Mois : novembre 2024

In a new study, the researchers administered human umbilical cord-derived mesenchymal stem cells (HUCMSCs) to aged mice and observed reduced degeneration in multiple organs, changes to microbial composition, metabolic alterations, improvements in behavior and ability, and reduced fearfulness [1].

Therapeutic potential

Earlier this year, we reported on a clinical trial in which administering HUCMSCs reduced frailty in older people. MSCs in general are known for their capacity for self-renewal and differentiation into multiple cell types. A growing body of research suggests that MSCs can be used as a tool for therapeutic purposes [2].

In this new study, the researchers used four-month-old mice of two different strains, senescence-accelerated mouse prone 8 (SAMP8), a mouse strain used as a model of age-related cognitive decline and, as a control, senescence-accelerated mouse resistant 1 (SAMR1), a strain that ages normally.

A group of 15 SAMP8 mice received HUCMSCs weekly for eight weeks. Additionally, researchers had SAMP8 and SAMR1 groups that didn’t receive HUCMSCs as a control. One week following the end of the experiment, the researchers took fecal and blood samples from now 6-month-old mice.

Improvements on many levels

Following MSC administration, the researchers tested the mice’s cognitive abilities. They observed increased curiosity, better motor coordination and balance, and reduced anxiety in mice treated with HUCMSCs compared to controls. However, there were no differences in a test that assessed spatial learning and memory.

On the molecular level, the researchers analyzed the genome for DNA single-strand breaks in the brain tissue. They performed additional analysis to specifically focus on exonic regions (DNA sections translated into proteins) and within 200 bp of transcription start sites (where many elements that regulate translation – the first step in protein production – are located).

Unsurprisingly, they noted more single-strand breaks in the faster-aging SAMP8 control mice compared to the SAMR1 controls. MSCs-treated mice fared better than their counterparts in the SAMP8 untreated controls regarding single-strand DNA breaks, but there were no significant differences between SAMP8 MSCs-treated and untreated SAMR1.

Together, this suggests that MSCs reduce age-related DNA damage, preserving genomic stability and neuroprotection, which the researchers hypothesized to play a role in improving cognitive function.

On the tissue level, MSC treatment led to significant improvements. For example, in the frontal lobe and hippocampal brain regions, which are responsible for learning, memory, and attention, the researchers observed “maintained structural integrity and normal glial cell distribution” in the mice treated with MSCs.

The cardiac tissue of the MSC-treated SAMP8 mice resembled that of the healthy cardiac tissue of the SAMR1 controls. The structures of the gastrointestinal, kidney, skeletal muscle, spleen, liver, and lung cells were also well-preserved, while controls exhibited more aging-related changes. The researchers also observed reduced inflammation in the lungs and spleens of MSC-treated mice compared to the control animals.

The authors emphasize that in some tissues (kidney, muscle, and spleen), the tissues of mice treated with MSCs surpassed that of controls, suggesting tissue rejuvenation properties of MSC treatment and its potential for regenerative medicine.

The impact on microbiota and metabolism

MSC treatment also resulted in changes to the mice’s microflora and metabolic profiles. While all three groups of mice share some microbial species in their guts, there were also significant differences.

For example, the researchers noted that following the MSC treatment, some bacterial species that are considered beneficial in humans were restored. On the metabolomic level, they noted that MSC treatment “increased levels of metabolites beneficial for cardiovascular health.”

The authors also linked the increased levels of one of the metabolites, namely 5-hydroxy-L-tryptophan, in MSC-treated mice to the reduced depression-like behavior that they observed in previous experiments. They suggest that an increase in this compound leads to the normalization of serotonin synthesis, a process linked to antidepressant properties.

More broadly, the researchers observed differences between experimental groups regarding a few metabolite pathways, including pathways related to fatty acid and amino acid metabolism, suggesting that MSC therapy has an impact on metabolism.

However, this impact was quite complex, and the authors pointed to both benefits and limitations of MSC treatment on the metabolome. They noticed that several metabolites exhibited changes in accordance with what would be expected, based on the previous research, which highlighted the benefits of MSC treatment on metabolic changes. However, researchers also noted some observations conflicted with those expectations suggesting MSC treatment has some limitations regarding its impact on metabolic changes. Those results need further investigation.

Understanding the mechanism

While investigating the molecular mechanism of MSC treatment still needs more investigation, the authors suggest that, based on these results and previous research, some possible molecular pathways that are in play. They also suggest that MSCs’ anti-inflammatory properties promote DNA damage-repair cycles, leading to reduced DNA damage in the brain. They point to the critical role of metabolism, which should be further investigated.

