12 Mar 2024

Almost half of a person's DNA consists of retrotransposons, remnants of ancient viral infections that have jumped around the human genome. Retrotransposons are typically kept under wraps by epigenetics, but tau can unleash those restraints, allowing retrotransposons to flare in tauopathies. This line of investigation is becoming an object of fascination both for drug testing and basic science.

In a preprint posted to medRxiv on February 28, scientists led by Bess Frost at the University of Texas Health in San Antonio describe a pilot study aiming to quiet fidgety retrotransposons. People with mild cognitive impairment took the HIV drug lamivudine. It seemed safe, and some neurodegeneration and neuroinflammation markers nudged toward normal. “This is proof of principle for using antiretrovirals in Alzheimer’s disease and is encouraging,” Andrew Satlin of Transposon Therapeutics, Westport, Connecticut, told Alzforum.

A second preprint, posted to bioRxiv on February 5 by Frost and colleagues, reports genomic evidence of what goes awry at retrotransposons in AD. People with the disease had as many new genetic insertions of the jumping genes as controls, but certain ones were less methylated, meaning more transcriptionally active. “These results reinforce the concept that retrotransposons get activated in AD,” said John Sedivy of Brown University, Providence, Rhode Island.

Tau can activate retrotransposons to spew double-stranded RNA and viral proteins. This rallies the immune system to clear the pseudo-invaders, but can also drive neurodegeneration (Jul 2018 news). Also called 3TC, lamivudine is a nucleoside analog that inhibits reverse transcriptase, an enzyme encoded by some retrotransposons to help them spread and embed into the genome. The drug stifled retrotransposon activity and neurodegeneration in tauopathy models (Vallés-Saiz et al., 2023; Wahl et al., 2023; Sun et al., 2023).

Lamivudine is FDA-approved to treat HIV and chronic hepatitis B, and epidemiological data indicate that people taking the drug long-term may be less likely to develop AD (Magagnoli et al., 2023). Might it curb AD markers and symptoms in clinical trials?

To find out, Campbell Sullivan, first author of the medRxiv preprint, and colleagues ran an open-label pilot study. Twelve people with MCI, ages 52 to 83, took a 300 mg lamivudine pill once daily for six months. This is standard dosing for HIV and hepatitis B. Nine participants were women; 10 were white. They took cognitive tests, gave cerebrospinal fluid samples at the beginning and end of the study, and blood samples at baseline and every two months.

The primary outcomes were safety, feasibility, blood-brain barrier penetration, and peripheral effects of lamivudine on reverse transcriptase activity. Secondary outcomes were changes in cognition and fluid biomarkers of neurodegeneration and neuroinflammation.

All 12 participants completed the trial. The only adverse event, gastrointestinal bleeding due to a peptic ulcer, happened in someone also taking daily aspirin. Lamivudine is considered safe for the general population, but this is the first time it has been tested in MCI.

Lamivudine was detected in the blood and CSF of all participants throughout the study, suggesting to the authors that it got into the brain. Avindra Nath of the National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, wasn’t so sure. “Just because the drug goes into the CSF doesn't mean it's getting into the brain,” he told Alzforum.

What did lamivudine do? Reverse transcriptase activity in the blood did not change after treatment, though this measure varied widely from person to person.

Scores on the Mini-Mental State Exam (MMSE) and Preclinical Alzheimer Cognitive Composite (PACC-5) trended worse after treatment. When the scientists removed scores from two people who had caught COVID-19 during the study, most of the difference between baseline and post-trial scores disappeared. COVID can worsen cognition (Mar 2022 news).

As for fluid biomarkers, the plasma Aβ42/40 ratio nudged up during the study, and CSF glial fibrillary acidic protein (GFAP) levels dropped (image below). The former suggests less brain amyloid pathology; the latter reduced astrogliosis. Neurofilament light and phosphotau-181 levels did not change.

