Biology subjects

Mortazavi, A.

Publications and source records attributed to Mortazavi, A..

At least 19 recordsLinked to original sources

bioRxiv2026

LEUTX mediates amplification of DUX4 signaling and aberrant myotube differentiation in facioscapulohumeral muscular dystrophy

Aberrant reactivation of an embryonic DUX4 transcription factor gene encoded in the D4Z4 macrosatellite repeats on chromosome 4q is considered the root cause of facioscapulohumeral muscular dystrophy (FSHD). While DUX4 target gene expression correlates with the clinical severity, DUX4 expression itself is very rare. How this limited DUX4 expression leads to definitive target gene activation and how these downstream genes contribute to FSHD pathology remain elusive. We previously found the evidence for LEUTX and ZSCAN4 representing two distinct DUX4 target subpathways. Here we present functional analyses in control and FSHD skeletal myocytes identifying LEUTX, but not ZSCAN4, as a major amplifier of DUX4 target gene expression. Furthermore, LEUTX uniquely disrupts myotube differentiation by impairing muscle gene induction and promoting persistent mitotic gene expression. Forced LEUTX expression causes aberrant DNA replication in myotube nuclei. A subset of misregulated genes is bound by LEUTX, strongly suggesting that they are direct targets of LEUTX. Notably, LEUTX requires the presence of DUX4 to gain access to DUX4 target gene promoters for their activation. Taken together, our results establish the critical role of LEUTX in DUX4 signal amplification and defective myotube differentiation, revealing distinct contributions of DUX4 target gene pathways in FSHD pathogenesis.

cell biology↗

bioRxiv2026

Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation

Understanding the genetic architecture of gene expression is fundamental to evolutionary biology and medicine. As part of the IGVF Consortium, we present a single-nucleus RNA-seq resource of 5.3 million nuclei across eight tissue groups, featuring seven F1 hybrids from C57BL/6J dams crossed with the other Collaborative Cross founder strains for comparison against parental strains. We identify 25,864 genes (91% of those detected) exhibiting non-conserved regulatory behavior in at least one of 92 cell types in one or more crosses. Our results show that while cis-acting variation primarily drives divergence, trans-acting effects are substantially more cell-type specific and sensitive to tissue environment. Notably, bulk tissue analyses frequently mask these signals, particularly in smaller populations such as astrocytes. Furthermore, increasing genetic divergence primarily expands the landscape of cis-acting variation, while trans-acting effects remain stable across genetic distances within species. This atlas establishes a foundational framework for decoding the complex interplay between genetic variation and cell-type-specific regulation across the mammalian body.

genomics↗

bioRxiv2026

Peptide signaling in the paraventricular thalamus contributes to disrupted adult reward behaviors after early-life adversity

Early-life adversity (ELA) is strongly linked to emotional disorders characterized by dysregulated reward behaviors including diminished motivation for and enjoyment of rewards (anhedonia). However, how transient ELA leads to enduring disruptions of reward behaviors remains unclear. Using activity-dependent genetic labeling during ELA, we previously found that the paraventricular thalamic nucleus (PVT) uniquely distinguishes ELA from typical rearing, and inhibiting ELA-activated PVT cells in adult ELA mice rescued reward behaviors in a sex-specific manner. However, the cellular mechanisms by which ELA alters the function of PVT neurons enduringly, to impact adult reward behaviors is unresolved. Here, we probed potential gene expression mechanisms by assessing reward-induced gene translation selectively in early-life activated (TRAPed) PVT cells, and identified genes regulated by reward in a sex-specific way. Combining data- and hypothesis-driven approaches, we targeted the corticotropin-releasing hormone receptor type 1 (CRHR1) as potentially mediating ELA-induced disruptions of reward behaviors. We find that CRISPR-Cas9-mediated Crhr1 deletion in TRAPed-PVT cells restores typical reward behaviors in ELA mice. Our results provide insight into the developmental origin of mental illness and identify potentially powerful molecular targets for prevention or mitigation of the consequences of ELA on reward behaviors germane to human mental illness.

neuroscience↗

bioRxiv2026

Single-Cell Genomics Decontamination with CellSweep

Single-cell genomics technologies enable high-throughput cell profiling, but technical contamination remains an obstacle to accurate downstream analysis. Free-floating ambient molecules released from lysed cells and global bulk contamination introduced during library preparation can distort molecular profiles. These artifacts can obscure cellular identities and reduce the reliability of differential analysis or clustering results. We present an efficient and effective approach to removing ambient and bulk contamination that can be applied to data generated from a wide variety of technologies. We show that our tool, CellSweep, outperforms other methods to remove artifacts using numerous benchmarks.

bioinformatics↗

bioRxiv2025

Genome-wide analysis of FSHD cell lines using Nanopore sequencing reveals allele-specific differences at DUX4 target genes and complex repeats