In these experiments, the researchers use intraperitoneal injection (IP), and not intravenous infusion, as preclinical studies have shown IP of MSCs as more effective in treating colitis [3]. Previous research suggests that IP-administered MSCs impact intestinal immune and inflammatory responses [4]. These researchers hypothesize that MSCs alter gut microbiota through modulation of intestinal immune function and microenvironment. A changed microbiome subsequently impacts metabolism and immune functions, resulting in a positive feedback loop. However, there is still a need to fully understand the mechanism by which MSCs influence gut microbiota.

This study has several limitations, one of which is sampling for microbiome analysis. Since samples were taken at a single time point, the researchers might have missed dynamic and long-term changes in the microbiome, factors important for potential use in therapies. Second, SAMP8/SAMR1 was used as a model for aging and dementia; however, those animals have some pathological features that are different from human dementia, which might impact how the results will translate to human research. Also, having more animals would have increased the statistical strength of these results.

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Literature

[1] Lian, J., Xia, L., Wang, G., Wu, W., Yi, P., Li, M., Su, X., Chen, Y., Li, X., Dou, F., & Wang, Z. (2024). Multi-omics evaluation of clinical-grade human umbilical cord-derived mesenchymal stem cells in synergistic improvement of aging related disorders in a senescence-accelerated mouse model. Stem cell research & therapy, 15(1), 383.

[2] Musiał-Wysocka, A., Kot, M., & Majka, M. (2019). The Pros and Cons of Mesenchymal Stem Cell-Based Therapies. Cell transplantation, 28(7), 801–812.

[3] Wang, M., Liang, C., Hu, H., Zhou, L., Xu, B., Wang, X., Han, Y., Nie, Y., Jia, S., Liang, J., & Wu, K. (2016). Intraperitoneal injection (IP), Intravenous injection (IV) or anal injection (AI)? Best way for mesenchymal stem cells transplantation for colitis. Scientific reports, 6, 30696.

[4] Sala, E., Genua, M., Petti, L., Anselmo, A., Arena, V., Cibella, J., Zanotti, L., D’Alessio, S., Scaldaferri, F., Luca, G., Arato, I., Calafiore, R., Sgambato, A., Rutella, S., Locati, M., Danese, S., & Vetrano, S. (2015). Mesenchymal Stem Cells Reduce Colitis in Mice via Release of TSG6, Independently of Their Localization to the Intestine. Gastroenterology, 149(1), 163–176.e20.

Scientists have found that both a ketogenic diet and oral supplementation with ketone bodies alleviate symptoms of multiple sclerosis, a serious autoimmune disorder, in a mouse model [1].

Keto and autoimmune diseases

In ketogenic diets, the vast majority of calories are derived from fat, some from protein, and almost none from carbohydrates. While a ketogenic diet might speed up weight loss, it has also been linked to increased cholesterol levels [2]. However, at least for some people, keto’s advantages might outweigh its drawbacks.

Ketogenetic diets are associated with reduced inflammation [3], and some studies have suggested possible benefits for people with autoimmune diseases [4]. However, the exact mechanisms are not fully understood yet. In this new study published in Cell Reports, scientists from the University of California San Francisco took a deep dive into the workings of these diets in a murine model of an autoimmune disease.

Less severity and incidence

For their experiments, the researchers chose so-called experimental autoimmune encephalomyelitis (EAE) mice. These are often used as a plausible if imperfect model of human multiple sclerosis (MS) since they recapitulate many aspects of this debilitating autoimmune disease.

First, the researchers wanted to know whether keto can protect normally raised mice from EAE. Ten days after a ketogenic diet was begun, the mice were inoculated with a compound that triggers EAE. Compared to mice on a high-fat diet (75% of calories from fat, 15% from carbohydrate, and 10% from protein), mice eating a ketogenic diet (90.5% from fat, 0% from carbohydrate, and 9.5% from protein) were more resistant to the disease, with both lower incidence and much less severe symptoms. The keto-eating mice also had a more favorable immune profile.

However, when the researchers performed the same experiment in mice with depleted microbiota, the two groups barely showed any difference, demonstrating that the protective effect of a keto diet is mediated by gut bacteria.

