Abstract
Human prion diseases are remarkable for long incubation times followed typically by rapid clinical decline. Seed amplification assays and neurodegeneration biofluid biomarkers are remarkably ...useful in the clinical phase, but their potential to predict clinical onset in healthy people remains unclear. This is relevant not only to the design of preventive strategies in those at-risk of prion diseases, but more broadly, because prion-like mechanisms are thought to underpin many neurodegenerative disorders. Here, we report the accrual of a longitudinal biofluid resource in patients, controls and healthy people at risk of prion diseases, to which ultrasensitive techniques such as real-time quaking-induced conversion (RT-QuIC) and single molecule array (Simoa) digital immunoassays were applied for preclinical biomarker discovery.
We studied 648 CSF and plasma samples, including 16 people who had samples taken when healthy but later developed inherited prion disease (IPD) (‘converters’; range from 9.9 prior to, and 7.4 years after onset). Symptomatic IPD CSF samples were screened by RT-QuIC assay variations, before testing the entire collection of at-risk samples using the most sensitive assay. Glial fibrillary acidic protein (GFAP), neurofilament light (NfL), tau and UCH-L1 levels were measured in plasma and CSF. Second generation (IQ-CSF) RT-QuIC proved 100% sensitive and specific for sporadic Creutzfeldt-Jakob disease (CJD), iatrogenic and familial CJD phenotypes, and subsequently detected seeding activity in four presymptomatic CSF samples from three E200K carriers; one converted in under 2 months while two remain asymptomatic after at least 3 years’ follow-up.
A bespoke HuPrP P102L RT-QuIC showed partial sensitivity for P102L disease. No compatible RT-QuIC assay was discovered for classical 6-OPRI, A117V and D178N, and these at-risk samples tested negative with bank vole RT-QuIC. Plasma GFAP and NfL, and CSF NfL levels emerged as proximity markers of neurodegeneration in the typically slow IPDs (e.g. P102L), with significant differences in mean values segregating healthy control from IPD carriers (within 2 years to onset) and symptomatic IPD cohorts; plasma GFAP appears to change before NfL, and before clinical conversion.
In conclusion, we show distinct biomarker trajectories in fast and slow IPDs. Specifically, we identify several years of presymptomatic seeding positivity in E200K, a new proximity marker (plasma GFAP) and sequential neurodegenerative marker evolution (plasma GFAP followed by NfL) in slow IPDs. We suggest a new preclinical staging system featuring clinical, seeding and neurodegeneration aspects, for validation with larger prion at-risk cohorts, and with potential application to other neurodegenerative proteopathies.
Mok et al. present longitudinal biofluid RT-QuIC and neurodegenerative biomarker analyses of individuals at risk of and symptomatic for prion disease. RT-QuIC can detect seeding activity up to almost 4 years before disease onset, while neurodegenerative marker trajectories differ between fast and slow inherited prion diseases.
See Minikel and Vallabh (https://doi.org/10.1093/brain/awad143) for a scientific commentary on this article.
If ever there were “charismatic megaflora” of the sea, the Laminariales (kelp) would undoubtedly meet that designation. From the Northeast Pacific kelp forests to the less diverse, but nonetheless ...dense, kelp beds ranging from the Arctic to the cold temperate waters of the Southern Hemisphere, kelp provide habitat structure and food for a variety of productive marine systems. Consequently, kelp are well represented in the literature, however, understanding their evolution has proven challenging. We used a 152‐gene phylogenomics approach to better resolve the phylogeny of the “derived” kelp families (viz., Agaraceae, Alariaceae, Laminariaceae, and Lessoniaceae). The formerly unresolved Egregia menziesii firmly joined a significantly expanded Arthrothamnaceae including Arthrothamnus, Cymathaere, Ecklonia, Macrocystis, Nereocystis, Pelagophycus, Postelsia, Pseudolessonia, Saccharina, and Streptophyllopsis, which rendered both the Laminariaceae and Lessoniaceae monogeneric. A published eight‐gene alignment, the most marker‐rich prior to this study, was expanded and analyzed to facilitate inclusion of Aureophycus. Although the topology was unchanged at the family level between the transcriptome data set relative to eight‐gene analyses, the superior resolving power of the former was clearly established.
Although human tumours are shaped by the genetic evolution of cancer cells, evidence also suggests that they display hierarchies related to developmental pathways and epigenetic programs in which ...cancer stem cells (CSCs) can drive tumour growth and give rise to differentiated progeny. Yet, unbiased evidence for CSCs in solid human malignancies remains elusive. Here we profile 4,347 single cells from six IDH1 or IDH2 mutant human oligodendrogliomas by RNA sequencing (RNA-seq) and reconstruct their developmental programs from genome-wide expression signatures. We infer that most cancer cells are differentiated along two specialized glial programs, whereas a rare subpopulation of cells is undifferentiated and associated with a neural stem cell expression program. Cells with expression signatures for proliferation are highly enriched in this rare subpopulation, consistent with a model in which CSCs are primarily responsible for fuelling the growth of oligodendroglioma in humans. Analysis of copy number variation (CNV) shows that distinct CNV sub-clones within tumours display similar cellular hierarchies, suggesting that the architecture of oligodendroglioma is primarily dictated by developmental programs. Subclonal point mutation analysis supports a similar model, although a full phylogenetic tree would be required to definitively determine the effect of genetic evolution on the inferred hierarchies. Our single-cell analyses provide insight into the cellular architecture of oligodendrogliomas at single-cell resolution and support the cancer stem cell model, with substantial implications for disease management.
