- Before Columbus: A 4,000-Year-Old Skeleton Reveals a Rare Leprosy Strain in the Americas SciTechDaily
- 4,000-year-old Mycobacterium lepromatosis genomes from Chile reveal long establishment of Hansen’s disease in the Americas Nature
- Ancient DNA reveals rare leprosy strain existed in the Americas for millennia Phys.org
Category: 8. Health
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Before Columbus: A 4,000-Year-Old Skeleton Reveals a Rare Leprosy Strain in the Americas – SciTechDaily
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Gut microbiota signatures predict gestational diabetes in first trimester
A new study has identified early-pregnancy gut microbiota signatures associated with the development of gestational diabetes mellitus, a metabolic disorder that carries substantial risks to both maternal and fetal health. The study, published in the American Society for Microbiology journal Microbiology Spectrum, provides new avenues for gestational diabetes prevention and management.
Gestational diabetes is a prevalent metabolic disorder characterized by abnormal glucose metabolism, primarily in the mid to late stages of pregnancy. Early intervention for gestational diabetes can substantially reduce complications for both mother and baby. Gestational diabetes significantly increases the risk of maternal complications such as gestational hypertension, polyhydramnios, and cesarean delivery, while also posing long-term health risks for the fetus, including asphyxia at birth and increased susceptibility to obesity and diabetes in adulthood.
In the new study, researchers from The Second Hospital, Southern Medical University, and the Third Affiliated Hospital of Guangzhou Medical University, all in Guangzhou, China, set out to identify gut microbiota dysbiosis that is strongly linked to the onset and progression of gestational diabetes that may serve as a critical early-warning biomarker. The scientists analyzed the fecal microbiota of 61 pregnant women during their first trimester of pregnancy using 16S rRNA sequencing. They then correlated these microbial profiles with oral glucose tolerance test results at 24-28 weeks of gestation and clinical delivery outcomes.
The researchers discovered that there were significant differences in gut microbiota composition between those with gestational diabetes and women who had healthy pregnancies. Based on their findings, the researchers developed an early diagnostic model for gestational diabetes, based on genus-level markers, with high diagnostic precision.
“These findings suggest that microbiota-based tools could enable early, non-invasive detection of gestational diabetes mellitus, offering new opportunities for prevention and personalized management,” write the study authors. “This research highlights the role of the gut microbiome in pregnancy and has important implications for improving maternal and fetal health outcomes.”
Source:
American Society for Microbiology
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Brain cells can burn fat to fuel activity
While glucose, or sugar, is a well-known fuel for the brain, Weill Cornell Medicine researchers have demonstrated that electrical activity in synapses—the junctions between neurons where communication occurs—can lead to the use of lipid or fat droplets as an energy source.
The study, published July 1 in Nature Metabolism, challenges “the long-standing dogma that the brain doesn’t burn fat,” said principal investigator Dr. Timothy A. Ryan, professor of biochemistry and of biochemistry in anesthesiology, and the Tri-Institutional Professor in the Department of Biochemistry at Weill Cornell Medicine.
The paper’s lead author, Dr. Mukesh Kumar, a postdoctoral associate in biochemistry at Weill Cornell Medicine who has been studying the cell biology of fat droplets, suggested that it makes sense that fat may play a role as an energy source in the brain like it does with other metabolically demanding tissues, such as muscle.
The research team was particularly intrigued by the DDHD2 gene, which encodes a lipase, or enzyme that helps break down fat. Mutations in DDHD2 are linked to a type of hereditary spastic paraplegia, a neurological condition that causes progressive stiffness and weakness in the legs, in addition to cognitive deficits.
Prior research by other investigators has demonstrated that blocking this enzyme in mice causes a build-up of triglycerides—or fat droplets that store energy—throughout the brain. “To me, this was evidence that maybe the reason we claim the brain doesn’t burn fat is because we never see the fat stores,” Dr. Ryan said.
Research demonstrates lipids have an important role
The current study explored whether the lipid droplets that build up in the absence of DDHD2 are used as fuel by the brain, particularly when glucose isn’t present, Dr. Ryan said.
Dr. Kumar found that when a synapse contains a lipid droplet filled with triglycerides in mice without DDHD2, neurons can break down this fat into fatty acids and send it to the mitochondria—the cell’s energy factories—so they can produce adenosine triphosphate (ATP), the energy the cell needs to function.
The process of being able to use the fat is controlled by the electrical activity of the neurons, and I was shocked by this finding. If the neuron is busy, it drives this consumption. If it’s at rest, the process isn’t happening.”
Dr. Timothy A. Ryan, professor of biochemistry and of biochemistry in anesthesiology
In another study, researchers injected a small molecule into mice to block the enzyme carnitine palmitoyltransferase 1 (CPT1), which helps transport fatty acids into the mitochondria for energy production. Blocking CPT1 prevented the brain from using fat droplets, which then led to torpor, a hibernation-like state, in which the body temperature rapidly plummets and the heartbeat slows. “This response convinced us that that there’s an ongoing need for the brain to use these lipid droplets,” Dr. Ryan said.
