publications

2024

1. bioRxiv

   

   Single-nucleus multi-omics identifies shared and distinct pathways in Pick’s and Alzheimer’s disease

   Zechuan Shi, Sudeshna Das, Samuel Morabito, and 12 more authors

   bioRxiv, 2024

   Abs HTML PDF

   The study of neurodegenerative diseases, particularly tauopathies like Pick’s disease (PiD) and Alzheimer’s disease (AD), offers insights into the underlying regulatory mechanisms. By investigating epigenomic variations in these conditions, we identified critical regulatory changes driving disease progression, revealing potential therapeutic targets. Our comparative analyses uncovered disease-enriched non-coding regions and genome-wide transcription factor (TF) binding differences, linking them to target genes. Notably, we identified a distal human-gained enhancer (HGE) associated with E3 ubiquitin ligase (UBE3A), highlighting disease-specific regulatory alterations. Additionally, fine-mapping of AD risk genes uncovered loci enriched in microglial enhancers and accessible in other cell types. Shared and distinct TF binding patterns were observed in neurons and glial cells across PiD and AD. We validated our findings using CRISPR to excise a predicted enhancer region in UBE3A and developed an interactive database (http://swaruplab.bio.uci.edu/scROAD) to visualize predicted single-cell TF occupancy and regulatory networks.

2. Immunity

   

   Innate immune training restores pro-reparative myeloid functions to promote remyelination in the aged central nervous system

   Vini Tiwari, Bharat Prajapati, Yaw Asare, and 16 more authors

   Immunity, 2024

   Abs HTML PDF

   The reduced ability of the central nervous system to regenerate with increasing age limits functional recovery following demyelinating injury. Previous work has shown that myelin debris can overwhelm the metabolic capacity of microglia, thereby impeding tissue regeneration in aging, but the underlying mechanisms are unknown. In a model of demyelination, we found that a substantial number of genes that were not effectively activated in aged myeloid cells displayed epigenetic modifications associated with restricted chromatin accessibility. Ablation of two class I histone deacetylases in microglia was sufficient to restore the capacity of aged mice to remyelinate lesioned tissue. We used Bacillus Calmette-Guerin (BCG), a live-attenuated vaccine, to train the innate immune system and detected epigenetic reprogramming of brain-resident myeloid cells and functional restoration of myelin debris clearance and lesion recovery. Our results provide insight into aging-associated decline in myeloid function and how this decay can be prevented by innate immune reprogramming.

3. Nat Neurosci

   

   Derivation and transcriptional reprogramming of border-forming wound repair astrocytes after spinal cord injury or stroke in mice

   Timothy M. O’Shea, Yan Ao, Shinong Wang, and 6 more authors

   Nature Neuroscience, 2024

   Abs HTML PDF

   Central nervous system (CNS) lesions become surrounded by neuroprotective borders of newly proliferated reactive astrocytes; however, fundamental features of these cells are poorly understood. Here we show that following spinal cord injury or stroke, 90% and 10% of border-forming astrocytes derive, respectively, from proliferating local astrocytes and oligodendrocyte progenitor cells in adult mice of both sexes. Temporal transcriptome analysis, single-nucleus RNA sequencing and immunohistochemistry show that after focal CNS injury, local mature astrocytes dedifferentiate, proliferate and become transcriptionally reprogrammed to permanently altered new states, with persisting downregulation of molecules associated with astrocyte–neuron interactions and upregulation of molecules associated with wound healing, microbial defense and interactions with stromal and immune cells. These wound repair astrocytes share morphologic and transcriptional features with perimeningeal limitans astrocytes and are the predominant source of neuroprotective borders that re-establish CNS integrity around lesions by separating neural parenchyma from stromal and immune cells as occurs throughout the healthy CNS.

4. Alzheimer’s & Dementia

   

   BIN1K358R suppresses glial response to plaques in mouse model of Alzheimer’s disease

   Laura Fernandez Garcia‐Agudo, Zechuan Shi, Ian F. Smith, and 24 more authors

   Alzheimer’s & Dementia, 2024

   Abs HTML PDF

   The BIN1 coding variant rs138047593 (K358R) is linked to Late‐Onset Alzheimer’s Disease (LOAD) via targeted exome sequencing. To elucidate the functional consequences of this rare coding variant on brain amyloidosis and neuroinflammation, we generated BIN1K358R knock‐in mice using CRISPR/Cas9 technology. These mice were subsequently bred with 5xFAD transgenic mice, which serve as a model for Alzheimer’s pathology. The presence of the BIN1K358R variant leads to increased cerebral amyloid deposition, with a dampened response of astrocytes and oligodendrocytes, but not microglia, at both the cellular and transcriptional levels. This correlates with decreased neurofilament light chain in both plasma and brain tissue. Synaptic densities are significantly increased in both wild‐type and 5xFAD backgrounds homozygous for the BIN1K358R variant. The BIN1 K358R variant modulates amyloid pathology in 5xFAD mice, attenuates the astrocytic and oligodendrocytic responses to amyloid plaques, decreases damage markers, and elevates synaptic densities. BIN1 rs138047593 (K358R) coding variant is associated with increased risk of LOAD. BIN1 K358R variant increases amyloid plaque load in 12‐month‐old 5xFAD mice. BIN1 K358R variant dampens astrocytic and oligodendrocytic response to plaques. BIN1 K358R variant decreases neuronal damage in 5xFAD mice. BIN1 K358R upregulates synaptic densities and modulates synaptic transmission.