There were possible signals of cooled neuroinflammation. CSF vascular endothelial growth factor receptor 1 (Flt1) and IL-15 are high in AD and linked to worse cortical thinning and cognitive decline (Janelidze et al., 2018). On lamivudine, CSF levels of Flt1 dropped, whereas plasma IL-15 rose. Little is known about plasma IL-15 in AD, with one small study finding it to be lower in people with AD than in controls and another study finding no difference (Rentzos et al., 2007; Johansson et al., 2017). CSF or plasma levels of 20 or 29 other markers of neuroinflammation, respectively, remained unchanged after lamivudine.

The small sample size of this study does not allow much interpretation, the scientists acknowledge. “It’s encouraging that there are hints of some biomarkers going in a positive direction,” said Satlin. “But, without controls and data from a few people, it is hard to make much of the clinical effects.”

Biomarker Signals? After six months of daily lamivudine, CSF levels of GFAP (left) nudged downward; plasma Aβ42/40 (right) rose slightly. [Courtesy of Sullivan et al., medRxiv, 2024.]

Frost is planning a placebo-controlled Phase 2b trial of lamivudine in AD and a Phase 2a trial in primary tauopathies. She hoped to add a third arm evaluating both lamivudine and Leqembi.

Sedivy and Meghan Riddle at Butler Hospital in Providence are heading a Phase 1 trial of lamivudine’s cousin, FDA-approved emtricitabine, in people with MCI or early stage AD, who either take the drug or a placebo daily for six months. The trial will wrap up mid-next year.

For its part, Transposon Therapeutics is studying the reverse transcriptase inhibitor censavudine (aka TPN-101) in Phase 2 trials for amyotrophic lateral sclerosis/frontotemporal dementia and progressive supranuclear palsy. The company reported positive data at AD/PD in Lisbon last week. A trial in AD is in planning as well, though Satlin said they have not decided on the Phase yet.

Clues in our Genes
How might reverse transcriptase inhibitors block retrotransposons from wreaking havoc in the brain? To learn more about these jumping genes, bioRxiv preprint first author Paulino Ramirez and colleagues analyzed DNA extracted from postmortem brain tissue from six controls and 12 people with AD, half at Braak stages III and half at V/VI. They used long-read whole-genome sequencing, a new technology that enables sequencing of previously unreadable parts of the genome, such as the repeat-rich segments often found in retrotransposons.

Controls and AD cases had the same overall number of new retrotransposon insertions in their genomes. However, DNA methylation analysis showed hypomethylation of LINE1 retrotransposons, which encode a reverse transcriptase, and of human endogenous retrovirus K (HERV-K) sequences. This implies that they were more transcriptionally active in AD, meaning cells might make more of the enzymes and viral proteins.

Andrew Yoo at the Washington University School of Medicine, St. Louis, was intrigued by this demethylation. “What directs enzymes that regulate methylation to these specific retrotransposon loci? And could it be a downstream consequence of age-associated changes in tau?” he wondered.

These epigenetic results track with RNA-Seq data showing increased expression of retrotransposon transcripts in AD brain tissue and blood samples (Jun 2018 news; Macciardi et al., 2022). “We knew retrotransposons were upregulated in AD, but we did not know which ones,” Sedivy said. He told Alzforum that he has unpublished long-read sequencing data very similar to Frost’s. “What she’s reporting is the tip of the iceberg,” added Sedivy.

Frost believes that by blocking LINE1 reverse transcriptase, lamivudine suppresses the overproduction of viral proteins and other virus-like nucleic acids from retrotransposons, ameliorating symptoms in AD models—and possibly in people.