Facioscapulohumeral muscular dystrophy (FSHD) is linked to a monoallelic contraction of primate-specific 3.3kb D4Z4 macrosatellite repeats on the disease-permissive chromosome 4q (4qA haplotype) with additional mutations of a chromatin regulator SMCHD1 acting as a disease modifier. DNA hypomethylation at the D4Z4 repeat and resulting abnormal derepression of the embryonic transcription factor DUX4 encoded in the D4Z4 repeat are the hallmark of FSHD. In order to investigate the impact of FSHD mutations within as well as outside of the disease loci, we performed Nanopore direct-RNA and genomic sequencing to characterize global and D4Z4-specific changes in isoform expression and DNA methylation using CRISPR-engineered human skeletal myoblast lines carrying FSHD mutations (D4Z4 contraction and SMCHD1 mutation) compared to the isogenic parental healthy control line. Nanopore sequencing allowed us to characterize the entire unedited control and contracted D4Z4 arrays as well as distinguish differential methylation patterns at the disease locus on chromosome 4qA from those at a nearly identical nonpathogenic D4Z4 repeat arrays on chromosome 10 and disease non-permissive 4qB allele. We observe hypomethylation both at the DUX4 locus and globally in FSHD mutant cell lines in myoblasts as well as in myotubes. DUX4 target gene expression is correlated with promoter hypomethylation. De novo haplotype phasing of genomic and RNA reads reveals allele- and isoform-specific expression of DUX4 target genes as well as highly expressed DUX4 target pseudogenes that may contribute to disease pathogenesis. Taken together, our results indicate significant impact of FSHD mutations not only on D4Z4 allele, but also DUX4 targets and repeat regions in the genome, which may be collectively contributing to the FSHD pathogenesis.

genomics↗

bioRxiv2025

Determining gene specificity from multivariate single-cell RNA sequencing data

An important application of single-cell genomics experiments is to identify genes specific to biological categories or experimental conditions. Although numerous approaches have been proposed to identify such genes, we consider an axiomatic approach based on defining properties that a specificity measure should have. This leads us to develop ember (Entropy Metrics for Biological ExploRation), which we show is the only method satisfying four key desired properties for a specificity measure. Applying ember to eight tissues from eight founder mouse strains, we find that gene specificity is often unintuitive: canonical markers can be supplanted, housekeeping genes are context-dependent, and mouse strain can drive unexpected cell type switching. Unsupervised learning on entropy metrics uncovers shared genes specialized to male gonads and kidney, as well as genes specific to non-consecutive developmental stages in the kidney. To facilitate further exploration of gene specificity in mice, we have also developed a comprehensive specificity database, along with a web interface, API and MCP server. Extending ember to a human PBMC dataset collected from 255 diverse individuals, we find that variation in PBMCs is largely localized to classical monocytes. We also find genes with unique specificity by sex, age and ancestral background. Together, these applications establish ember as a powerful tool and provide a roadmap for elucidating the impact of human genetic variation using the murine model.

bioinformatics↗

bioRxiv2025

Dogme: A nextflow pipeline for reprocessing nanopore RNA and DNA modifications

MotivationThe Oxford Nanopore Technologies (ONT) platform allows for the direct detection of RNA and DNA modifications from unamplified nucleic acids, which is a significant advantage over other platforms. However, the rapid updates to ONT basecalling models and the evolving landscape of computational tools for modification detection bring about challenges for reproducible and standardized analyses. To address these challenges, we developed Dogme, which is a Nextflowbased workflow that automates the processing of ONT data, including basecalling, alignment, modification detection, and transcript quantification. Dogme automates the reprocessing of ONT POD5 files by integrating basecalling using Dorado, read mapping using minimap2 and subsequent analysis steps such as running modkit. The pipeline supports three major types of ONT sequencing data - direct RNA (dRNA), complementary DNA (cDNA), and genomic DNA (gDNA) - enabling comprehensive analyses across different library preparations. Dogme facilitates detection of diverse RNA modifications supported by Dorado such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), inosine, pseudouridine, 2-Omethylation (Nm) and DNA methylation, while concurrently quantifying full-length transcript isoforms LR-Kallisto for transcript quantification for dRNA and cDNA. ResultsWe applied Dogme to three separate mouse C2C12 myoblast replicates using direct RNA sequencing on MinION flow cells. We detected an average of 147,879 m6A, 86,673 m5C, 21,242 inosine, 24,540 pseudouridine, and 83,841 2- O-methylation sites per replicate with 96,581 m6A, 43,446 m5C, 8,825 inosine, 10,048 pseudouridine, and 30,157 2-O- methylation sites detected in all three biological replicates. The pipeline produced reproducible modification profiles and transcript expression levels across replicates, demonstrating its utility for integrative long-read transcriptomic and epigenomic analyses. AvailabilityDogme is implemented in Nextflow and is freely available under the MIT license at https://github.com/mortazavilab/dogme, with documentation provided for installation and usage.

genomics↗

bioRxiv2025

Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains captures global and local expression variation

