Virus World

But doubts remain about whether cell reprogramming technique could one day help.  A decade after Kyoto University biologist Shinya Yamanaka won a share of a Nobel Prize for discovering a cocktail of proteins that reprogram adult cells into versatile stem cells, two teams argue the proteins can turn back the clock for entire organisms—perhaps one day humans. One group at a biotech used gene therapy to deliver some of the so-called Yamanaka factors into old mice, and modestly extended their life span. And a separate team followed a similar strategy to reverse aging-like changes in genetically engineered mice.  In both cases, the Yamanaka factors appear to have restored part of the animals’ epigenome, chemical modifications on DNA and proteins that help regulate gene activity, to a more youthful state. But scientists not involved in the work say suggestions of age reversal are premature. “These studies use reprogramming factors to reverse epigenetic changes that happen during aging,” says Matt Kaeberlein, a geroscientist at the University of Washington, Seattle, but that’s a far cry from making an old animal young again. Several groups had already found genetically engineered mice that begin expressing Yamanaka factors in adulthood show reversal of certain aging symptoms. To explore an approach that might lead to a more practical treatment for people, San Diego–based company Rejuvenate Bio injected elderly (124-week-old) mice with adeno-associated viruses (AAVs) carrying genes for three of the factors, collectively known as OSK.

These animals lived another 18 weeks on average, compared with 9 weeks for a control group, the company reported in a preprint on bioRxiv this month. They also partially regained patterns of DNA methylation—a type of epigenetic mark—typical of younger animals. Although some studies have suggested Yamanaka factors can promote cancer, Noah Davidsohn, Rejuvenate’s chief scientific officer and co-founder, says the company has so far found no obvious negative effects in mice given the gene therapy. “I would say it is provocative—possibly a breakthrough,” says Steven Austad of the University of Alabama, Birmingham, who studies the biology of aging. “But it will need to be replicated and the mechanism explored before we can say for sure.” The second study, published yesterday in Cell, is from a team led by Harvard Medical School geneticist David Sinclair, who has backed several controversial “antiaging” interventions over the past 2 decades. (Rejuvenate’s approach grew from an earlier collaboration between Sinclair and Davidsohn, but Sinclair isn’t involved in the company’s research, Davidsohn says.) Sinclair’s team set out to test his “information theory of aging,” which posits that our bodies get old because of the cumulative loss of epigenetic marks. Cells’ DNA repair mechanisms, operating throughout a lifetime to fix DNA cuts and other damage, are what degrade these marks, he argues.

To test the theory in mammals, the team genetically engineered a mouse strain that, when given a particular drug, makes an enzyme that cuts their DNA at 20 sites in the genome, which are then faithfully repaired. Widespread changes in cells’ DNA methylation patterns and gene expression followed, consistent with Sinclair’s theory. The mice ended up with an epigenetic signature more like that of older animals, and their health deteriorated. Within weeks, they lost hair and pigment; within months, they showed multiple signs of frailty and tissue aging. To see whether the epigenetic degradation was reversible, the researchers injected some of these elderly seeming mice with AAVs carrying OSK genes, which Sinclair’s group recently reported could reverse loss of vision in aging rodents. Analyses of the mice’s muscles, kidneys, and retinas suggest the cocktail reversed some of the epigenetic changes induced by the DNA breaks. The findings point to a way to drive an animal’s age “forwards and backwards at will,” Sinclair says, and support the idea of epigenome-targeting treatments for aging in humans. Molecular biologist Wolf Reik, director of the Altos Cambridge Institute of Science (opened last year by rejuvenation-focused company Altos Labs), praised the sophistication and thoroughness of the Harvard team’s study, but says the team’s indirect way of inducing epigenetic changes with dramatic DNA breaks that could have other effects makes it hard to prove those changes are what’s causing aging. It’s also unclear how well mice with induced DNA breaks mimic naturally aging animals, says Jan Vijg, a geneticist at the Albert Einstein College of Medicine. He and others stress that aging is a complex process with multiple contributing factors, and that in both papers, the effects of OSK treatment were moderate: a small extension of life span in one, and a partial reversal of artificially induced symptoms in the other. “The jump that now aging is a program” that can be wound backward isn’t justified by the research, Vijg says. Still, both groups want to move their work toward the clinic. Rejuvenate is examining the mechanisms underlying the treatment’s action and tweaking its delivery and composition, Davidsohn says. “OSK might not be the final set” of factors, he adds. Sinclair says his team is already testing AAV-delivered OSK in the eyes of monkeys. “If those studies in monkeys go well and everything looks safe enough for humans, the plan is to immediately apply to the FDA [Food and Drug Administration] to do a study in one or more [age-related] diseases of blindness.”

