Nairn, Angus C.

Abstract Introduction: Biomarkers that reflect pathologic processes affecting neuronal function during preclinical and early stages of Alzheimer's disease (AD) are needed to aid drug development. Methods: A targeted, stable isotope, quantitative mass spectrometry‐based investigation of longitudinal changes in concentrations of previously identified candidate biomarkers was performed in cerebrospinal fluid (CSF) of Alzheimer's Disease Neuroimaging Initiative participants who were classified as cognitively normal (CN; n = 76) or with mild cognitive impairment (MCI; n = 111) at baseline. Results: Of the candidate biomarkers, the CSF concentration of neuronal pentraxin 2 (NPTX2), a protein involved in synaptic function, exhibited rates of change that were significantly different between three comparison groups (i.e., CN vs. MCI participants; AD pathology positive vs. negative defined by phosphorylated tau181/amyloid beta1‐42 ratio; and clinical progressors vs. non‐progressors). The rate of change of NPTX2 also significantly correlated with declining cognition. Discussion: CSF NPTX2 concentration is a strong prognostic biomarker candidate of accelerated cognitive decline with potential use as a therapeutic target.

AbstractBackgroundMany biomarkers have been identified which are relevant to studies of Alzheimer’s disease (AD), especially pertaining to the evolution of amyloid plaque, tau tangle pathology and loss of brain tissue. There remains, however, the need for additional biomarkers that reflect pathologic processes affecting neuronal function during pre‐clinical and prodromal stages, to help accelerate drug development efforts.MethodA retrospective investigation of longitudinal changes in concentrations of five analytes (CgA, NPTX2, VGF, SCG2, FABP3) was performed in CSF of ADNI subjects. Rates of longitudinal change in these candidate proteins were compared between: a) Cognitively normal subjects (CN; n = 76) versus subjects with mild cognitive impairment (MCI; n = 111) at baseline; b) Subjects categorized as p‐Tau181/Aβ1‐42 ratio positive versus negative at baseline; and c) ‘Progressors’, i.e., subjects who progressed from CN to MCI or MCI to Dementia within a predefined period versus subjects categorized as ‘non‐progressors’. Following a pre‐specified analysis plan involving mixed‐effects linear models adjusting for relevant covariates, the association between changes in each analyte’s concentration and subjects’ clinical progression was quantified.ResultNPTX2, a protein involved in synaptic function, showed the strongest association with baseline clinical diagnosis of MCI, and a positive p‐Tau181/Aβ1‐42 ratio – the biomarker profile indicative of AD. Differences in the rates of decline in NPTX2 concentration between subjects classified as CN and MCI as well as between p‐Tau181/Aβ1‐42 ratio positive and negative subjects were highly significant (p=0.008 and p<0.0001 resp.), suggesting a complex interaction between the rate of decline in subjects at various stages along the disease continuum. Of the five analytes, only the rates of change in NPTX2 concentrations differed between progressors and non‐progressors (mean difference: 0.08 ± 0.02 ng/mL/year); p = 0.0004), further validating the association of changes in NPTX2 concentration and clinical prognosis. Additional exploratory analyses indicated the presence of a correlation between NPTX2 rates of change and declining cognition measured by MMSE (coef. = 0.3, p = 0.02), and Adas‐Cog 13 (coef. = ‐0.3, p = 0.01).ConclusionThese results suggest that NPTX2 concentration may serve as a prognostic biomarker of accelerated cognitive decline in at least a subset of individuals with AD.

INTRODUCTION The human cerebral cortex has undergone an extraordinary increase in size and complexity during mammalian evolution. Cortical cell lineages are specified in the embryo, and genetic and epidemiological evidence implicates early cortical development in the etiology of neuropsychiatric disorders such as autism spectrum disorder (ASD), intellectual disabilities, and schizophrenia. Most of the disease-implicated genomic variants are located outside of genes, and the interpretation of noncoding mutations is lagging behind owing to limited annotation of functional elements in the noncoding genome. RATIONALE We set out to discover gene-regulatory elements and chart their dynamic activity during prenatal human cortical development, focusing on enhancers, which carry most of the weight upon regulation of gene expression. We longitudinally modeled human brain development using human induced pluripotent stem cell (hiPSC)–derived cortical organoids and compared organoids to isogenic fetal brain tissue. RESULTS Fetal fibroblast–derived hiPSC lines were used to generate cortically patterned organoids and to compare oganoids’ epigenome and transcriptome to that of isogenic fetal brains and external datasets. Organoids model cortical development between 5 and 16 postconception weeks, thus enabling us to study transitions from cortical stem cells to progenitors to early neurons. The greatest changes occur at the transition from stem cells to progenitors. The regulatory landscape encompasses a total set of 96,375 enhancers linked to target genes, with 49,640 enhancers being active in organoids but not in mid-fetal brain, suggesting major roles in cortical neuron specification. Enhancers that gained activity in the human lineage are active in the earliest stages of organoid development, when they target genes that regulate the growth of radial glial cells. Parallel weighted gene coexpression network analysis (WGCNA) of transcriptome and enhancer activities defined a number of modules of coexpressed genes and coactive enhancers, following just six and four global temporal patterns that we refer to as supermodules, likely reflecting fundamental programs in embryonic and fetal brain. Correlations between gene expression and enhancer activity allowed stratifying enhancers into two categories: activating regulators (A-regs) and repressive regulators (R-regs). Several enhancer modules converged with gene modules, suggesting that coexpressed genes are regulated by enhancers with correlated patterns of activity. Furthermore, enhancers active in organoids and fetal brains were enriched for ASD de novo variants that disrupt binding sites of homeodomain, Hes1, NR4A2, Sox3, and NFIX transcription factors. CONCLUSION We validated hiPSC-derived cortical organoids as a suitable model system for studying gene regulation in human embryonic brain development, evolution, and disease. Our results suggest that organoids may reveal how noncoding mutations contribute to ASD etiology. Summary of the study, analyses, and main results. Data were generated for iPSC-derived human telencephalic organoids and isogenic fetal cortex. Organoids modeled embryonic and early fetal cortex and show a larger repertoire of enhancers. Enhancers could be divided into activators and repressors of gene expression. We derived networks of modules and supermodules with correlated gene and enhancer activities, some of which were implicated in autism spectrum disorders (ASD).