approach in people, they have some encouraging evidence from studies in mouse models of medulloblastoma, an aggressive brain cancer that’s diagnosed in hundreds of children each year.
The team, including Daniel Heller, Memorial Sloan Kettering Cancer Center, New York, NY, and Praveen Raju, Icahn School of Medicine at Mount Sinai, New York, NY, wanted to target a protein called P-selectin. The protein is found on blood vessel cells at sites of infection, injury, or inflammation, including cancers. The immune system uses such proteins to direct immune cells to the places where they are needed, allowing them to exit the bloodstream and enter other tissues.
Heller’s team thought they could take advantage of P-selectin and its molecular homing properties as a potential way to deliver cancer drugs to patients. But first they needed to package the drugs in particles tiny enough to stick to P-selectin like an immune cell.
That’s when they turned to a drug-delivery construct called a nanoparticle, which can have diameters a thousand times smaller than that of a human hair. But what’s pretty unique here is the nanoparticles are made from chains of sugar molecules called fucoidan, which are readily extracted from a type of brown seaweed that grows in Japan. It turns out that this unlikely ingredient has a special ability to attract P-selectin.
In the new study, the researchers decided to put their novel fucoidan nanoparticles to the test in the brain, while building on their previous animal work in the lungs [2]. That work showed that when fucoidan nanoparticles bind to P-selectin, they trigger a process that shuttles them across blood vessel walls.
This natural mechanism should also allow nanoparticle-packaged substances in the bloodstream to pass through vessel walls in the BBB and into the surrounding brain tissue. The hope was it would do so without damaging the BBB, a critical step for improving the treatment of brain tumors.
In studies with mouse models of medulloblastoma, the team loaded the nanoparticles with a cancer drug called vismodegib. This drug is approved for certain skin cancers and has been tested for medulloblastoma. The trouble is that the drug on its own comes with significant side effects in children at doses needed to effectively treat this brain cancer.
The researchers found that the vismodegib-loaded nanoparticles circulating in the mice could indeed pass through the intact BBB and into the brain. They further found that the particles accumulated at the site of the medulloblastoma tumors, where P-selectin was most abundant, and not in other healthy parts of the brain. In the mice, the approach allowed the vismodegib treatment to work better against the cancer and at lower doses with fewer side effects.
This raised another possibility. Radiation is a standard therapy for children and adults with brain tumors. The researcher found that radiation boosts P-selectin levels specifically in tumors. The finding suggests that radiation targeting specific parts of the brain prior to nanoparticle treatment could make it even more effective. It also may help to further limit the amount of cancer-fighting drug that reaches healthy brain cells and other parts of the body.
The fucoidan nanoparticles could, in theory, deliver many different drugs to the brain. The researchers note their promise for treating brain tumors of all types, including those that spread to the brain from other parts of the body. While much more work is needed, these seaweed-based nanoparticles may also help in delivering drugs to a wide range of other brain conditions, such as multiple sclerosis, stroke, and focal epilepsy, in which seizures arise from a specific part of the brain. It’s a discovery that brings new meaning to the familiar adage that good things come in small packages.
References:
[1] P-selectin-targeted nanocarriers induce active crossing of the blood-brain barrier via caveolin-1-dependent transcytosis. Tylawsky DE, Kiguchi H, Vaynshteyn J, Gerwin J, Shah J, Islam T, Boyer JA, Boué DR, Snuderl M, Greenblatt MB, Shamay Y, Raju GP, Heller DA. Nat Mater. 2023 Mar;22(3):391-399.
[2] P-selectin is a nanotherapeutic delivery target in the tumor microenvironment. Shamay Y, Elkabets M, Li H, Shah J, Brook S, Wang F, Adler K, Baut E, Scaltriti M, Jena PV, Gardner EE, Poirier JT, Rudin CM, Baselga J, Haimovitz-Friedman A, Heller DA. Sci Transl Med. 2016 Jun 29;8(345):345ra87.
Links:
Medulloblastoma Diagnosis and Treatment (National Cancer Institute/NIH)
Brain Basics: Know Your Brain (National Institute of Neurological Disorders and Stroke/NIH)
The Daniel Heller Lab (Memorial Sloan Kettering Cancer Center, New York, NY)
Praveen Raju (Mount Sinai, New York, NY)
NIH Support: National Cancer Institute; National Institute of Neurological Disorders and Stroke
Connecting the Dots: Oral Infection to Rheumatoid Arthritis
Posted on by Lawrence Tabak, D.D.S., Ph.D.
To keep your teeth and gums healthy for a lifetime, it’s important to brush and floss each day and see your dentist regularly. But what you might not often stop to consider is how essential good oral health really is to your overall well-being. The mouth, after all, is connected to the rest of the body, and oral infections can contribute to problems elsewhere.
