Therapeutic Targeting of Proteostasis in Amyotrophic Lateral Sclerosis—a Systematic Review and Meta-Analysis of Preclinical Research

Funding This work was supported by AMS: 210JMG 3102 R45620 and CSO and MNDS: 217ARF R45951. Medical Research Council (MRC UK; MR/L016400/1).Peer reviewedPublisher PD

Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes

<div><p>RNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family genes that mediate these pathways suggests that defensive RNAi is ancient, and probably shared by most animal (metazoan) phyla. Indeed, while vertebrates had been thought an exception, it has recently been argued that mammals also possess an antiviral RNAi pathway, although its immunological relevance is currently uncertain and the viral small RNAs (viRNAs) are not easily detectable. Here we use a metagenomic approach to test for the presence of viRNAs in five species from divergent animal phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga—which represents an independent origin of multicellularity from plants, fungi, and animals. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify viRNAs derived from those viruses. We identified 21U small RNAs derived from an RNA virus in the brown alga, reminiscent of plant and fungal viRNAs, despite the deep divergence between these lineages. However, contrary to our expectations, we were unable to identify canonical (i.e. <i>Drosophila-</i> or nematode-like) viRNAs in any of the animals, despite the widespread presence of abundant micro-RNAs, and somatic transposon-derived piwi-interacting RNAs. We did identify a distinctive group of small RNAs derived from RNA viruses in the mollusc. However, unlike ecdysozoan viRNAs, these had a piRNA-like length distribution but lacked key signatures of piRNA biogenesis. We also identified primary piRNAs derived from putatively endogenous copies of DNA viruses in the cnidarian and the echinoderm, and an endogenous RNA virus in the mollusc. The absence of canonical virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response. Alternatively, these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, with cryptic viRNAs not detectable through simple metagenomic sequencing of wild-type individuals. In either case, our findings show that the antiviral RNAi responses of arthropods and nematodes, which are highly divergent from each other and from that of plants and fungi, are also highly diverged from the most likely ancestral metazoan state.</p></div

Distinct neuroinflammatory signatures exist across genetic and sporadic ALS cohorts

Acknowledgments This research was funded in part by the Wellcome Trust (108890/Z/15/Z) to OMR, a Pathological Society and Jean Shanks Foundation grant (JSPS CLSG 202002) to JMG and JOS, an NIH grant (5-R01-NS127186-02) to JMG, FMW, and JOS, a Motor Neuron Disease (MND) Scotland grant to JMG and CRS (2021/MNDS/RP/8440GREG), and a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (215454/Z/19/Z) to CRS. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. This work would not be possible without the resources of the Edinburgh Brain Bank. The authors declare no conflicts of interest.Preprin

Distinct neuroinflammatory signatures exist across genetic and sporadic amyotrophic lateral sclerosis cohorts

Acknowledgements This work would not be possible without the resources of the Edinburgh Brain Bank, and the tissue donors and their families. Funding This research was funded in part by the Wellcome Trust (108890/Z/15/Z) to O.M.R., a Pathological Society of Great Britain & Ireland and Jean Shanks Foundation grant (JSPS CLSG 202002) to J.M.G. and J.O., a National Institutes of Health (NIH) grant (5-R01-NS127186-02) to J.M.G., F.M.W., and J.O., a Motor Neuron Disease (MND) Scotland grant to J.M.G. and C.R.S. (2021/MNDS/RP/8440GREG), and a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (215454/Z/19/Z) to C.R.S.Peer reviewedPublisher PD

pTDP-43 aggregates accumulate in non-central nervous system tissues prior to symptom onset in amyotrophic lateral sclerosis : a case series linking archival surgical biopsies with clinical phenotypic data

Acknowledgements The authors would like to thank the staff at the NHS Lothian BioResource (Vishad Patel and Craig Marshall) and the NHS Grampian biorepository (Joan Wilson) and the staff and corefunded resources of the imaging and histology core facility at the Institute of Medical Sciences (Gillian Milne, Lucinda Wight, and Debbie Wilkinson). This study was funded by the Pathological Society/Jean Shanks Foundation (JSPS CLSG 202002 to JMG and JO’S), The Royal Society (RGS\R1\221396 to JMG) and the Wellcome Trust (108890/Z/15/Z to OR). Funders had no role in study design, data collection, data analyses, interpretation, or writing the manuscriptPeer reviewedPostprin

Systematic, comprehensive, evidence-based approach to identify neuroprotective interventions for motor neuron disease: using systematic reviews to inform expert consensus