Implications for future research
This research may encourage the further investigation of neurodegenerative conditions and the role of lipids in the brain. Glucose fluctuations or low levels of glucose can occur with aging or neurological disease, but fatty acids broken down from lipid droplets may help to maintain the brain’s energy, Dr. Kumar said. “We don’t know where this research will go in terms of neurodegenerative conditions, but some evidence suggests that accumulation of fat droplets in the neurons may occur in Parkinson’s disease,” he said.
Researchers also need to better understand the interplay between glucose and lipids in the brain, Dr. Ryan said. “By learning more about these molecular details, we hope to ultimately unlock explanations for neurodegeneration, which would give us opportunities for finding ways to protect the brain.”
This research was supported in part by the National Institute of Neurological Disorders and Stroke and the National Cancer Institute, both part of the National Institutes of Health, through grant numbers NS036942, NS11739 and F31CA278383. Additional support was provided by Aligning Science Across Parkinson’s through grant number ASAP-000580.
Source:
Journal reference:
Kumar, M., et al. (2025). Triglycerides are an important fuel reserve for synapse function in the brain. Nature Metabolism. doi.org/10.1038/s42255-025-01321-x.
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Younger children in school face higher mental health risks
Schoolchildren born late in the year are at greater risk of developing mental health problems compared with their older peers, according to a new study.
A recent study by the Norwegian University of Science and Technology (NTNU) has found that children born in October, November or December are statistically more often identified as having a mental health diagnosis than their classmates born earlier in the year. The findings apply to both boys and girls, and regardless of whether they were born full term or prematurely.
Extensive research material
The researchers have followed over one million Norwegians aged 4 to 17 years (all born between 1991 and 2012) through Norwegian health registries.
The aim of the study was to identify what are known as ‘relative age effects’. In other words, whether children and adolescents born late in the year are more frequently diagnosed with mental health disorders than their peers born early in the year (January, February and March).
Our findings show that the youngest members of a school class tend to be diagnosed with a mental illness more frequently than the oldest.
This is most obvious with regard to ADHD, where we saw an increase in incidence of 20-80 per cent for the youngest class members, depending on whether the children were born full term or prematurely.”
Christine Strand Bachmann, a PhD research fellow at the Norwegian University of Science and Technology (NTNU’s) Department of Public Health and Nursing
The researchers found the same trend for ‘other neuropsychiatric disorders’. These include delayed developments in areas such as language, academic skills and motor skills.
The study has been published in BMJ Peadiatrics Open.
Additional risks for premature girls
In addition, the youngest premature girls were at a significantly greater risk of being diagnosed with emotional disorders, such as anxiety, depression and adaptation disorders, compared with the oldest premature girls in the same year group.
“We know that children and adolescents born prematurely are already more vulnerable to poor mental and social health compared with children and young people born full term. For those born prematurely, the risks associated with being born late in the year comes in addition to this vulnerability.
“We believe that these findings, which show an increase in the number of psychological diagnoses for the youngest class members, can partly be linked to the way in which we organize our education system. The school system is unable to adequately provide for children with normal, but more immature behaviour. Possible solutions include flexible school start dates or additional support.”
In addition to being a researcher at NTNU, Christine Strand Bachmann is also a consultant at the Neonatal Intensive Care Unit, Children and Adolescent Medicine Department, St. Olavs Hospital.
Source:
Norwegian University of Science and Technology
Journal reference:
Bachmann, C. S., et al. (2025). Relative age as a risk factor for psychiatric diagnoses in children born preterm and to term: a cohort study. BMJ Paediatrics Open. doi.org/10.1136/bmjpo-2024-003186.
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Omega-6 Fatty Acids Do Not Raise Inflammatory Markers, Study Shows
In a large community-based study, researchers at Fatty Acid Research Institute observed weak but statistically significant inverse associations between several types of inflammatory biomarkers with omega-6 fatty acids.
This image shows Oenothera biennis, a flower that produces an oil containing a high content of linolenic acid. Image credit: Georg Slickers / CC BY-SA 4.0.
“Chronic inflammation is recognized as an important risk factor for a variety of health disorders,” said Fatty Acid Research Institute’s president William Harris and his colleagues.
“Omega-6 fatty acids, particularly linoleic (LA) and arachidonic acid (AA), have been shown to be either pro- or anti-inflammatory, and researchers have advocated both for and against reducing their dietary intake.”
The authors relied on data from the Framingham Offspring Study, a well-known research cohort from the Boston area.
The Framingham Offspring Study is a landmark longitudinal research initiative that follows the children of participants in the original Framingham Heart Study to investigate genetic and lifestyle factors influencing cardiovascular and metabolic health.