The molecule that can replace ketogenesis

A ketogenic diet works by remodeling the body’s energy metabolism. When glucose is abundant, it is preferentially used as fuel. However, in a ketogenic environment, glucose is scarce, so the body switches to producing energy from fat using a process known as beta-oxidation. Fatty acids must be broken down into small molecules called ketone bodies, such as beta-hydroxybutyrate (βHB), which are transported across the body to be used as an alternative source of fuel.

In recent years, direct ketone supplementation via compounds such as ketone salts or esters has been tested as a way to recapitulate the benefits of ketogenic diets without the downsides. The researchers introduced a new group of mice fed the unhealthy high-fat diet supplemented with a ketone ester. This group was virtually indistinguishable from the original ketogenic diet group in terms of EAE incidence and severity.

“What was really exciting was finding that we could protect these mice from inflammatory disease just by putting them on a diet that we supplemented with these compounds,” said Peter Turnbaugh of the Benioff Center for Microbiome Medicine, a leading author on the study.

The gut connection

Interestingly, while most of the βHB production under KD happens in the liver, the beneficial effects of both keto diets and keton ester supplementation on MS seemed to be mediated by βHB production in intestinal epithelial cells. Mice genetically modified so that they could not produce βHB in the gut were not protected against MS regardless of their diet.

The researchers already knew that the gut microbiome was a crucial element, so they started hunting for bacterial species. After extensive screening, the researchers focused on Lactobacillus murinus and a metabolite it produces called indole lactic acid (ILA). ILA is known to alleviate autoimmune responses by inhibiting the production of the pro-inflammatory cytokine interleukin 17 (IL-17) by Th17, a subset of T cell strongly associated with autoimmune diseases.

Both treating MS mice with ILA and populating their guts with L. murinus alleviated the symptoms. The researchers concluded that ΒHB production specifically in the gut or oral supplementation with a ketone ester benefits ILA-producing bacteria, including L. murinus. This increases the production of ILA, which, in turn, leads to the observed anti-MS effect.

“The big question now is how much of this will translate into actual patients,” Turnbaugh said. “But I think these results provide hope for the development of a more tolerable alternative to helping those people than asking them stick to a challenging restrictive diet.”

Surprisingly, we discovered that oral delivery of a βHB-KE can mimic the protective effects of a KD. If this finding holds in humans, βHB supplementation alone could offer a viable therapeutic alternative to the full KD. The translational implications are profound, as KDs are difficult to maintain and can have negative side effects. Our identification of βHB as a key player provides a way to circumvent these barriers and provides a more general proof of concept for the ability to distill the activity of a complex diet down to a single bioactive molecule.

We would like to ask you a small favor. We are a non-profit foundation, and unlike some other organizations, we have no shareholders and no products to sell you. All our news and educational content is free for everyone to read, but it does mean that we rely on the help of people like you. Every contribution, no matter if it’s big or small, supports independent journalism and sustains our future.

Yes I will donate

Literature

[1] Alexander, M., Upadhyay, V., Rock, R., Ramirez, L., Trepka, K., Puchalska, P., … Turnbaugh, P. J. (n.d.). A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity. Cell Reports.

[2] Burén, J., Ericsson, M., Damasceno, N. R. T., & Sjödin, A. (2021). A ketogenic low-carbohydrate high-fat diet increases LDL cholesterol in healthy, young, normal-weight women: a randomized controlled feeding trial. Nutrients, 13(3), 814.

[3] Pinto, A., Bonucci, A., Maggi, E., Corsi, M., & Businaro, R. (2018). Anti-oxidant and anti-inflammatory activity of ketogenic diet: new perspectives for neuroprotection in Alzheimer’s disease. Antioxidants, 7(5), 63.

[4] Brenton, J. N., Banwell, B., Bergqvist, A. C., Lehner-Gulotta, D., Gampper, L., Leytham, E., … & Goldman, M. D. (2019). Pilot study of a ketogenic diet in relapsing-remitting MS. Neurology: Neuroimmunology & Neuroinflammation, 6(4), e565.

In a groundbreaking Nature paper, researchers have developed synthetic regulatory sequences that could prevent targeted gene therapies from having effects in unwanted cell types.

More than methylation

While methylation is the most well-known regulator of gene expression, it isn’t the only thing that determines what is to be expressed when. Cis-regulatory elements (CREs), so called because they sit near the DNA sequences they regulate, are responsible for expressing the genes that are specific to each cell type [1]. While they are technically non-coding, as they do not directly code for functional proteins, CREs are critical to epigenomic function.