Published in Science (Jan.13, 2023): https://doi.org/10.1126/science.adg6801 

See also:

 https://doi.org/10.1101/2023.01.04.522507 

https://doi.org/10.1016/j.cell.2022.12.027 

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged at the end of 2019 and caused the devastating global pandemic of coronavirus disease 2019 (COVID-19), in part because of its ability to effectively suppress host cell responses1–3. In rare cases, viral proteins dampen antiviral responses by mimicking critical regions of human histone proteins4–8, particularly those containing post-translational modifications required for transcriptional regulation9–11. Recent work has demonstrated that SARS-CoV-2 markedly disrupts host cell epigenetic regulation12–14. However, how SARS-CoV-2 controls the host cell epigenome and whether it uses histone mimicry to do so remain unclear. Here we show that the SARS-CoV-2 protein encoded by ORF8 (ORF8) functions as a histone mimic of the ARKS motifs in histone H3 to disrupt host cell epigenetic regulation.

ORF8 is associated with chromatin, disrupts regulation of critical histone post-translational modifications and promotes chromatin compaction. Deletion of either the ORF8 gene or the histone mimic site attenuates the ability of SARS-CoV-2 to disrupt host cell chromatin, affects the transcriptional response to infection and attenuates viral genome copy number. These findings demonstrate a new function of ORF8 and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Further, this work provides a molecular basis for the finding that SARS-CoV-2 lacking ORF8 is associated with decreased severity of COVID-19. The SARS-CoV-2 protein ORF8 functions as a mimic of histone H3 to disrupt host cell epigenetic regulation.

Published in Nature (Oct. 5, 2022): 

https://doi.org/10.1038/s41586-022-05282-z 

An immune response that likely evolved to help fight infections appears to be the mechanism that drives human immunodeficiency virus (HIV) into a latent state, lurking in cells only to erupt anew, researchers at Duke Health report. Publishing Nov. 14 in the journal Nature Microbiology, the research team provides new insights into the vexing process that makes HIV particularly stealthy, but could also play a role in other viral infections. "HIV has proven to be incurable because of a small number of latently HIV-infected T-cells that are untouched by both antiviral drugs and the immune response," said senior author Bryan R. Cullen, Ph.D., professor in the Department Molecular Genetics and Microbiology at Duke University School of Medicine. "These cells, which are very long lived, can spontaneously emerge from latency and start producing HIV even years after infection, thus necessitating the life-long use of antiretrovirals," Cullen said. "The origin of these latently infected cells has remained unknown despite considerable effort." The findings from Cullen and colleagues offer important insights, pointing to a protein complex called SMC5/6, which is involved in a host cell's chromosome function and repair. HIV enters the body, infects the immune system's CD4+ T-cells, then makes a genome-length DNA molecule that it integrates into a host cell chromosome where it is then copied to generate viral RNAs and proteins. If this so-called DNA provirus is prevented from integrating into the host cell DNA, for example by a drug that blocks this process, then it fails to make any viral RNAs and proteins and becomes inert. In contrast, DNA proviruses that are able to integrate are normally able to drive a productive HIV infection.

Cullen and his team found that in a small number of infected cells, the SMC5/6 protein complex initiates a process that silences the DNA provirus before it integrates into a host cell chromosome. These proviruses remain inert even after integration and result in latent infections, lying low until prompted to erupt into an active infection. "Our research suggests that latency results not from any intrinsic properties of the infecting HIV but rather from an unfortunate side effect of a cellular innate immune response that probably evolved to silence invasive foreign DNA," Cullen said. The researchers found that a molecule that shuts down SMC5/6's silencing action showed promising results as a potential therapeutic strategy as it inhibited the establishment of latent HIV infections. Reactivated proviruses are vulnerable to natural immune system responses and anti-retroviral drugs. "Although antiretroviral therapies can reduce the viral load in AIDS patients to below the level of detection, these drugs fail to eradicate HIV-1," Cullen said. "While there has been considerable effort expended on trying to develop therapies that can activate latent HIV-1 and help antiretroviral therapies clear the body of infectious virus, this effort has so far failed to identify drugs that are both effective and non-toxic. Our study represents a potentially important step toward achieving this goal." "Clearly, understanding the mechanism that results in HIV-1 latency may provide insights into how latent HIV-1 proviruses can be reactivated and then destroyed," Cullen said. In addition to Cullen, study authors include Ishak D. Irwan and Hal P. Bogerd.