Launched in 1971, it has provided decades of valuable insights into chronic disease risk and prevention.
The cohort’s rigor and continuity make it one of the most trusted sources for understanding long-term health trajectories.
This was a cross-sectional study, meaning that the LA and AA levels were measured in the same blood samples as the 10 inflammation-related biomarkers in 2,700 individuals.
The relationships between the levels of these two omega-6 fatty acids and 10 separate blood/urine biomarkers of inflammation and oxidative stress were statistically evaluated.
After adjusting (controlling statistically) for multiple other potentially confounding factors (age, race, sex, smoking, blood lipid levels, blood pressure, body weight, etc.), the researchers found that higher LA levels were associated with statistically significantly lower levels of five of the 10 biomarkers, and in no case was higher LA related to higher levels of any biomarker.
For AA, higher levels were linked with lower concentrations of four markers, and, like LA, there were no statistically significant associations with higher levels of inflammation/oxidation.
“These new data show clearly that people who have the highest levels of LA (and AA) in their blood are in a less inflammatory state than people with lower levels,” Dr. Harris said.
“This finding is exactly the opposite of what one would expect if omega-6 fatty acids were ‘proinflammatory’ — in fact, they appear to be anti-inflammatory.”
“In the flurry of news stories about the harms of seed oils — the primary sources of LA in the diet — many voices are calling for reducing Americans’ intakes of LA.”
“This is not a science-based recommendation, and this study — in addition to many more — point in precisely the opposite direction: instead of lowering LA intakes, raising intakes appears to be a healthier recommendation.”
“These findings contradict a narrative, not previous research findings.”
“There are many studies in the medical literature that are consistent with our findings here.”
The study was published June 22 in the journal Nutrients.
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Heidi T.M. Lai et al. 2025. Red Blood Cell Omega-6 Fatty Acids and Biomarkers of Inflammation in the Framingham Offspring Study. Nutrients 17 (13): 2076; doi: 10.3390/nu17132076
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Epilepsy self-management program shows promising results
Epilepsy is among the most common neurological conditions, marked by unpredictable seizures, accidents and injuries, reduced quality of life, stigma and-in the worst case-premature death.
But a program-developed over several years by a Case Western Reserve University-led research team-that teaches people with epilepsy how to “self-manage” their disorder is showing positive results.
The program has been found to help people with epilepsy reduce related health complications and improve their mood and quality of life, according to a new study recently published in the peer-reviewed journal, Epilepsy & Behavior.
Results of this study provide a model for broad and practical expansion of the program to people with epilepsy.”
Martha Sajatovic, the L. Douglas Lenkoski MD Professor in Psychiatry at the Case Western Reserve University School of Medicine
Sajatovic, who co-led the study funded by the U.S. Centers for Disease Control and Prevention (CDC), is also the Willard Brown Chair in Neurological Outcomes Research and director of the Neurological and Behavioral Outcomes Center at University Hospitals Cleveland Medical Center. The study was also co-led by Gena Ghearing, formerly at the University of Iowa and now a professor of neurology at the Icahn School of Medicine at Mount Sinai in New York. Collaborators also included researchers at the University of Cincinnati.
Self-managing the disorder
Epilepsy is a chronic health condition triggered by abnormal electrical activity in the brain
in which individuals experience recurrent-and usually unpredictable-seizures. According to the CDC:
- 1.2% of the United States population has active epilepsy. That’s about 3 million adults and 470,000 children nationally.
- Epilepsy can last a lifetime and may be triggered by events like stroke and traumatic brain injury.
Given that people with chronic health conditions often have limited contact with their healthcare providers, self-management interventions have gained increasing attention for their potential benefit.
In particular, how well epilepsy patients manage the condition depends on their daily behavior, such as consistently taking medication, proper nutrition, exercise, stress management and avoiding activities or triggers that can make it more likely for seizures to occur, such as being sleep-deprived.
With that in mind, the CDC’s Managing Epilepsy Well (MEW) network has led the development, testing and growth of various successful epilepsy self-management approaches over the last dozen years.
Among them is a program Sajatovic and the Case Western Reserve team developed, called SMART, to support people with epilepsy who have experienced health complications, including poorly controlled seizures.
How it works
SMART features remote self-management training sessions for groups of six to 10 people with epilepsy. They meet by video conferencing for about an hour weekly for eight to 10 weeks.
The sessions are led by a nurse and “peer educator”-a person with epilepsy trained to deliver the detailed curriculum designed to help people learn to better manage and cope with their epilepsy and improve their overall well-being. Participants also get written resource materials to help them continue to practice refining their epilepsy self-management skills.
“Many people who participate in our SMART program have never been in a group with other people with epilepsy and find this a particularly valuable and rewarding part of the program,” Sajatovic said.
