How the eye cleans itself up
Investigators at the University of Copenhagen and the University of California at Berkeley have demonstrated that the eye possesses a glymphatic system for the clearance of metabolic waste that is similar to that of the brain. Like the brain, the eye has high metabolic activity, but it is not connected to the lymph system that clears metabolic waste from much of the body. In earlier work, the team had demonstrated that the brain clears metabolic waste through a glial-based or “glymph” system that ultimately connects to the lymphatic system. In their current study, the researchers demonstrated that the eye also uses a glial-based system to dispose of metabolic waste, and that in two separate mouse models, such transport was impaired under the conditions found during early stage glaucoma. The team reported its findings in the March 25, 2020, issue of Science Translational Medicine.
In blood stem cells, selection drives driver mutations early on
Scientists at the University of Cambridge have demonstrated that in blood-forming stem cells, precancerous mutations are under positive selection long before the development of overt disease. The accumulation of mutations in cancer-associated genes, which is termed clonal hematopoiesis when it happens in blood-forming stem cells, is a universal feature of aging. Such mutations increase the risk of leukemia, but there is disagreement over whether such accumulation occurs by random chance, or whether such mutations are under positive selection before any overt disease state. In their work, the authors sequenced blood cells from roughly 50,000 individuals and demonstrated that positive selection rather than random genetic drift was the major force shaping clonal hematopoiesis. They plan to use their data to develop risk predictors for not just blood cancers, but also other blood diseases and cardiovascular disease. Their work appeared in the March 27, 2020, issue of Science.
Dead cells do tell tales
Researchers at the University of Virginia have profiled the metabolites released by apoptotic cells, and they identified metabolites by which those cells communicated and influenced physiological processes. Ninety percent of cell deaths are programmed, occurring via apoptotic mechanisms, and the metabolites secreted by apoptotic cells control developmental and regenerative processes. The researchers demonstrated that the release of metabolites from apoptotic cells “is not simply due to passive emptying of cellular contents and instead is a regulated process,” during which cells secreted specific metabolites while their membrane was still intact. “Functionally, the apoptotic metabolite secretome induced specific gene programs in healthy neighboring cells, including suppression of inflammation, cell proliferation, and wound healing. Furthermore, a cocktail of apoptotic metabolites reduced disease severity in mouse models of inflammatory arthritis and lung-graft rejection,” the authors wrote. “These data advance the concept that apoptotic cells are not inert cells waiting for removal, but instead release metabolites as ‘good-bye’ signals to actively modulate outcomes in tissues.” The team reported its findings in the March 19, 2020, issue of Nature.
Selective TGF-beta inhibition helps checkpoint blockade
Scientists at Scholar Rock Inc. have published research demonstrating that specific inhibition of transforming growth factor beta (TGF-beta) was able to overcome primary resistance to checkpoint blockade with PD-1 inhibitors. Checkpoint inhibition leads to profound remissions, but it is only effective in a minority of treated patients, in part because tumor cells have multiple immunosuppressive mechanisms. Secretion of TGF-beta is one of those mechanisms, and TGF-beta inhibitors offer a possible avenue to sensitizing resistant tumors to checkpoint blockade. However, nonspecific inhibition has been plagued by toxicity problems. In their experiments, the researchers demonstrated that tumors preferentially expressed TGF-b1, one of three forms of TGF-beta. In an animal study, the TGF-b1 selective inhibitor SRK-181, which works by preventing release of the growth factor from a larger prodomain complex, was able to increase the effectiveness of checkpoint blockers, without cardiotoxicity that has prevented the use of less specific inhibitors. “Together, the results presented herein demonstrate that highly selective inhibition of TGF-b1 activation overcomes a key mechanism of primary resistance to [checkpoint blockade] that has been observed in the clinical setting and recapitulated in preclinical models,” the authors wrote. Their work appeared in the March 25, 2020, issue of Science Translational Medicine.
How lung tumors seed to brain
Researchers at Massachusetts General Hospital have identified drivers of brain metastases in lung cancers, uncovering potential targets for trying to treat or prevent such metastases. Half of lung adenocarcinoma patients develop brain metastases, and once a metastasis is present in the brain, the outlook for patients becomes far worse. The researchers compared copy number alterations from 73 brain metastases to roughly 500 primary lung tumors, and found that amplifications of the transcription factors MYC and YAP1, and the protease MMP13, were significantly more frequent in brain metastases than primary tumors, as were deletions of the cell cycle regulator CDKN2A/B. Beyond the specific drivers identified, the work is proof of principle that “genomic characterization of large collections of metastases represents a feasible strategy to uncover potential avenues for the prevention and treatment of metastasis.” The researchers published their results in the March 23, 2020, issue of Nature Genetics.