Study cited published in Nature Microbiology (Nov. 14, 2022):

https://doi.org/10.1038/s41564-022-01264-z 

Scientists have created a first-of-its-kind mouse model of the COVID-19 disease, capable of revealing how the SARS-CoV-2 virus wreaks havoc on multiple organ systems in the animal's body. While this experimental model doesn't directly correspond to human coronavirus cases, it's a breakthrough in other ways, giving us a potential test system for exploring how the deadly respiratory pathogen extends way beyond the respiratory system in many cases of infection. "This mouse model is a really powerful tool for studying SARS-CoV-2 in a living system," explains cardiologist Arjun Deb from UCLA. Mouse models of COVID-19 have been engineered before, but none have gotten us to this point, the researchers say, by demonstrating what extra-pulmonary manifestations of COVID-19 look like. That's been a significant limitation for animal-based research into the virus's progression, and it's due to a couple of reasons. While mouse cells contain an analogue of the ACE2 receptor that the SARS-CoV-2 uses to bind to human cells, the virus doesn't seem to attach to the mouse version of the molecule. Genetically engineering mice with the human version of ACE2 provides a workaround of sorts, but before now, scientists hadn't succeeded in inducing multiple organ failure in mice, which could mimic the way human cases of extra-pulmonary infection tend to present. The shortfall may have been because prior studies used nasal inoculation on mice, infecting the animals with SARS-CoV-2 through the nose, which doesn't seem to develop into full-blown, system-wide coronavirus infections in mice.

In the new study, led by first author Shen Li, a cardiologist at UCLA, the team got around this by injecting the virus into the bloodstreams of engineered mice, where it could reach the human version of ACE2 (called hACE2) in the heart and other vital organs. Unfortunately for the subjects, the experimental tweaks worked. And while it wasn't a good outcome for the mice involved, being able to study systemically induced toxicity in SARS-CoV-2-infected mice could significantly expand our knowledge of the virus's branching capabilities in human cases. Such knowledge is sorely needed. "Among COVID-19 patients, those who have organs involved other than the lungs are most at risk of a bad outcome," Deb says. "So we felt it was really important to understand how the virus affects those other organs." In the experiment, systemic administration of the infection provoked rapid results. Within seven days, the infected mice "demonstrated profound morbidity, severely restricted activity, and were found huddled at the corner of the cage", in contrast with a control group of similarly engineered mice who were spared the infection, remaining healthy. In the same amount of time, the infected mice lost up to about 25 percent of their body weight due to sharply reduced food consumption, necessitating euthanisation. The infected mice also had damaged spleens, irregular heart activity and blood pressure, and altered levels of immune cells – all symptoms resembling human cases of COVID-19.

After the animals were euthanised, analysis of their organs revealed changes in gene expression in multiple tissues, disrupting cellular processes that generate energy in the body. "If a virus snuffs out the energy-generating pathways in multiple organs of the body, that's going to really wreak havoc," Deb explains.  Beyond these effects, the infected mice also bore numerous signs of epigenetic changes, which could explain the altered gene expression evident in multiple organs. It's not known for sure, but the impacts of this could potentially be felt long after an infection has been beaten by the immune system – and, hypothetically speaking, could be the basis of the prolonged symptoms experienced by COVID-19 'long haulers'. "Although the physiological significance of SARS-CoV-2 altered DNA methylation patterns is not clear from our study, our model provides proof of concept that such epigenetic changes do occur soon after SARS-CoV-2 infection and can potentially led to persistent transcriptional changes affecting tissue homeostasis and organ function," the authors write in their paper. "Such epigenetic changes potentially occurring in humans with COVID-19 could lead to symptoms from persistent changes in dysregulated gene expression in infected tissues even in the absence of tissue viral burden."...

Cited Research Published in JCI Insight (Dec. 7, 2020):

https://doi.org/10.1172/jci.insight.145027