The study
SMART’s effectiveness was measured in two independent research studies. The published report summarizes the results of a clinical research study of 160 people with epilepsy. Half used the SMART program; half did not.
Compared to the control group, people with epilepsy who participated in the SMART program demonstrated reduced complications of the condition as well as improved mood and quality of life and an increase in the ability to manage their epilepsy.
“This new clinical trial confirms the positive effects of SMART and also demonstrates how effective a simple and relatively inexpensive telehealth delivery can be,” Sajatovic said.
What’s ahead
The study team at Case Western Reserve has made substantial progress to refine, implement and expand the SMART program in community settings by collaborating with the Epilepsy Association in Cleveland, the Epilepsy Alliance of Ohio and the Epilepsy Association of Western and Central Pennsylvania, as well as with epilepsy treatment centers in Ohio and in Iowa.
“I am most excited about the possibility of establishing successful models of delivering SMART that can be used by clinical-care teams and by epilepsy-focused social services agencies,” Sajatovic said. “I am hopeful that we can make the SMART program available to as many people with epilepsy as possible.”
Source:
Case Western Reserve University
Journal reference:
Sajatovic, M., et al. (2025). Development and feasibility testing of an implementation evaluation tool: Recommendations from the managing epilepsy well (MEW) network research collaborative. Epilepsy & Behavior. doi.org/10.1016/j.yebeh.2025.110488.
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Mayo Clinic AI Tool Allows Rapid, Precise Identification of 9 Types of Dementia From Single Brain Scan
Mayo Clinic researchers have developed an artificial intelligence–based clinical decision support system (CDSS) that could help clinicians identify patterns of brain activity associated with 9 types of dementia, including Alzheimer disease, from a single FDG-PET brain scan.1 The tool, called StateViewer, was trained and validated on more than 3,600 brain scans and in a new study achieved a sensitivity of 0.89 ± 0.03 and an area under the receiver operating characteristic (ROC) curve of 0.93 ± 0.02 in distinguishing neurodegenerative phenotypes.1
T: David T Jones, MD
B: Leland Barnard, PhD
In the radiologic reader study, which compared the tool’s integration into standard workflow, clinical readers using StateViewer had 3.3 ± 1.1 times greater odds of making a correct diagnosis than those using standard-of-care practices. It also enabled nearly twice the speed of interpretation. The research was published June 27, 2025, in Neurology.1
StateViewer has the potential to remedy a core challenge in dementia care: identifying the disease early and precisely, even when multiple conditions are present, the Mayo team said in a statement.2 “Every patient who walks into my clinic carries a unique story shaped by the brain’s complexity,” lead author David Jones, MD, neurologist and director of the Mayo Clinic Neurology Artificial Intelligence Program, said in the Mayo statement. The intricacy of the brain drew Jones to neuroscience in the first place, he added, and supports his deep “commitment to clearer answers. StateViewer reflects that commitment — a step toward earlier understanding, more precise treatment and, one day, changing the course of these diseases.”2
The system uses a neighbor-matching algorithm to compare an individual patient’s FDG-PET scan with a large reference dataset of confirmed dementia cases. It then produces color-coded brain activity maps highlighting regions that match specific disease patterns. Among the 9 syndrome the tool is designed to detect are Alzheimer disease, Lewy body dementia, posterior cortical atrophy, and frontotemporal dementia.1
The discovery cohort consisted of 3,671 individuals (mean age 68 years, 49% women), drawn from 3 research studies and clinical patient populations. All patients had FDG-PET imaging within 2.5 years of diagnosis. The system’s classification performance was externally validated in the Alzheimer’s Disease Neuroimaging Initiative dataset. While promising, the authors noted that the discovery cohort may not fully represent broader clinical populations.1
Mayo Clinic researchers plan further evaluation of StateViewer across a range of clinical environments. The tool’s use of a widely available imaging modality and its visual interpretability could help expand access to specialist-level insights in clinics that lack neurology expertise.2 Access to neurologists is extremely limited, particularly in low income and rural areas where financial, time, and travel restrictions put specialist appointments out of reach or where wait times can be extreme. The broader goal for StateViewer is to expand the technology beyond the Mayo Clinic where it could be “transformative on a global scale in the near future and expand access to these data-driven insights.”3
Dr. Jones partnered with Mayo Clinic data scientist Leland Barnard, PhD to build the system. “As we were designing StateViewer, we never lost sight of the fact that behind every data point and brain scan was a person facing a difficult diagnosis and urgent questions,” he said in a statement. “Seeing how this tool could assist physicians with real-time, precise insights and guidance highlights the potential of machine learning for clinical medicine.”2
References
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Barnard L, Botha H, Corriveau-Lecavalier N, et al. An FDG-PET-based machine learning framework to support neurologic decision making in Alzheimer disease and related disorders. Neurology. 2025;105(2). doi:10.1212/WNL.0000000000213831
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Murphy S. Mayo Clinic’s AI tool identifies 9 dementia types, including Alzheimer’s, with one scan. News release. Mayo Clinic. June 27, 2025. Accessed July 1, 2025. https://newsnetwork.mayoclinic.org/discussion/mayo-clinics-ai-tool-identifies-9-dementia-types-including-alzheimers-with-one-scan/
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Lindquist SB. Mayo Clinic neurology AI program tests platform to detect brain diseases. News release. Mayo Clinic. December 17, 2024. Accessed July 1, 2025. https://newsnetwork.mayoclinic.org/discussion/mayo-clinic-neurology-ai-program-tests-platform-to-detect-brain-diseases/
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Association between dietary insulin index and risk of depression, anxiety, and sleep disturbance in a group of Iranian physically active adults | BMC Psychology
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HIV treatment linked to risk of early knee osteoarthritis
Acquired immune deficiency syndrome, or AIDS, caused by the human immunodeficiency virus (HIV), weakens the body’s immune system and can be life-threatening if left untreated. Although there is currently no cure for AIDS, the widespread use of antiretroviral therapies has successfully transformed what was once a fatal diagnosis into a manageable chronic condition. Given this increased life expectancy, the focus has now shifted to non-AIDS comorbidities such as cancer, diabetes, and even osteoarthritis (OA), since HIV-infected individuals are at a higher risk of developing these conditions than the general population. However, there has been controversy regarding the premature aging of knee joints and the prevalence of OA in HIV-infected individuals.