Incidentally, Frost told Alzforum, her team also spotted retrotransposons nestled next to, or embedded with, AD risk variants of 23 genes, including the lipid transporter gene ABCA7. Frost wondered whether the jumping genes might explain some of the risk signal at these loci. “No one was able to see these retrotransposons before because they were really hard to sequence,” she said. “We need more data to see if these elements drive disease.”—Chelsea Weidman Burke

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References

News Citations

1. Jumping Genes Rampant in Tau Flies 26 Jul 2018
2. Mild COVID Infection Can Shrink Brain, Speed Cognitive Decline 12 Mar 2022
3. Tau Aggregates Awaken Genetic Relics in the Brain 8 Jun 2018

Therapeutics Citations

1. Leqembi
2. Emtricitabine
3. TPN-101

Paper Citations

1. Vallés-Saiz L, Ávila J, Hernández F. Lamivudine (3TC), a Nucleoside Reverse Transcriptase Inhibitor, Prevents the Neuropathological Alterations Present in Mutant Tau Transgenic Mice. Int J Mol Sci. 2023 Jul 6;24(13) PubMed.
2. Wahl D, Smith ME, McEntee CM, Cavalier AN, Osburn SC, Burke SD, Grant RA, Nerguizian D, Lark DS, Link CD, LaRocca TJ. The reverse transcriptase inhibitor 3TC protects against age-related cognitive dysfunction. Aging Cell. 2023 May;22(5):e13798. Epub 2023 Mar 22 PubMed.
3. Sun Z, Kwon J-S, Ren Y, Chen S, Cates K, Lu X, Walker CK, Karahan H, Sviben S, Fitzpatrick JA, Valdez C, Houlden H, Karch CM, Bateman RJ, Sato C, Mennerick SJ, Diamond MI, Kim J, Tanzi RE, Holtzman DM, Yoo AS. Endogenous recapitulation of Alzheimers disease neuropathology through human 3D direct neuronal reprogramming. 2023 May 25 10.1101/2023.05.24.542155 (version 1) bioRxiv.
4. Magagnoli J, Yerramothu P, Ambati K, Cummings T, Nguyen J, Thomas C, Wang S-b, Cheng K, Juraev M, Dholkawala R, Nagasaka A, Ambati M, Nagasaka Y, Ban A, Ambati V, Sutton SS, Gelfand B, Ambati J. Reduction of human Alzheimer's disease risk and reversal of mouse model cognitive deficit with nucleoside analog use. 2023 Mar 21 10.1101/2023.03.17.23287375 (version 1) medRxiv.
5. Janelidze S, Mattsson N, Stomrud E, Lindberg O, Palmqvist S, Zetterberg H, Blennow K, Hansson O. CSF biomarkers of neuroinflammation and cerebrovascular dysfunction in early Alzheimer disease. Neurology. 2018 Aug 28;91(9):e867-e877. Epub 2018 Jul 27 PubMed.
6. Rentzos M, Paraskevas GP, Kapaki E, Nikolaou C, Zoga M, Tsoutsou A, Rombos A, Vassilopoulos D. Circulating interleukin-15 in dementia disorders. J Neuropsychiatry Clin Neurosci. 2007 Summer;19(3):318-25. PubMed.
7. Johansson P, Almqvist EG, Wallin A, Johansson JO, Andreasson U, Blennow K, Zetterberg H, Svensson J. Reduced cerebrospinal fluid concentration of interleukin-12/23 subunit p40 in patients with cognitive impairment. PLoS One. 2017;12(5):e0176760. Epub 2017 May 2 PubMed.
8. Macciardi F, Giulia Bacalini M, Miramontes R, Boattini A, Taccioli C, Modenini G, Malhas R, Anderlucci L, Gusev Y, Gross TJ, Padilla RM, Fiandaca MS, Head E, Guffanti G, Federoff HJ, Mapstone M. A retrotransposon storm marks clinical phenoconversion to late-onset Alzheimer's disease. Geroscience. 2022 Jun;44(3):1525-1550. Epub 2022 May 19 PubMed.

External Citations

1. Phase 1 trial

Further Reading

Papers

1. Martinez de Lagran M, Elizalde-Torrent A, Paredes R, Clotet B, Dierssen M. Lamivudine, a reverse transcriptase inhibitor, rescues cognitive deficits in a mouse model of down syndrome. J Cell Mol Med. 2022 Aug;26(15):4210-4215. Epub 2022 Jun 28 PubMed.

News

1. Attack From Within: How Ancient Viruses Resurface to Spread Tau 14 Apr 2023