The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and ...PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein–protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.
Associations between procedure volumes and outcomes can inform minimum volume standards and the regionalization of health services. Robot-assisted surgery continues to expand globally; however, data ...are limited regarding which hospitals should be using the technology.BACKGROUNDAssociations between procedure volumes and outcomes can inform minimum volume standards and the regionalization of health services. Robot-assisted surgery continues to expand globally; however, data are limited regarding which hospitals should be using the technology.Using administrative health data for all residents of Ontario, Canada, this retrospective cohort study included adult patients who underwent a robot-assisted radical prostatectomy (RARP), total robotic hysterectomy (TRH), robot-assisted partial nephrectomy (RAPN), or robotic portal lobectomy using 4 arms (RPL-4) between January 2010 and September 2021. Associations between yearly hospital volumes and 90-day major complications were evaluated using multivariable logistic regression models adjusted for patient characteristics and clustering at the level of the hospital.STUDY DESIGNUsing administrative health data for all residents of Ontario, Canada, this retrospective cohort study included adult patients who underwent a robot-assisted radical prostatectomy (RARP), total robotic hysterectomy (TRH), robot-assisted partial nephrectomy (RAPN), or robotic portal lobectomy using 4 arms (RPL-4) between January 2010 and September 2021. Associations between yearly hospital volumes and 90-day major complications were evaluated using multivariable logistic regression models adjusted for patient characteristics and clustering at the level of the hospital.A total of 10,879 patients were included, with 7567, 1776, 724, and 812 undergoing a RARP, TRH, RAPN, and RPL-4, respectively. Yearly hospital volume was not associated with 90-day complications for any procedure. Doubling of yearly volume was associated with a 17-min decrease in operative time for RARP (95% confidence interval CI - 23 to - 10), 8-min decrease for RAPN (95% CI - 14 to - 2), 24-min decrease for RPL-4 (95% CI - 29 to - 19), and no significant change for TRH (- 7 min; 95% CI - 17 to 3).RESULTSA total of 10,879 patients were included, with 7567, 1776, 724, and 812 undergoing a RARP, TRH, RAPN, and RPL-4, respectively. Yearly hospital volume was not associated with 90-day complications for any procedure. Doubling of yearly volume was associated with a 17-min decrease in operative time for RARP (95% confidence interval CI - 23 to - 10), 8-min decrease for RAPN (95% CI - 14 to - 2), 24-min decrease for RPL-4 (95% CI - 29 to - 19), and no significant change for TRH (- 7 min; 95% CI - 17 to 3).The risk of 90-day major complications does not appear to be higher in low volume hospitals; however, they may not be as efficient with operating room utilization. Careful case selection may have contributed to the lack of an observed association between volumes and complications.CONCLUSIONThe risk of 90-day major complications does not appear to be higher in low volume hospitals; however, they may not be as efficient with operating room utilization. Careful case selection may have contributed to the lack of an observed association between volumes and complications.
Steatotic livers represent a potentially underutilized resource to increase the donor graft pool; however, 1 barrier to the increased utilization of such grafts is the heterogeneity in the definition ...and the measurement of macrovesicular steatosis (MaS). Digital imaging software (DIS) may better standardize definitions to study posttransplant outcomes. Using HALO, a DIS, we analyzed 63 liver biopsies, from 3 transplant centers, transplanted between 2016 and 2018, and compared macrovesicular steatosis percentage (%MaS) as estimated by transplant center, donor hospital, and DIS. We also quantified the relationship between DIS characteristics and posttransplant outcomes using log-linear regression for peak aspartate aminotransferase, peak alanine aminotransferase, and total bilirubin on postoperative day 7, as well as logistic regression for early allograft dysfunction. Transplant centers and donor hospitals overestimated %MaS compared with DIS, with better agreement at lower %MaS and less agreement for higher %MaS. No DIS analyzed liver biopsies were calculated to be >20% %MaS; however, 40% of liver biopsies read by transplant center pathologists were read to be >30%. Percent MaS read by HALO was positively associated with peak aspartate aminotransferase (regression coefficient= 1.04 1.08 1.12 , p <0.001), peak alanine aminotransferase (regression coefficient = 1.04 1.08 1.12 , p <0.001), and early allograft dysfunction (OR= 1.10 1.40 1.78 , p =0.006). There was no association between HALO %MaS and total bilirubin on postoperative day 7 (regression coefficient = 0.99 1.01 1.04 , p =0.3). DIS provides reproducible quantification of steatosis that could standardize MaS definitions and identify phenotypes associated with good clinical outcomes to increase the utilization of steatite livers.
