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Study identifies an epigenetic regulator that suppresses pathogenic events in rheumatoid arthritis

Study identifies an epigenetic regulator that suppresses pathogenic events in rheumatoid arthritis

Rheumatoid arthritis (RA) is characterized by chronic inflammation of synovium, eventually leading to joint destruction. Epigenetic alteration (the mechanism of gene expression regulation without DNA sequence changes), such as low levels of DNA methylation, is one of the factors which worsens the RA state. However the mechanism by which the alterations occur remains largely unknown.

In the present study, we identified an epigenetic regulator UHRF1 that was remarkably up-regulated in synovial fibroblasts (SF) from arthritis model mice and RA patients. Previous study showed that UHRF1 is a key player in the maintenance of DNA methylation, although the function for RA is unknown. To understand UHRF1 function for arthritis, we generated mice with SF-specific UHRF1 conditional knockout (cKO) and experimental arthritis was induced.

cKO mice exhibited more severe arthritic phenotypes than the littermate control. Next, to reveal UHRF1 function in SF, RNA-seq and MBD-seq were performed using SF obtained from the control and cKO mice. Integrative genome-wide analyses of the transcriptome and methylome showed that expression of several cytokines was up-regulated in UHRF1-deficient SF accompanied by reduced DNA methylation signatures.

Also, UHRF1 expression in synovium was negatively correlated with several pathogenesis in RA patients. These data suggested that RA pathogenesis is exacerbated when UHRF1 levels are low in SF. Finally, we assessed whether UHRF1 stabilization contributes to improvement of arthritis pathogenesis. Ryuvidine, which was identified as a candidate chemical compound to the stabilize UHRF1 protein, was administrated in arthritis model mice.

The results showed that arthritis pathogenesis was ameliorated by treatment with Ryuvidine. Also, the development of organoids derived from RA-SF was suppressed by Ryuvidine.

This study demonstrated that UHRF1 expressed in SF with RA has a protective role in suppressing multiple pathogenic events in arthritis, suggesting that targeting UHRF1 could be a therapeutic strategy for RA.

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Interactive web portal details the extent of splicing events in noncoding sequences

Interactive web portal details the extent of splicing events in noncoding sequences

An online tool reveals the extent of gene-restructuring events in noncoding sequences.

An interactive web portal developed by scientists at KAUST offers a platform for cancer researchers to interrogate how RNA splicing in noncoding parts of genes fuels the growth of different types of tumors.

The new resource, named SpUR (short for Splicing in Untranslated Regions) and freely available online, details more than 1,000 splicing events found frequently in cancers in noncoding regions of mRNA located just downstream of protein-coding stop signals. The sites and expression levels of these events are catalogued and visualized for nearly 8,000 samples across 10 cancer types and corresponding normal tissues.

With the tool, independent research teams can now further probe the role of individual splice events in cancer development and progression.

These events could become candidates to study RNA dysregulations in cancer for academic researchers. Or they could serve as a primary source for the development of RNA-based anti-cancer drugs.”


Xin Gao, acting associate director of the Computational Bioscience Research Center and deputy director of the Smart Health Initiative at KAUST

Computer scientist Gao, together with postdoc Bin Zhang and research engineer Adil Salhi, created the SpUR database in collaboration with researchers at the Cancer Science Institute of Singapore.

The research showed that splicing in downstream sequences of a gene (known as 3′ untranslated regions, or 3′ UTRs) is pervasive in cancers, especially in genes linked to tumor aggression. Consequently, patients whose cancers harbor more of these gene-restructuring events tend to have poorer survival outcomes.

As a proof of principle, the researchers designed splice-switching agents known as antisense oligonucleotides (ASOs) that could block this splicing process in 3′ UTRs. When administered to liver cancer cells, these drugs helped repress tumor growth. And since the same kinds of splicing events are “ubiquitously expressed across different cancer types,” Gao notes, this type of therapeutic strategy “could be helpful to develop broad-spectrum anti-cancer drugs.”

One potential target:CTNNB1, which is a gene that provides instructions for making a protein called beta-catenin. Drug companies have long tried to target beta-catenin, given its central role in many cancer-signaling pathways, but with only limited success. The study from Gao and his collaborators showed that splicing in the 3′ UTR ofCTNNB1is widespread across cancers of the liver, breast, colon, kidney, lung and other organs, and that a spliced variant is the predominant driver of tumor progression.

In a mouse model of liver cancer, blocking this splicing resulted in complete tumor regression. An ASO therapy directed atCTNNB1splicing could therefore have broad utility in patients, and, as Gao points out, it is not likely to be the only one.

Source:

Journal reference:

Chan, J.J., et al. (2022) Pan-cancer, pervasive upregulation of 3’UTR splicing drives tumorigenesis. Nature Cell Biology. doi.org/10.1038/s41556-022-00913-z.