2023

1. Molecular Neurodegeneration

   

   A Trem2R47H mouse model without cryptic splicing drives age- and disease-dependent tissue damage and synaptic loss in response to plaques

   Kristine M. Tran, Shimako Kawauchi, Enikö A. Kramár, and 26 more authors

   Molecular Neurodegeneration, 2023

   Abs HTML PDF

   The TREM2 R47H variant is one of the strongest genetic risk factors for late-onset Alzheimer’s Disease (AD). Unfortunately, many current Trem2 R47H mouse models are associated with cryptic mRNA splicing of the mutant allele that produces a confounding reduction in protein product. To overcome this issue, we developed the Trem2R47H NSS (Normal Splice Site) mouse model in which the Trem2 allele is expressed at a similar level to the wild-type Trem2 allele without evidence of cryptic splicing products.

2. bioRxiv

   Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s Disease

   Emily Miyoshi^*, Samuel Morabito^*, Caden M. Henningfield, and 21 more authors

   bioRxiv, 2023

   Abs HTML PDF

   The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3′ end choice. Detecting and quantifying transcript isoforms across tissues, cell types, and species has been extremely challenging because transcripts are much longer than the short reads normally used for RNA-seq. By contrast, long-read RNA-seq (LR-RNA-seq) gives the complete structure of most transcripts. We sequenced 264 LR-RNA-seq PacBio libraries totaling over 1 billion circular consensus reads (CCS) for 81 unique human and mouse samples. We detect at least one full-length transcript from 87.7% of annotated human protein coding genes and a total of \textbackslashtextasciitilde200,000 full-length transcripts, \textbackslashtextasciitilde40% of which have novel exon junction chains. To capture and compute on the three sources of transcript structure diversity, we introduce a gene and transcript annotation framework that uses triplets representing the transcript start site, exon junction chain, and transcript end site of each transcript. Using triplets in a simplex representation demonstrates how promoter selection, splice pattern, and 3′ processing are deployed across human tissues, with nearly half of multitranscript protein coding genes showing a clear bias toward one of the three diversity mechanisms. Evaluated across samples, the predominantly expressed transcript changes for 74% of protein coding genes. In evolution, the human and mouse transcriptomes are globally similar in types of transcript structure diversity, yet among individual orthologous gene pairs, more than half (57.8%) show substantial differences in mechanism of diversification in matching tissues. This initial large-scale survey of human and mouse long-read transcriptomes provides a foundation for further analyses of alternative transcript usage, and is complemented by short-read and microRNA data on the same samples and by epigenome data elsewhere in the ENCODE4 collection.

2022

1. STAR Protoc

   

   Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue

   Zechuan Shi^*, Sudeshna Das^*, Samuel Morabito, and 2 more authors

   STAR Protocols, 2022

   Abs HTML PDF

   Single-nucleus ATAC sequencing (snATAC-seq) employs a hyperactive Tn5 transposase to gain precise information about the cis-regulatory elements in specific cell types. However, the standard protocol of snATAC-seq is not optimized for all tissues, including the brain. Here, we present a modified protocol for single-nuclei isolation from postmortem frozen human brain tissue, followed by snATAC-seq library preparation and sequencing. We also describe an integrated bioinformatics analysis pipeline using an R package (ArchRtoSignac) to robustly analyze snATAC-seq data. For complete details on the use and execution of this protocol, please refer to Morabito et al. (2021).

2018

1. Pedosphere

   

   Elevated CO2 Accelerates Phosphorus Depletion by Common Bean (Phaseolus vulgaris) in Association with Altered Leaf Biochemical Properties

   Zhong Ma, Jennifer Flynn, Grant Libra, and 1 more author

   Pedosphere, 2018

   Abs HTML PDF

   Phosphorus (P) is a major limiting factor for plant productivity in many ecosystems and agriculture. The projected increase in atmospheric CO2 is likely to result in changes in plant mineral consumption and growth. We studied P depletion by common bean (Phaseolus vulgaris) cultured hydroponically under ambient (377 ± 77 μmol mol−1) or elevated (650 ± 32 μmol mol−1) CO2 in media of low or high P. Under elevated CO2 compared to ambient CO2, the maximum P depletion rate increased by 98% at low P and 250% at high P, and P was depleted about 2–5 weeks sooner; leaf acid phosphatase (APase) activity and chlorophyll content both increased significantly; root-to-shoot ratio increased significantly at high P, although it was unaffected at low P; lateral root respiration rate showed no change, suggesting that CO2 did not affect P depletion via metabolic changes to the roots; the total biomass at final harvest was significantly higher at both low and high P. Our data showed that the increased rate and amount of P depletion during plant growth under elevated CO2 occurred in association with alterations in leaf biochemical properties, i.e., enhanced activities of leaf APase and increased leaf chlorophyll content.