Manipulating existing CREs in engineered cells is one thing, but it’s not clear if the CREs generated by evolution will always be the ideal candidates for specific therapeutic applications in specific cell types. A decade ago, researchers began seriously asking if it might be possible to generate CREs to more precisely do what we want [2]. Having functional control of CREs would allow therapies to apply only to specific cell types, potentially offering massive improvements to gene therapies that aren’t yet good enough for clinical use [3].

However, the number of potential sequences that could be inserted into a mere 200 base pairs of DNA is far larger than the number of atoms in the universe. Basic computational algorithms, therefore, will not suffice to find CREs that work. A substantial amount of previous work has gone into this topic between then and now, attempting to discover why CREs work the way they do and looking to develop a regulatory ‘grammar’ and a more complete understanding [4]. Very recently, researchers have developed CREs for use in Drosophila flies [5].

However, fruit flies aren’t mice, let alone people, and it was unclear if this process could create sequences for use in cells that can be transplanted into larger animals. These researchers appear to have done it.

A new algorithm with real-world effects

Previous work was focused on looking at the epigenetic downstream effects of CREs, but these researchers used MPRA, a system that can accurately gauge the directeffects of any given CRE. To train their model, Malinois, these researchers used sequences derived from three cell lines: bone marrow cells, liver cells, and nerve cancer cells. Even without being directly informed as to their effects, Malinois was able to accurately predict the activity of more than sixty thousand existing, natural CREs. Its predictions of epigenetic behavior were in line with experimental results in all three cell types.

Malinois, however, is just a prediction algorithm. To actually generate new CRE sequences, the researchers developed Computational Optimization of DNA Activity (CODA), which can be used with multiple algorithms. Their intention was to develop sequences that have maximal effects on one of the three cell types and minimal effects on the other two.

At first, the algorithm was attracted to certain motifs, yielding 36,000 of similar-looking sequences. However, after an algorithmic tweak to penalize re-use, CODA created 15,000 more synthetic sequences and compared them to 12,000 natural sequences.identified primarily by location and 12,000 more natural sequences identified by Malinois.

The location-based sequences were found to be less specific and have less effect than the Malinois-identified sequences, but the synthetic sequences were stronger still, having more specificity to each of the desired cell types. Even when CODA’s preferred motifs weren’t used, 92.4% of its generated sequences were still specific to a cell type, compared to 73.6% of the Malinois-identified sequences and only 40.6% of the location-identified sequences. Under far more stringent conditions for specificity, more than half of CODA’s sequences made the cut, while far fewer of the natural sequences did.

These synthetic sequences were found to be higher in useful content than the natural sequences, and rather than being mostly activatory for the desired cell types, these synthetic sequences actively repressed activation in off-target types.

To confirm their cellular findings, the researchers injected living zebrafish and mouse embryos with gene therapies that used these synthetic CREs. The therapies were found to be specific to cell type in these living animals, both before and after birth.

This represents a sea-change for researchers of gene therapies. There are always plenty of cell types for which expressing a gene therapy modification would be highly negative. If therapies that use these synthetic sequences can prevent this from happening, it bodes well for a wide variety of potential therapies, including those that target age-related diseases.

We would like to ask you a small favor. We are a non-profit foundation, and unlike some other organizations, we have no shareholders and no products to sell you. All our news and educational content is free for everyone to read, but it does mean that we rely on the help of people like you. Every contribution, no matter if it’s big or small, supports independent journalism and sustains our future.

Yes I will donate

Literature

[1] Donohue, L. K., Guo, M. G., Zhao, Y., Jung, N., Bussat, R. T., Kim, D. S., … & Khavari, P. A. (2022). A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation. Cell genomics, 2(11).

[2] Levo, M., & Segal, E. (2014). In pursuit of design principles of regulatory sequences. Nature Reviews Genetics, 15(7), 453-468.

[3] Deverman, B. E., Ravina, B. M., Bankiewicz, K. S., Paul, S. M., & Sah, D. W. (2018). Gene therapy for neurological disorders: progress and prospects. Nature Reviews Drug Discovery, 17(9), 641-659.

[4] Movva, R., Greenside, P., Marinov, G. K., Nair, S., Shrikumar, A., & Kundaje, A. (2019). Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays. PLoS One, 14(6), e0218073.

[5] de Almeida, B. P., Schaub, C., Pagani, M., Secchia, S., Furlong, E. E., & Stark, A. (2024). Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo. Nature, 626(7997), 207-211.