Butyrate affects regulatory B cells, rheumatoid arthritis
Scientists at University College London have demonstrated that dietary supplementation with butyrate, a short-chain fatty acid and a metabolite produced by the gut microbiome, improved the symptoms of rheumatoid arthritis (RA) in mice by increasing the activity of regulatory B cells. Like regulatory T cells, regulatory B cells suppress immunity, both by activating regulatory T cells themselves and by producing anti-inflammatory interleukin-10, interleukin-35 and TGF-beta. Butyrate supplementation required the microbiome to be effective, and shifted the microbiota to increase relative abundance of Allobaculum, Bifidobacterium and Rhodosprillaceae unclassified. Those bacteria produced higher levels of the serotonin-derived metabolite 5- hydroxyindole-3-acetic acid (5-HIAA), which activated regulatory B cells via the aryl hydrocarbon receptor. “Based on our results, we propose the hypothesis that butyrate overcomes the need for inflammatory stimuli in Breg differentiation by increasing the availability of the 5-HIAA, which directly activates AhR and IL-10 transcription,” the authors wrote. “This hypothesis needs further exploration and could offer important immunological and physiological groundwork for future therapeutic interventions.” Their work appeared in the March 25, 2020, issue of Cell Metabolism.
Lamin A/C’s presence in nucleus, absence from membrane both problematic in progeria
A team at the University of Chicago has gained new insights into the role of Lamin A/C, a protein that causes the premature aging syndrome Hutchinson-Guilford progeria syndrome (progeria) when it is mutated. Lamin A/C binds Lamin-associated domains to the membrane of the nucleus, and loss of those domains when the protein is mutated is thought to be the key cellular mechanism underlying its role in progeria. However, the authors showed that when mutated Lamin A/C migrated to the interior of the nucleus, it bound to enhancer elements and changed the transcription of genes whose expression is changed in progeria. “These results suggest that Lamin A/C regulates gene expression by enhancer binding. Disruption of the gene regulatory rather than LAD tethering function of Lamin A/C may underlie the pathogenesis of disorders caused Q9 Q2 by LMNA mutations,” the authors wrote. Their work appeared in the March 23, 2020, issue of Developmental Cell.
Females, males have different metabolic response to intermittent fasting
Researchers at the University of Sydney have discovered that male and female mice responded differently to the same regimen of daily food restriction in terms of both food intake and metabolic changes. Timed food restriction, in the form of either a short daily feeding window or alternate-day fasting, appears to be a way of duplicating the benefits of caloric restriction without actually restricting calories. Animal research has led to insights into the molecular underpinning of intermittent fasting’s effects – in males, as most studies have used exclusively male mice. The University of Sydney team compared the effects of food restriction during the animals’ active cycle, and showed that although male and female animals showed the same effects on glucose tolerance during restricted feeding, females had both a different behavioral response, with more compensatory food intake, and different changes in lipid metabolism in the liver. The authors wrote that their results “highlight the intrinsic biological and metabolic disparities between male and female mice, emphasizing the growing need for the inclusion of both sexes in scientific research… [and] illustrate sex-specific metabolic pathways that regulate lipogenesis, obesity and overall metabolic health.” They reported their findings in the March 23, 2020, online issue of the Journal of Physiology.
Ditching PAMs expands CRISPR
Investigators at Massachusetts General Hospital have developed a new variant of Cas9 that eliminates the need for a protospacer adjacent motif (PAM) for CRISPR genome editing, opening up almost the entire genome to targeting via CRISPR. In CRISPR’s natural role as a primitive bacterial immune system, PAMs make sure that the Cas9 can tell the difference between self and nonself. However, PAMs limit the areas of the genome that can be targeted, and even though different CAS nucleases recognize different motifs, some areas of the genome remain untargetable. By engineering Cas9 to relax its requirement for a PAM, the authors developed two Cas9 variants with broader targeting abilities: SpG, which was capable of targeting an expanded set of PAMs, and a near-PAMless variant called SpRY. “By developing SpCas9 variants capable of high-resolution editing, we demonstrate that protein engineering can eliminate biological constraints that limit applications of CRISPR-Cas enzymes,” the authors wrote, concluding that “the vast majority of the genome is now targetable.” They reported their findings in the March 26, 2020, online issue of Science.