A sporadic case of neurodegenerative disease likely represents the culmination of myriad gene-expression changes in the brain. How to make sense of the chaos, let alone restore order? In the January Nature Medicine, researchers led by Daniel Geschwind at the University of California, Los Angeles, identified two key networks of dysregulated genes—one in neurons, the other in glia—in multiple animal models of frontotemporal dementia (FTD) and Alzheimer’s disease. The same two gene networks were compromised in postmortem brain samples from people with these diseases. The researchers zeroed in on a microRNA and histone deacetylases as key drivers of these networks.
- In P301L-tau mice, cadres of genes changed expression in diseased brain regions.
- The same networks are perturbed in postmortem samples from multiple neurodegenerative diseases.
- Suppressing microRNA-203 and histone deacetylases restored network expression.
“This Herculean systems-level approach identified important pathogenic pathways in neurodegeneration that may be targetable by antisense oligonucleotides or small molecules,” commented Thomas Kukar of Emory University School of Medicine in Atlanta.
In recent years, researchers have started measuring co-expression changes that correlate with neurodegeneration (May 2013 webinar; Jun 2018 news). However, distinguishing changes that cause neurodegeneration from those that merely respond to it has proven difficult. Identifying therapeutic targets among such gene networks has been harder still. Animal models, while useful, are highly inbred, yielding insights that may not translate to other mice, let alone to people.
Grappling with these issues, co-first authors Vivek Swarup and Flora Hinz and colleagues searched for common gene-expression patterns that underpin neurodegeneration, and for ways to modulate those changes. Reasoning that tau pathology is a common denominator across many neurodegenerative disorders, including FTD and AD, the researchers analyzed gene expression in mice expressing the P301L mutant of human tau. They crossed the mice to three background strains, then compared gene-expression profiles among the offspring. At six months, hyperphosphorylated tau and gliosis were evident in the hippocampus, cortex, and brain stem, though cells were not dying yet. Compared with wild-type mice, all three tau transgenics had marked—and similar—changes in gene expression in these affected brain regions. Some expression changes also occurred in the cerebellum but often in the opposite direction, whereby the most upregulated genes in the cerebellum tended to be downregulated in the cortex. Since the cerebellum was spared from tau pathology, the expression changes there may reflect a protective response.
Common Change. On different genetic backgrounds, tau pathology came with common changes in gene expression over time. [Courtesy of Swarup et al., Nature Medicine, 2019.]
The researchers hypothesized that common gene-expression changes in affected regions across the different tau strains represented a neurodegenerative signature. To test this, they ran a weighted gene co-expression network analysis, zeroing in on two modules. One contained neuronal genes involved in synaptic function; the other comprised microglial and astrocyte genes involved in neuroinflammation. Lo and behold, the synaptic module contained genes previously implicated in FTD and progressive supranuclear palsy, including SLC32A1, NSF, and ELAVL2. AD risk genes, such as TREM2, ApoE, CLU, and C1q, populated the inflammatory module. Regions of the brain afflicted with early stage tau pathology were marked by suppression of the neurodegeneration-associated synaptic module, aka NAS, while showing an uptick of the inflammatory module (NAI).
When do these gene-expression changes occur in the course of disease? Geschwind said they happen in response to tau pathology, but prior to overt neurodegeneration. This suggested to him that the co-expression changes may contribute to early disease, rather than simply being a consequence of neuronal damage.
Wondering if these gene cliques pop up in other models of neurodegeneration, the scientists found NAS and NAI to be up- and downregulated, respectively, in affected brain regions of PS2APP, APP/PS1, and CRND8 AD models. In a progranulin gene mutation model of FTD, similar changes appeared over time, suggesting that this neurodegenerative signature holds across multiple disease etiologies.
Raffaele Ferrari of University College London considered this important. “This indicates that some of the neurodegenerative processes across neurological conditions are the same or similar, suggesting that effective therapeutic measures could target multiple different neurological conditions almost equally,” Ferrari wrote to Alzforum. He is a member of the International Frontotemporal Dementia Genomics Consortium, which co-authored the study.
It’s not just mice, either. Homologous modules emerged in postmortem brain samples from people with a range of neurodegenerative diseases. Both NAS and NAI networks were dysregulated in the cortices, but not cerebella, of people with tau-positive and tau-negative FTD, as well as in people with GRN-positive and GRN-negative FTD. Using mass spectrometry to test a subset of postmortem brain samples, the researchers concluded that these changes occurred at the protein level as well. The modules also cropped up in postmortem samples of people with AD, amyotrophic lateral sclerosis (ALS), and progressive supranuclear palsy (PSP), but not in samples from people with non-neurodegenerative brain disorders such as depression or schizophrenia. In people who had Aβ plaques, but no tau tangles or dementia, expression of these modules appeared normal.