Serpentinization of ultramafic rocks drives geochemical exchange between the hydrosphere, biosphere and lithosphere in surficial environments and at depth. Precious metals are implicated in these ...hydration reactions because of the well-known association between peridotite-hosted Au and placer platinum-group mineral (PGM) deposits sourced from serpentinized ophiolite complexes at surface. However, the distribution of precious metals in mantle rocks and their mode of occurrence at the onset of serpentinization are not well understood because early-stage features are typically obliterated with progressive hydration. Herein we report electron probe microanalysis (EPMA) and laser ablation inductively coupled mass spectrometry (LA-ICPMS) spot and mapping results for a suite of base metal sulphide (pentlandite, pyrrhotite, chalcopyrite), native metal (Cu and Fe) and Ni-Fe alloy (awaruite) from variably serpentinized peridotite and pyroxenite (Late Permian to Early Triassic Nahlin ophiolite, Cache Creek terrane; Atlin, British Columbia, Canada). Pentlandite and pyrrhotite occur with magmatic clinopyroxene and Cr-spinel as ultrafine inclusions (few μm) and as coarser interstitial base metal sulphides (≤200 μm) that are enveloped by native metal (Cu and Fe) and Ni-Fe alloy. Because native Fe- and awaruite-bearing mineral assemblages require reduced and/or low-fS2 conditions, we suggest that these replacement textures document destabilization of base metal sulphide phases during the conversion of olivine to serpentine and magnetite. Desulphurization reactions decoupled precious metals from relict pentlandite at the microscale, with Ag, Pd, Pt and Au partitioning from sulphides into both awaruite and native metal (Cu and Fe) at concentrations up to 100s of ppm. New high-resolution LA-ICPMS maps also point to clusters of ultrafine PGM, tellurides, bismuthides and metal alloys that were either remobilized within the serpentinized mesh and/or represent the completely desulphidized product of ultrafine, intergranular base metal sulphide. Other PGE (Os and Ir) are mostly hosted within relict pentlandite and/or pyrrhotite that were preserved during incomplete desulphurization, along with lesser microscale remobilization of these elements into ultrafine veins. New whole-rock PGE (nickel-sulphide fire-assay; NiS-FA) results demonstrate that precious metal remobilization was limited to the microscale during the earliest stages of serpentinization, which, in the case of Au, is consistent with its low solubility within such reduced, low fS2 fluids. Precious metal mobility during the early stages of serpentinization may therefore depend on the stability of Ni-Fe alloy, native metal (Cu and Fe) and PGM. Progressive serpentinization, complete replacement of olivine and destabilization of the reduced, low-fS2 mineral assemblage likely represents an important process to liberate, transport and concentrate precious metals within more oxidized and/or sulphur-bearing fluids in surficial and deep subduction environments.
•Alloy and native metal replace base metal mantle sulphide during serpentinization.•Osmium and iridium mostly immobile during serpentinization.•Gold, silver, platinum and palladium partition into alloy and native metal.•Precious metal remobilization mostly limited to the microscale.•New LA-ICPMS geochemical imaging method and data integration tools.
Purpose
Neurologic and endothelial injury biomarkers are associated with prolonged delirium during critical illness and may reflect injury pathways that lead to poor long-term outcomes. We ...hypothesized that blood–brain barrier (BBB), neuronal, and endothelial injury biomarkers measured during critical illness are associated with cognitive impairment and disability after discharge.
Methods
We enrolled adults with respiratory failure and/or shock and measured plasma concentrations of BBB (S100B), neuronal (UCHL1, BDNF), and endothelial (E-selectin, PAI-1) injury markers within 72 h of ICU admission. At 3 and 12 months post-discharge, we assessed participants’ global cognition, executive function, and activities of daily living (ADL). We used multivariable regression to determine whether biomarkers were associated with outcomes after adjusting for relevant demographic and acute illness covariates.
Results
Our study included 419 survivors of critical illness with median age 59 years and APACHE II score 25. Higher S100B was associated with worse global cognition at 3 and 12 months (
P
= 0.008;
P
= 0.01). UCHL1 was nonlinearly associated with global cognition at 3 months (
P
= 0.02). Higher E-selectin was associated with worse global cognition (
P
= 0.006 at 3 months;
P
= 0.06 at 12 months). BDNF and PAI-1 were not associated with global cognition. No biomarkers were associated with executive function. Higher S100B (
P
= 0.05) and E-selectin (
P
= 0.02) were associated with increased disability in ADLs at 3 months.
Conclusions
S100B, a marker of BBB and/or astrocyte injury, and E-selectin, an adhesion molecule and marker of endothelial injury, are associated with long-term cognitive impairment after critical illness, findings that may reflect mechanisms of critical illness brain injury.
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