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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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Cell stress-related biochemical events may be partly driving Parkinson’s disease

Cell stress-related biochemical events may be partly driving Parkinson's disease

Parkinson’s disease may be driven in part by cell stress-related biochemical events that disrupt a key cellular cleanup system, leading to the spread of harmful protein aggregates in the brain, according to a new study from scientists at Scripps Research.

The discovery, published in The Journal of Neuroscience in February 2022, offers a clear and testable hypothesis about the progression of Parkinson’s disease, and may lead to treatments capable of significantly slowing or even stopping it.

We think our findings about this apparent disease-driving process are important for developing compounds that can specifically inhibit the process of disease spread in the brain.”


Stuart Lipton, MD, PhD, study senior author, Step Family Endowed Chair, founding co-director of the Neurodegeneration New Medicines Center, and professor in the Department of Molecular Medicine at Scripps Research

Parkinson’s disease affects roughly one million people in the United States. Its precise trigger is unknown, but it entails the deaths of neurons in a characteristic sequence through key brain regions. The killing of one small set of dopamine-producing neurons in the midbrain leads to the classic Parkinsonian tremor and other movement impairments. Harm to other brain regions results in various other disease signs including dementia in late stages of Parkinson’s. A closely related syndrome in which dementia occurs early in the disease course is called Lewy Body Dementia (LBD), and affects about 1.4 million people in the U.S.

In both diseases, affected neurons contain abnormal protein aggregations, known as Lewy bodies, whose predominant ingredient is a protein called alpha-synuclein. Prior studies have shown that alpha-synuclein aggregates can spread from neuron to neuron in Parkinson’s and LBD, apparently transmitting the disease process through the brain. But precisely how alpha-synuclein aggregates build up and spread in this way has been unclear.

One clue, uncovered by Lipton’s lab and others in prior research, is that the Parkinson’s/LBD disease process generates highly reactive nitrogen-containing molecules including nitric oxide. In principle, these reactive nitrogen molecules could disrupt important cellular systems, including “housekeeping” systems that normally keep protein aggregates under control.

In the new study, the Scripps Research team demonstrated the validity of this idea by showing that a type of nitrogen-molecule reaction called S-nitrosylation can affect an important cellular protein called p62, triggering the buildup and spread of alpha-synuclein aggregates.

The p62 protein normally assists in autophagy, a waste-management system that helps cells get rid of potentially harmful protein aggregates. The researchers found evidence that in cell and animal models of Parkinson’s, p62 is S-nitrosylated at abnormally high levels in affected neurons. This alteration of p62 inhibits autophagy, causing a buildup of alpha-synuclein aggregates. The buildup of aggregates, in turn, leads to the secretion of the aggregates by affected neurons, and some of these aggregates are taken up by nearby neurons.

“The process we observed seems very similar to what is seen in Parkinson’s and LBD brains,” says study first author Chang-Ki Oh, PhD, a staff scientist in the Lipton laboratory.

The researchers also tested postmortem brains of LBD patients, and again found that levels of S-nitrosylated p62 were abnormally high in affected brain areas-;supporting the idea that this process occurs in humans.

Lipton and Oh say that S-nitrosylation of proteins becomes more likely in many situations of cellular stress, including the presence of protein aggregates. Thus, this chemical modification of p62 could be a key factor in a self-reinforcing process that not only stresses brain cells beyond their limits, but also spreads the source of stress to other brain cells.

The team is now working to develop drug-like compounds that specifically inhibit the S-nitrosylation of p62. Although it would take years to develop such compounds as potential commercial drugs, they could, in principle, slow the Parkinson’s/LBD disease process or prevent its further spread in the brain after it begins, Lipton says.

Source:

Journal reference:

Oh, C., et al. (2022) S-Nitrosylation of p62 Inhibits Autophagic Flux to Promote α-Synuclein Secretion and Spread in Parkinson’s Disease and Lewy Body Dementia. Journal of Neuroscience. doi.org/10.1523/JNEUROSCI.1508-21.2022.