Objectives: Motor neuron disease (MND) is an incurable progressive neurodegenerative disease with limited treatment options. There is a pressing need for innovation in identifying therapies to take to clinical trial. Here, we detail a systematic and structured evidence-based approach to inform consensus decision making to select the first two drugs for evaluation in Motor Neuron Disease-Systematic Multi-arm Adaptive Randomised Trial (MND-SMART: NCT04302870), an adaptive platform trial. We aim to identify and prioritise candidate drugs which have the best available evidence for efficacy, acceptable safety profiles and are feasible for evaluation within the trial protocol. Methods: We conducted a two-stage systematic review to identify potential neuroprotective interventions. First, we reviewed clinical studies in MND, Alzheimer’s disease, Huntington’s disease, Parkinson’s disease and multiple sclerosis, identifying drugs described in at least one MND publication or publications in two or more other diseases. We scored and ranked drugs using a metric evaluating safety, efficacy, study size and study quality. In stage two, we reviewed efficacy of drugs in MND animal models, multicellular eukaryotic models and human induced pluripotent stem cell (iPSC) studies. An expert panel reviewed candidate drugs over two shortlisting rounds and a final selection round, considering the systematic review findings, late breaking evidence, mechanistic plausibility, safety, tolerability and feasibility of evaluation in MND-SMART. Results: From the clinical review, we identified 595 interventions. 66 drugs met our drug/disease logic. Of these, 22 drugs with supportive clinical and preclinical evidence were shortlisted at round 1. Seven drugs proceeded to round 2. The panel reached a consensus to evaluate memantine and trazodone as the first two arms of MND-SMART. Discussion: For future drug selection, we will incorporate automation tools, text-mining and machine learning techniques to the systematic reviews and consider data generated from other domains, including high-throughput phenotypic screening of human iPSCs

The discovery, distribution, and evolution of viruses associated with drosophila melanogaster

Drosophila melanogaster is a valuable invertebrate model for viral infection and antiviral immunity, and is a focus for studies of insect-virus coevolution. Here we use a metagenomic approach to identify more than 20 previously undetected RNA viruses and a DNA virus associated with wild D. melanogaster. These viruses not only include distant relatives of known insect pathogens, but also novel groups of insect-infecting viruses. By sequencing virus-derived small RNAs we show that the viruses represent active infections of Drosophila. We find that the RNA viruses differ in the number and properties of their small RNAs, and we detect both siRNAs and a novel miRNA from the DNA virus. Analysis of small RNAs also allows us to identify putative viral sequences that lack detectable sequence similarity to known viruses. By surveying >2000 individually collected wild adult Drosophila we show that more than 30% of D. melanogaster carry a detectable virus, and more than 6% carry multiple viruses. However, despite a high prevalence of the Wolbachia endosymbiont—which is known to be protective against virus infections in Drosophila—we were unable to detect any relationship between the presence of Wolbachia and the presence of any virus. Using publicly available RNA-seq datasets we show that the community of viruses in Drosophila laboratories is very different from that seen in the wild, but that some of the newly discovered viruses are nevertheless widespread in laboratory lines and are ubiquitous in cell culture. By sequencing viruses from individual wild-collected flies we show that some viruses are shared between D. melanogaster and D. simulans. Our results provide an essential evolutionary and ecological context for host-virus interaction in Drosophila, and the newly reported viral sequences will help develop D. melanogaster further as a model for molecular and evolutionary virus research

Correction: Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes.

[This corrects the article DOI: 10.1371/journal.pgen.1007533.]

Phylogenetic relationships of virus-like contigs from the dog whelk.

<p>Mid-point rooted maximum likelihood phylogenetic trees for each of the virus-like contigs associated with viRNAs in the dog whelk (<i>Nucella lapillus</i>). New virus-like contigs described here are marked in red, sequences marked ‘TSA’ are derived from public transcriptome assemblies of the species named, and the scale is given in amino acid substitutions per site. Panels are: (A) rhabdoviruses related to lyssaviruses, inferred using the protein sequence of the nucleoprotein (the only open reading frame available from this contig, which is likely an EVE); (B) orthomyxoviruses related to influenza and thogoto viruses, inferred using the protein sequence of PB1; (C) rhabdoviruses and chuviruses, inferred from the RNA polymerase. Support values and accession identifiers are presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s002" target="_blank">S2 Fig</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s019" target="_blank">S3 Data</a>, and alignments in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s018" target="_blank">S2 Data</a>. Given the high level of divergence, alignments and inferred trees should be treated as tentative.</p

Small RNAs from TE-like contigs.

<p>The threecolumns show (left to right): the distribution of 20-30nt small RNAs along the length of a TE-like contig; the size distribution of small RNA reads (U red, G yellow, C blue, A green); and the sequence ‘logo’ of unique sequences for the dominant sequence length. Read counts above the x-axis represent reads mapping to the positive sense (coding) sequence, and counts below the x-axis represent reads mapping to the complementary sequence. For the sequence logos, the upper and lower plots show positive and negative sense reads respectively, and the y-axis of each measures relative information content in bits. Where available, reads from the oxidised library are shown (A-F), but other libraries display similar distributions (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s008" target="_blank">S8 Fig</a>). These examples from sponge (A), sea anemone (B), starfish (C), earthworm (D), dog whelk (E-F) and brown alga (G) were chosen to best illustrate the presence of the ‘ping pong’ signature, but other examples are shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s008" target="_blank">S8 Fig</a>. Note that the size distribution of TE-derived small RNAs varies substantially among species, and that the dog whelk (E and F) displays at least two distinct patterns, one (F) reminiscent of that seen for some RNA virus contigs (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.g003" target="_blank">Fig 3C</a>). The data required to plot these figures is provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007533#pgen.1007533.s014" target="_blank">S5 Table</a>.</p