Together, the findings suggested that while distinct genetic pathways instigate different neurodegenerative diseases, somewhere early in the pathogenic process gene-expression changes converge to compromise synaptic function and stoke neuroinflammation.
What controls this dysregulation? The researchers investigated microRNAs, which can suppress expression of groups of genes. Going back to the P301L-tau strain, they found altered expression of multiple microRNA networks in affected regions.
The single most upregulated microRNA was miR-203, which was elevated in autopsy tissue from people with AD and FTD. Its expression tracked up when NAS expression fell, suggesting miR-203 shuts down these neuronal genes. Indeed, overexpressing miR203 in cultured neurons or in the brains of wild-type mice suppressed genes in the synaptic module. In one-month-old P301L-tau mice, miR203 overexpression silenced multiple synaptic genes and increased apoptosis, whereas knocking down miR-203 prevented these changes.
The researchers also searched for small molecules that might counteract these neurodegenerative gene-expression changes. They screened Connectivity Map (CMap), a public resource of gene-expression responses to drugs, for compounds predicted to correct NAS and NAI changes. Four of the top 10 hits were histone deacetylase inhibitors. CMap analysis predicted these drugs would lift suppression of genes in the synaptic module, but suppress the inflammatory module. They researchers tested two HDAC inhibitors: scriptaid, which was the top hit, and suberanilo-hydroxamic acid. SAHA, also known as vorinostat, is currently undergoing a dose-finding trial in people with mild AD (see clinicaltrials.gov). Both compounds reduced cell death in neurons overexpressing miR-203, although SAHA became toxic above a concentration of 1 μM. In iPSC-derived neurons from people with FTD or AD, 0.5 μM SAHA restored expression of many genes in the NAS module. Neurons do not express many of the genes in the NAI module, and the researchers have yet to test whether the drugs restore normal expression to genes in that glial network.
Geschwind was surprised that histone deacetylase inhibitors emerged so clearly from the screen. He noted this does not mean they will make suitable drugs, given their potential for toxicity. Rather, he sees the finding as proof of principle that therapeutic approaches can emerge from complex gene network data.
Gerold Schmitt-Ulms of the University of Toronto said the study raises key questions, including how histone deacetylases and miR203 control the gene modules, and whether their inhibition can prevent cell death in vivo. “Dissecting the molecular underpinnings of their action may not be trivial, because both histone deacetylases and microRNAs typically have relatively low target specificity,” he added.
Peter Nelson of the University of Kentucky in Lexington was impressed that such a massive, multifaceted study would zoom in on specific therapeutic strategies. That said, Nelson is leery of a “one size fits all” approach to treating neurodegenerative disease. “There may be common nodes and bottlenecks, but these diseases are triggered by inherently different processes,” he said.
Noting that miR-203 is not normally expressed in the brain, Nelson wondered what its physiological relevance there might be. Walter Lukiw of Louisiana State University in New Orleans noted the same. Geschwind, however, considers miR203’s absence from the healthy brain a plus, since it would be a target only in the diseased brain.
In a joint comment to Alzforum, Evgenia Salta, Annerieke Sierksma, and Bart De Strooper of KU Leuven in Belgium praised the study for its thorough and systematic approach. They also cautioned that it relied on transcriptomics of bulk brain cells. “In light of recent reports on the many distinct, transcriptionally defined, microglial subtypes that seem to be differentially impacted by brain pathology or aging, analyzing modules that seemingly relate to a pool of different cell types, for instance microglia, astrocytes, and endothelia, precludes the ability to isolate the contribution of individual cell types to distinct forms of neurodegeneration,” they wrote. Geschwind agreed, and said that moving forward his lab will analyze these neurodegenerative networks using single-cell transcriptomics.—Jessica Shugart
Research Models Citations
- Swarup V, Hinz FI, Rexach JE, Noguchi KI, Toyoshiba H, Oda A, Hirai K, Sarkar A, Seyfried NT, Cheng C, Haggarty SJ, International Frontotemporal Dementia Genomics Consortium, Grossman M, Van Deerlin VM, Trojanowski JQ, Lah JJ, Levey AI, Kondou S, Geschwind DH. Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia. Nat Med. 2019 Jan;25(1):152-164. Epub 2018 Dec 3 PubMed.