A good case in point comes from a study just published in the journal Science Translational Medicine. The study, though small, offers some of the most convincing evidence yet for a direct link between gum, or periodontal, disease and the rheumatoid arthritis that flares most commonly in the hands, wrists, and knees [1]. If confirmed in larger follow-up studies, the finding suggests that one way for people with both diseases to contend with painful arthritic flare-ups will be to prevent them by practicing good oral hygiene and controlling their periodontal disease.
For many years, there had been suggestions that the oral bacteria causing periodontal disease might contribute to rheumatoid arthritis. For instance, past studies have found that periodontal disease occurs even more often in people with rheumatoid arthritis. People with both conditions also tend to have more severe arthritic symptoms that can be more stubbornly resistant to treatment.
What’s been missing is the precise underlying mechanisms to confirm the connection. To help connect the dots, a research team, which included Dana Orange, Rockefeller University, New York, NY, and William Robinson, Stanford University, Stanford, CA, decided to look closer.
They looked first in the blood, not directly at an arthritic joint or an inflamed periodontium, the tissues that hold a tooth in place. They were interested in whether telltale changes in the blood of people with rheumatoid arthritis correlated with the start of another painful flare-up in one or more of their joints.
One of those possible changes involves proteins that carry a particular chemical modification that places the amino acid citrulline on their surface. These citrulline-marked proteins are found in many parts of the human body, including the joints. Intriguingly, they also are present on bacteria, including those in the mouth.
Because of this bacterial connection, the researchers looked in the blood for a specific set of antibodies known as ACPAs, short for anti-citrullinated protein antibodies. They recognize citrullinated proteins that are foreign to the body and mark them for attack.
But the attack isn’t always perfectly aimed, and studies have shown the presence of ACPAs in the joints of people with rheumatoid arthritis is associated with increasing disease activity and more frequent arthritis flares. Periodontal disease, too, is especially common in people with rheumatoid arthritis who have abnormally high levels of circulating ACPAs.
In the new study, the researchers followed five women with rheumatoid arthritis for one to four years. Two of them had severe periodontal disease while the other three had no periodontal disease.
Each week, the study volunteers provided a small blood sample for researchers to study changes at the level of RNA, the genetic material that encodes proteins. They also studied changes in certain immune cells, along with any changes in their medication, dental care, or arthritis symptoms. For additional information, they also looked at blood and joint fluid samples from 67 other people with and without arthritis, including individuals with healthy gums or mild, moderate, or severe periodontal disease.
Overall, the evidence shows that people with more severe periodontal disease experienced repeated influxes of oral bacteria into their blood even when they hadn’t had a recent dental procedure. These findings suggested that when their inflamed gums became more damaged and “leaky,” bacteria in the mouth could spill into the bloodstream.
The researchers also found that those oral invaders carried many citrullinated proteins. Once they got into the bloodstream, inflammatory immune cells detected them and released ACPAs.
The researchers showed in the lab that those antibodies bind the same oral bacteria detected in the blood of people with periodontal disease and rheumatoid arthritis. In fact, those with both conditions had a wide variety of genetically distinct ACPAs, as would be expected if their immune systems were challenged repeatedly over time with oral bacteria.
The overarching idea is that these antibodies prime the immune system to attack oral bacteria. But after it gets started, the attack mistakenly expands and targets citrullinated proteins in the joints. That triggers a flare-up in a joint and the characteristic inflammation, stiffness, and joint damage.
While more study is needed to fill in the molecular details, this discovery raises an encouraging possibility. Taking care of your teeth and periodontal disease isn’t just a wise idea to maintain good oral health over a lifetime. For some of the approximately 1 million Americans with rheumatoid arthritis, it may help to manage and perhaps even prevent a painful flare-up in one or more of their affected joints.
Reference:
[1] Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis. Brewer RC, Lanz TV, Hale CR, Sepich-Poore GD, Martino C, Swafford AD, Carroll TS, Kongpachith S, Blum LK, Elliott SE, Blachere NE, Parveen S, Fak J, Yao V, Troyanskaya O, Frank MO, Bloom MS, Jahanbani S, Gomez AM, Iyer R, Ramadoss NS, Sharpe O, Chandrasekaran S, Kelmenson LB, Wang Q, Wong H, Torres HL, Wiesen M, Graves DT, Deane KD, Holers VM, Knight R, Darnell RB, Robinson WH, Orange DE. Sci Transl Med. 2023 Feb 22;15(684):eabq8476.
Links:
Rheumatoid Arthritis (National Institute of Arthritis and Musculoskeletal and Skin Diseases)
Periodontal (Gum) Disease (National Institute of Dental and Craniofacial Research/NIH)
Oral Hygiene (NIDCR)
Dana Orange (Rockefeller University, New York NY)
Robinson Lab (Stanford University, Stanford, CA)
NIH Support: National Institute of Arthritis and Musculoskeletal and Skin Diseases; National Institute of Allergy and Infectious Diseases; National Human Genome Research Institute; National Institute of General Medical Sciences; National Center for Advancing Translational Sciences; National Cancer Institute
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