Now, in a study published online on June 03, 2025, in the journal Bone Research, a team of researchers led by Dr. Zanjing Zhai at Shanghai Jiaotong University in Shanghai, China, has investigated the link between protease inhibitors (PIs), a class of drugs used to manage HIV, and the potential acceleration of OA development. In addition, they explored the underlying biological mechanisms that were responsible for this association.
First, they studied a group of 151 HIV-infected individuals to observe if PIs (specifically, a combination of the drugs lopinavir and ritonavir) had any association with early development of OA in the knee. “Patients receiving PIs scored lower on the Knee Injury and Osteoarthritis Outcome Score questionnaire compared to those not receiving these medications, suggesting worse functional outcomes,” Dr. Zhai explains. Furthermore, X-ray imaging revealed a higher incidence of OA in the knees of patients treated with PIs.
The researchers then evaluated the effect of various anti-HIV drugs on chondrocytes, the specialized cells comprising cartilage—a tissue in the knee joints that undergoes deterioration in patients with OA. Experiments on cultured chondrocytes as well as mice showed that among 25 anti-HIV drugs screened, lopinavir had the most detrimental effect on chondrocytes. Lopinavir treatment accelerated chondrocyte degradation and promoted senescence, a process in which cells permanently cease growth and division, thereby contributing to the OA development.
How exactly do PIs accelerate OA development? To answer this, the researchers focused on the gene Zmpste24, which plays a role in arthritis and aging processes and has been previously reported to be inhibited by lopinavir. Interestingly, they found that lopinavir’s effects on chondrocytes were dependent on Zmpste24 expression. When the gene was ‘knocked out’ or not expressed, lopinavir no longer exacerbated chondrocyte degradation and senescence or worsened cartilage degeneration in mice.
To understand the mechanism by which lopinavir-induced inhibition of Zmpste24 accelerates OA, they explored the underlying biological pathways and genes affected in this process. They found that Zmpste24 inhibition compromises nuclear membrane stability, which disrupts the interaction between Usp7 and Mdm2 proteins. This disruption activates the p53 signaling pathway, ultimately accelerating cartilage senescence. The study also revealed increasing the expression of Zmpste24 can have the opposite effect, i.e., it can reduce the OA severity in mice.
How does this study impact the millions of people worldwide who are currently living with HIV? “This study provides new insights into PI-containing regimens and their relation to early OA development in people living with HIV and unveils a new mechanism underlying Zmpste24-related senescence,” explains Dr. Zhai. “Based on our findings, people living with HIV with elevated risk for knee OA should carefully consider their treatment options and choose other regimens when other effective alternatives are available.”
Source:
Shanghai Jiaotong University
Journal reference:
Kong, K., et al. (2025). AIDS patients suffer higher risk of advanced knee osteoarthritis progression due to lopinavir-induced Zmpste24 inhibition. Bone Research. doi.org/10.1038/s41413-025-00431-2.
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The role of cd8+ t cells in tissue regeneration
In this interview, News Med talks to Prof. Uwe Ritter about the role of advanced imaging techniques in uncovering the role of CD8+ T cells in tissue regeneration.
What are the main goals of your research into immune cell interactions and tissue regeneration?
My work focuses on exploring immune cell interactions and tissue regeneration through cutting-edge imaging technologies, most notably the image processing and analysis pipelines of 3D skin models. These models are beneficial for characterizing regular T cells (Tregs) in wound healing.
