Comparative interactomics analysis of different ALS-associated proteins identifies converging molecular pathways

Amyotrophic lateral sclerosis (ALS) is a devastating neurological disease with no effective treatment available. An increasing number of genetic causes of ALS are being identified, but how these genetic defects lead to motor neuron degeneration and to which extent they affect common cellular pathways remains incompletely understood. To address these questions, we performed an interactomic analysis to identify binding partners of wild-type (WT) and ALS-associated mutant versions of ATXN2, C9orf72, FUS, OPTN, TDP-43 and UBQLN2 in neuronal cells. This analysis identified several known but also many novel binding partners of these proteins. Interactomes of WT and mutant ALS proteins were very similar except for OPTN and UBQLN2, in which mutations caused loss or gain of protein interactions. Several of the identified interactomes showed a high degree of overlap: shared binding partners of ATXN2, FUS and TDP-43 had roles in RNA metabolism; OPTN- and UBQLN2-interacting proteins were related to protein degradation and protein transport, and C9orf72 interactors function in mitochondria. To conf

Understanding ALS: insights from genetics, genomics and functional biology

Amyotrophic lateral sclerosis is a progressive neurological disorder. It is characterized by the selective degeneration of central and peripheral motor neurons, leading to muscle wasting and weakness, and subsequent paralysis. Patients die on average 3 to 5 years after disease onset, mostly due to respiratory failure. Progress in understanding the genetic background of ALS has recently begun to improve our understanding of pathogenic changes underlying the disease. However, both at the preclinical and clinical levels, many questions remain to be addressed. In this thesis, we expand the knowledge on ALS pathogenesis by combining different approaches from genetics, genomics and functional biology. First, we used gene expression profiling to study ALS pathogenesis in the SOD1-G93A mouse model of ALS. We show that blood gene expression profiles can be used to distinguish transgenic from wild-type mice by studying overlap and differences in gene expression of different tissues in this mouse model. Also, we used gene expression profiling to study the effect of the only currently available drug for ALS, riluzole, in SOD1-G93A mice. Several pathways were identified as influenced by riluzole treatment, including ubiquitin-mediated proteolysis, RNA-protein interaction and mitochondrial function. Changed RNA-protein interaction has recently emerged as important pathogenic mechanism in ALS. Therefore, we next investigated the occurrence of rare variants in previously ALS-associated genomic regions on human chromosome 9 and 19 and found that rare variants in the coding parts of these regions were not associated with ALS. We have confirmed the presence of FUS variants in a cohort of Dutch ALS patients, at equal frequencies as has been described in other studies. We then focused on further studying cellular mechanisms associated with FUS-caused ALS. ALS-linked mutations in FUS often lead to cytosolic mislocalization of the protein. We therefore performed a protein-interaction screen and determined numerous FUS-interacting proteins, including SMN and FMRP. Both SMN and FMRP are involved in neurological disease (SMA and FXS, respectively) and, in addition, genetic variation in SMN has been shown to be associated with ALS. Genetic variation in FMRP, however, is not associated with ALS, as described in this thesis. Subsequently, we showed that both SMN and FMRP are sequestered into FUS-associated cytosolic protein aggregates in primary neuron models. The sequestration of these proteins into cytosolic protein aggregates leads to their depletion from the axon, the endogenous expression site of the proteins. This impairs their normal function, as both SMN and FMRP have specific axonal functions. Depletion of SMN by ALS-mutant FUS aggregates leads to morphological defects, particularly at the growth cone, in primary cortical neurons. When the effect of protein sequestration of FMRP was studied in a zebrafish model of FUS, we observed a decrease in integrity of the neuromuscular junction. Importantly, each defect could be rescued by restoring expression of SMN and FMRP, respectively. These findings illustrate how protein aggregation in ALS leads to sequestration of proteins, depleting them from endogenous sites of expression and thereby leading to defects in axonal connectivity. Approaches to decrease protein aggregation toxicity and tackle connectivity defects are promising therapeutic strategies for ALS

Author Correction: Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Correction to: Nature Genetics https://doi.org/10.1038/s41588-021-00973-1, published online 6 December 2021. In the version of this article initially published, the affiliation for Nazli Başak appeared incorrectly. Nazli Başak is at Koç University, School of Medicine, KUTTAM-NDAL, Istanbul, Turkey, and not Bogazici University. The error has been corrected in the HTML and PDF versions of the article

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press