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Hemophilia A Gene Therapy Reduced Bleeding Events, Need for Clotting Factors

Hemophilia A Gene Therapy Reduced Bleeding Events, Need for Clotting Factors

The phase 3 trial of valoctocogene roxaparvovec for severe hemophilia A showed it reduced bleeding events as well as the use of factor VIII concentrates.

A phase 3 trial of valoctocogene roxaparvovec, a gene therapy for severe hemophilia A, showed it reduced bleeding events as well as the use of factor VIII concentrates and increased endogenous production of clotting factors.

Severe hemophilia A, defined as a factor VIII level of 1 IU/dL or lower, carries the highest risk of spontaneous and traumatic bleeding, resulting in loss of limbs, chronic pain, decreased quality of life, and higher risk of mortality. About 1 in 5000 males is born with the rare disease, and about 60% have the most severe form, according to the National Organization for Rare Disorders.

Outcomes for individuals with hemophilia A, caused by a deficient F8 gene, have improved with factor VIII concentrates that are used prophylactically, but bleeding events are not eliminated.

If approved by the FDA, the adeno-associated virus (AAV) vector gene therapy would be sold as Roctavian by BioMarin, which funded the study. The FDA has granted valoctocogene roxaparvovec Regenerative Medicine Advanced Therapy and Breakthrough Therapy designations; according to press reports, it could be priced as high as $3 million, making it the most expensive therapy to date.

Writing in The New England Journal of Medicine, the authors said the gene therapy enables steady production of factor VIII without additional prophylactic measures. However, the authors also said, “The expression of the transferred gene appears to decline over time; further study is needed to address whether repeat treatment will be necessary or possible.”1

Participants in the trial (GENEr8-1) were 134 adult men 18 years or older who had previously been treated with clotting-factor prophylaxis for at least 1 year, 2 of whom were living with HIV. At baseline, 61.9% of the participants were receiving factor VIII prophylaxis with standard half-life products, 27.6% with extended half-life products, and 17.9% with plasma-derived products. None of the participants were receiving emicizumab (Helimbra), a humanized bispecific monoclonal antibody that joins both factor IXa and X, which are proteins necessary to activate the natural coagulation cascade and restore the blood clotting process.

Exclusion criteria for the open-label, single-group, multicenter, phase 3 study included those who had preexisting anti-AAV5 antibodies, factor VIII inhibitors, or significant liver disease.

Patients received a single infusion of valoctocogene roxaparvovec at a dose of 6×1013 vector genomes per kilogram of body weight, and investigators examined the change from baseline in factor VIII activity (measured with a chromogenic substrate assay) during weeks 49 through 52 after infusion.

Secondary end points included the change in annualized factor VIII concentrate use and bleeding rates.

Overall, 134 participants received an infusion and completed more than 51 weeks of follow-up. The analysis included data from 132 HIV-negative participants, including 112 participants enrolled from a prospective noninterventional study.

Results showed:

  • A decline in annualized rates of factor VIII use of 98.6% and treated bleeding of 83.8% (P <.001 for both comparisons)
  • A median factor VIII activity level of 5 IU/dL or higher in 88.1% of participants

As for safety, all participants had at least 1 adverse event (AE); 22 of 134 (16.4%) reported serious AEs.

Elevations in alanine aminotransferase levels occurred in 115 of 134 participants (85.8%) and were managed with glucocorticoids. The other most common AEs were headache (38.1%), nausea (37.3%), and elevations in aspartate aminotransferase levels (35.1%).

There were no deaths in the trial or withdrawals due to AEs, and there was no thrombosis or development of factor VIII inhibitors.

The investigators wrote that “intra- and interindividual variability in factor VIII activity after gene transfer were notable.” Seven participants had a median factor VIII activity level of greater than 150 IU/dL; 12 participants had a median factor VIII activity level of less than 3 IU/dL, measured by chromogenic assay; and 2 participants, measured by a 1-stage assay, had a factor VIII activity level of less than 1 IU/dL.

The causes of the variability are not fully known; the authors said biologic variables and molecular events related to gene transfer and expression may impact endogenous factor VIII production.

There were a few limitations to the study. The 2 participants with HIV were excluded from the primary analysis, and so generalizing the results to that population may be constrained. In addition, direct comparisons to emicizumab cannot be made because the participants had previously been using factor VIII concentrates, but the authors said “the annualized rates of treated bleeding here were similar to those reported with long-term emicizumab prophylaxis.”

In an accompanying editorial, the author called valoctocogene roxaparvovec “a new choice for care that could be truly transformative and liberating for eligible men with hemophilia” and called on payers, policymakers, and others to get ready for its entrance.2

Reference

1. Ozelo MC, Mahlangu J, Pasi KJ, et al; GENEr8-1 Trial Group. Valoctocogene roxaparvovec gene therapy for hemophilia A. N Engl J Med. 2022;386:1013-1025. doi:10.1056/NEJMoa2113708

2. Thornberg CD. Prepare the way for hemophilia A gene therapy. N Engl J Med. 2022;386:1081-1082. doi:10.1056/NEJMe2200878