I am also using machine learning to analyze organoid cultures, particularly focused on investigating the impact of CD8+ T cells on tissue remodeling and the decryption of cell-cell interactions in situ.
Mouse experiments involving the depletion of Tregs (pan depletion, subset-specific depletion, or induced depletion) have shown that Tregs are involved in immune regulation, metabolism, and tissue repair. These Tregs are characterized by the expression of amphiregulin and Foxp3.
The repair function in murine systems is well established, but we would like to know whether or not there are equivalent tissue repair Tregs in humans.
Michael Sforer’s group analyzed mouse and human tissues to investigate this equivalence. They analyzed blood, subcutaneous fat, and skin, performing single-cell attacks to look for any overlap in markers expressed by human or mouse Tregs to detect the phenotype of tissue repair Tregs in humans.
This research revealed that it was possible to detect tissue Tregs in humans that express CCR8 and are positive for basic leucine zipper ATF-like transcription factor (BATF). These are comparable to tissue Tregs from the mouse immune system.
Could you explain how imaging pipelines support the investigation of tissue regeneration processes?
In the example I discussed, molecular analysis revealed that these tissue Tregs included Tfh, a molecular helper T cell differentiation program. This discovery offers a major advantage because we can generate Tfh-like tissue Tregs and naive T cells and look for functional analysis or tissue repair functions.
The pipeline for this experiment involved isolating the tissue Tregs from PBMCs from blood and enriching them with CD25. We performed FACS sorting for the markers CD45 and CD45RA. We isolated antigen-naive Tregs and stimulated those naive Tregs with IL-2 to generate IL-2-derived Tregs. This allowed us to use Tfh-like Tregs similar to tissue Tregs, adding components such as IL-2, IL-12, IL-21, IL-23, and TGF-b.
We added TransAct IL-2 to these T cells, allowing us to further activate and harvest the supernatant from these Tregs. This process gave us two supernatants from the IL-2 Tregs and putative repair Tregs from the tissue itself.
What makes 3D skin models particularly useful for studying Tregs in wound healing? Could you expand on your work in this area?
We contacted Florian Gruber in Vienna and Dirk Becker in Würzburg because this group had established a very useful 3D skin model involving growing human epidermal keratinocytes in plastic (PET) tubes.
As the keratinocytes grow, they build up a strong epidermal compartment. A dermal punch can then be used to punch a hole into the epidermal compartment, and the keratinocytes start to close this area. This is essentially wound healing.
We aimed to determine whether supernatants from Tfh-like Tregs or IL-2 Tregs better accelerate wound healing. Using a time kinetic approach, we cut the epidermal pieces in a cryostat.
We aimed to measure the newly built stratum corneum in this structure. We needed to develop a software-based solution for dissecting structures from this epidermal compartment because we wanted to quantify the new stratum corneum in relation to the root healing effect of supernatant from the different Tregs I mentioned.
The challenge was achieving the sophisticated color and structural separation to properly discern the epidermal tissue, the stratum granulosum, the stratum basale, and the polycarbonate matrix of the 3D skin model.
The software detected the structures present in the epidermal compartment, reducing the impact of the background by subtracting the shades that do not correlate with the epidermal compartment. This is what allowed the stratum corneum to be detected.
The software can be used to measure the number of keratinocytes in the epidermal compartment, and it is possible to use advanced color separation using special settings for tissue detection, polycarbonate detection, and more.
The software’s capabilities were key to answering whether the supernatant could increase the wound healing in the system. The results showed that the IL-2 Treg supernatants did not have a significant impact on wound healing, but the Tfh-like cells supernatant saw the square micrometer of the stratum corneum become normalized.
This technique can be reproduced via other methods such as trans-epithelial electrical resistance (TEER) measurements. Comparing these measurements showed similarity between the different approaches, confirming that the technique was working.
We developed a detection algorithm that could dissect the pink shades of tissue. We also showed that tissue Tregs from humans are CCR8- and BAFT-positive and that these Tregs could accelerate wound healing in more complex wound-healing systems.
Image Credit: Komsan Loonprom/Shutterstock.com
How are you using machine learning with organoid cultures to study CD8+ T cells?
CD8+ T cells are well known for their ability to kill virus-infected cells or tumor cells. CD8+ T cells in the dysfunctional state (called exhaustion) are positive for PD1, TIGIT, and other markers.
Immunity is not black and white, however. In systems like liver hepatocellular carcinoma or NASH, it has been shown that CD8+ T cells that are PD1+ and TIGIT+ are reactive. They are not exhausted and can promote fibrosis or tumor progression.
We want to know whether these CD8+ T cells are involved in tissue reconstruction. When CD8+ T cells kill infected cells, we see tissue destruction that requires remodeling. Therefore, we can ask whether CD8+ T cells can also induce tissue regeneration.
To investigate this, we isolated those T cells and stimulated those CD8+ T cells using CD3 and CD28 beads. We took the resulting supernatant and performed an easy scratch assay. Activated naive T cells are not useful in wound healing, but we did observe that activated PD1+, TIGIT+, and activated central memory T cells can induce wound healing.
We also wanted to know whether CD8+ cells can promote organoids’ reorganization. To investigate this, we isolated CD8+ T cells using the TexMACS medium, activated those T cells (because only activated CD8+ T cells can induce wound healing), and added them to organoids.
Organoids are simple tissue-engineered cell-based in vitro models that recapitulate many aspects of the complex structures and functions of corresponding in vivo tissues. Organoids are tissue-derived and we can derive them from adult stem cells.
Cancer stem cells are induced through pretense stem cells, so this is not a problem. We can generate organoids in a Matrigel dome, so we opted to use this approach.
For example, we wanted to know what happens when the organoids come into close contact with lymphocytes. This had not been done before our study because measuring and dissecting organoids from lymphoids is very difficult.
With this in mind, our goal was to develop a machine learning pipeline suitable for detecting organ structures within the complex co-culture and high-throughput conditions. This had to include the characterization of organ formation, including numbers, size, and shape.
We began by deriving organoids from the bile duct and combining them with CD8+ T cells. Then, we started working in collaboration with TissueGnostics to develop an organoid detection app.
A number of problems had to be addressed at the beginning of this process. For example, we saw contour mimicry whereby cells look like organoids but are not organoids. We also saw contour fusion, with a fusion of two organoids that are difficult to dissect, and contour disruption, which makes it difficult for the algorithm to detect the organoid structure.
The software takes the organoid image, converts it to grayscale, and performs a background correction. The software then allows one to see the membrane of the organoids, distinguishing between the membrane and the organoids and the background of the lymphocytes and other structures. Corrections can be applied as required to better split the background from the organoids and implement a layer specification of the organoids.
It is also possible to adjust size and compactness when you are not confident or happy with the results.
We used the classifier machine learning system to improve this new system. For example, it is possible to train the algorithm by manually marking the tissue and marking the organoid boundary.
This type of manual delineation is time-consuming, but it was a useful quality control measure. We used a linear regression model to compare organoid size using both manual detection and software detection, confirming that the app is very precise and that it can be used to perform studies.
Results showed an increase in CD8+ cells from different donors. We measured the total area and sum of the organoids, showing an increase in organoid development in the presence of CD8+ T cells.
Our findings also indicate that the cytotoxic effector program of CD8+ cells is closely linked to a regeneration program, both of which are evoked upon a teaser stimulation. CD8+ T cells can kill other cells, but they also induce a tissue regeneration program.
What are your visions for decoding cell-cell interactions in situ using advanced imaging technologies?
I think we will be able to effectively decode cell-cell interactions in a few years. Cell communication between immunological cells such as T cells or dendritic cells is often based on autocrine signaling or juxtaposition processes. These processes influence tissue homeostasis and immune response to tumors and pathogens.
There are signaling molecules involved, for example, cytokines, metabolites, receptor proteins that bind specific surface molecules, signaling pairs, cell junctions, and secondary messengers. In terms of understanding this communication, we know the alphabet, but we do not currently understand the sentences.
Many people are already working with single-cell RNA-seqs and single-cell FACS analysis, allowing them to describe the transcriptome and phenotype of each single cell. However, we still do not know which cell has been in contact with other cells or which cell is responsible for activating other cells. These questions cannot be answered via single-cell analysis.
We can generate single-cell raw data at the transcriptome, proteome, or metabolome level, but this is the limit at the moment.
We can perform very simple in vitro experiments. For example, we can evaluate OT-1 T cells specific for ovalbumin by adding ovalbumin to an in vitro culture with dendritic cells and measuring the immune response of the dendritic and T cells.
We can also use laser scanning microscopy to measure the membrane overlaps of cells (immunological synapse) to characterize the phenotype of cells that interact with dendritic cells. This approach is very precise, but it only describes the phenotypes.
We can also do this in situ, measuring cell boundaries via the StrataQuest software. This allows us to calculate the potential contact area of cells, analyzing the cells that are in direct contact with the analyzed cell to characterize its neighbors. However, this method does not show whether cells are in communication.
We have performed experiments. We took APCs, defined endogen, a T cell receptor, and added ovalbumin. We then measured single-cell and double-cell effects with RNAseq and dcRNAseq. After sorting the droplets, we analyzed the phenotype modification or the transcriptome of those cells interacting in terms of their phenotype modification or non-phenotype modification.
How does your work in this area correlate with the PIC-seq methods developed by Ido Amit’s lab?
It is closely aligned. In 2020, an excellent publication by Ido Amit described a similar approach to ours. They did exactly the same. They kept it simple, used APCs, defined a TCR receptor, isolated the T cells and dendritic cells, and then conjugated doublets. They then performed single-cell analysis and physically interacting cells (PIC) analysis.
This allowed them to develop a PIC-seq algorithm that enabled the dissection of dendritic cells and T cells. This PIC-seq approach allowed the team to analyze the core signature of the attached dendritic cells or T cells.
This is very important because this approach removes the need to isolate and dissect doublets, allowing us to begin to characterize the crosstalk of physically interacting cells.
However, it is important to note that this approach is only possible when the two cell subsets are transcriptionally distant. When they are transcriptionally related, this technique is not functional.
I became fascinated with this technique and wrote an opinion article about it that was published this year. I explained that it is possible to analyze single cells, analyze PICs, sequence single cells on the PICs, and run the PIC-seq. This is based on the pre-processing, integration, deconvolution, and differentiation of the data.
My idea was that it is also possible to define the gene expression profiles of PICs grouped by the contributing T cell or myeloid identity. For example, it would be possible to characterize migratory DCs based on their genes, plasmacytoid DCs, DC-1, DC-2, or monocytes. A similar definition is possible with T cells, for example, characterizing a naive T cell, CD4+ Treg, CD8+ CTL, or an activated T cell.
When we know the profile of physically interacting cells based on experimental data with ovalbumin or other antigens, we can determine the gene profiles of migratory antigen-presenting TCs and know exactly what they are producing.
This allows us to create a panel, choosing antibodies with fluorescence, for example, and performing multiplex staining.
This requires a microscope capable of imaging multiple channels. The key advantage of this approach is that we can detect the cells that are genuinely interacting based on the presence of specific markers.
What types of research do you see potentially evolving from these approaches?
This approach is potentially valuable for mouse systems where, for example, we can infect mice with pathogens, and because we know we have a resistant phenotype and a chronic phenotype, we can detect the gene modules that correlate to adaptive immunity by T cells or dendritic cells that correlate to immune pathology.
There are differences between viruses, protozoans, and bacteria, but this approach could lead to the creation of a multicenter-based contextual and PIC atlas, featuring relevant gene modules and a pathogen-specific background.
For example, during the immune response of the PICs, we may see shared expressions of genes also induced by protozoans or bacteria. The software could be used to detect genes that are exclusively induced by virus infection. We could isolate these genes using future software packages, demonstrate these findings, and relate these back to the in situ situation, clearly showing or describing the cells in communication in a pathogen-specific manner.
These findings could also eliminate the need to work with dendritic and T-cells. We may see this concept expand into other systems, such as tumor immunology. It may become possible to characterize gene models associated with tumor-killing based on the interaction between cells and the expression of genes that are specifically induced during tumor-killing processes.
This type of computational analysis will allow us to pinpoint biomarkers, for example, that are associated with tumor immune cell interaction. The advantages of these systems are clear: they allow us to deepen our understanding of tumor immune communications, identify tumor gene modules, and characterize tumor escape mechanisms.
I also think this will improve the interpretation of tumor-effector cell interactions in situ, which will be crucial for evaluating tumor progression and treatment activities.
About Prof. Uwe Ritter
Prof. Uwe Ritter is a principal investigator in the Department of Immunology, Leibniz institute for Immunotherapy. His research is focused on studying the immune system’s response to various antigens in the skin-associated lymphatic tissue (SALT). He and his team aim to manipulate critical immune checkpoints in myeloid cells to potentially reprogram dysfunctional immune reactions. Their work integrates cutting-edge technologies – notably in-situ contextual tissue cytometry and high-resolution imaging – to gain deeper insights into tissue structure and function.
About TissueGnostics
TissueGnostics (TG) is an Austrian company focusing on integrated solutions for high content and/or high throughput scanning and analysis of biomedical, veterinary, natural sciences, and technical microscopy samples.
TG has been founded by scientists from the Vienna University Hospital (AKH) in 2003. It is now a globally active company with subsidiaries in the EU, the USA, and China, and customers in 30 countries.
TissueGnostics portfolio
TG scanning systems are currently based on versatile automated microscopy systems with or without image analysis capabilities. We strive to provide cutting-edge technology solutions, such as multispectral imaging and context-based image analysis as well as established features like Z-Stacking and Extended Focus. This is combined with a strong emphasis on automation, ease of use of all solutions, and the production of publication-ready data.
The TG systems offer integrated workflows, i.e. scan and analysis, for digital slides or images of tissue sections, Tissue Microarrays (TMA), cell culture monolayers, smears, and other samples on slides and oversized slides, in Microtiter plates, Petri dishes and specialized sample containers. TG also provides dedicated workflows for FISH, CISH, and other dot structures.
TG analysis software apart from being integrated into full systems is fully standalone capable and supports a wide variety of scanner image formats as well as digital images taken with any microscope.
TG cooperations
TG continuously cooperates with research groups and other companies in the industry to provide novel tools and applications to its customers.
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