Mapping the impact of genomic variation on gene expression facilitates an understanding of the molecular basis of complex phenotypic traits and disease predisposition. Mouse models provide a controlled and reproducible framework for capturing the breadth of genomic variation observed in different genotypes across a wide variety of tissues. As part of the IGVF consortiums effort to catalog the effects of genetic variation, we uniformly characterized the transcriptomes of eight tissues from each mouse founder strain used to derive the Collaborative Cross strains, comprising five classical laboratory inbred strains and three wild-derived inbred strains. We sequenced samples from four male and four female replicates per tissue using single-nucleus RNA-seq to generate an "8-cube" dataset of 5.2 million nuclei across 106 cell types and cell states. As expected, the overall extent of transcriptome variation correlates positively with genetic divergence across the strains with the greatest differential between PWK/PhJ and CAST/EiJ. At the individual tissue level, heart and brain are relatively more similar across strains compared with gonads, adrenal, skeletal muscle, kidney, and liver. Further analyses revealed substantial strain variation, often concentrated in a few cell types as well as cell-state signatures that especially reflect strain-associated immune and metabolic trait differences. The founder 8-cube dataset provides rich transcriptome variation signatures to help explain strain-specific phenotypic traits and disease states, as illustrated by examples in tissue-resident immune cells, muscle degeneration, kidney sex differences, and the hypothalamicpituitary-adrenal axis. This data further provides a systematic foundation for the analysis of these tissues in the founder strains as well as the Collaborative Cross.

genomics↗

bioRxiv2025

A reliable in vitro rumen culture system and workflow for screening anti-methanogenic compounds

Arguably the biggest man-made challenge of the century is to halt the progression of the climate change. Livestocks methane (CH4) emissions, a greenhouse gas with a higher global warming potential than carbon dioxide (CO2), represent a prime target for reducing anthropogenic impact. While the reduction of enteric methane emissions through feed additives has been demonstrated, potent and affordable compounds inhibiting methanogenesis in ruminants are hardly established. Reliable methods for reproducible cultivation of the rumen microbiome in the laboratory are an essential tool for the study of methanogenesis. We have developed a versatile setup that allows for the cultivation of ruminal fluid in a benchtop configuration. This setup combines, miniaturises and improves existing systems. We use everyday labware to create a setup capable of the long term cultivation of primary cultures extracted from the rumen of slaughtered cows. We describe the detailed preparation and cultivation procedure and demonstrate the expected function of the setup. The efficacy of the system is demonstrated through the administration of various concentrations of state-of-the-art methanogenesis inhibitors, including lyophilised Asparagopsis taxiformis (AT) powder, bromoform (BF), iodoform (IF), 3-nitrooxypropanol (3-NOP), rapeseed oil and BF dissolved in rapeseed oil. The parameters of the system exhibit a change in accordance with the literature. In comparison with conventional methodologies, our system offers enhanced versatility and ease of use. Furthermore, a novel approach for the quantification of the exhaled gases, CH4 and CO2, is presented.

microbiology↗

bioRxiv2025

Multi-modal analysis of satellite cells reveals early impairments at pre-contractile stages of myogenesis in Duchenne muscular dystrophy

Recent studies on the role of myogenic satellite cells (SC) in Duchenne muscular dystrophy (DMD) documented altered division capacities and impaired regeneration potential of SC in DMD patients and animal models. It remains unknown, however, if SC-intrinsic effects trigger these deficiencies at pre-contractile stages of myogenesis rather than resulting from the pathologic environment. Addressing this, we isolated SC from muscle biopsies of a porcine DMD model for characterization. Traction force microscopy (TFM) revealed that DMD SC produce a significantly higher strain energy than wild-type cells (WT; 0.136 {+/-} 0.016 {micro}J vs. 0.057 {+/-} 0.008 {micro}J). By RNA-seq, we identified 1,390 differentially expressed genes and proteomics measurements detected 1,261 proteins with altered abundance in DMD vs. WT. Dysregulated pathways uncovered by Gene Ontology (GO) enrichment analysis included sarcomere organization, focal adhesion, and response to hypoxia. We integrated the data using multi-omics factor analysis (MOFA) and identified five factors accounting for the variance with an overall higher contribution of the transcriptomic (61.95 %) than the proteomic data (54.02 %). Our findings suggest SC impairments result from their inherent genetic abnormality rather than environmental influences. The observed biological changes are independent and not reactive to the pathological surrounding of DMD muscle.

pathology↗

bioRxiv2024

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, The ENCODE consortium mapped biochemical signals across many cell types and tissues and integrated these data to develop a Registry of 0.9 million human and 300 thousand mouse candidate cis-Regulatory Elements (cCREs) annotated with potential functions1. We have expanded the Registry to include 2.35 million human and 927 thousand mouse cCREs, leveraging new ENCODE datasets and enhanced computational methods. This expanded Registry covers hundreds of unique cell and tissue types, providing a comprehensive understanding of gene regulation. Functional characterization data from assays like STARR-seq, MPRA, CRISPR perturbation, and transgenic mouse assays now cover over 90% of human cCREs, revealing complex regulatory functions. We identified thousands of novel silencer cCREs and demonstrated their dual enhancer/silencer roles in different cellular contexts. Integrating the Registry with other ENCODE annotations facilitates genetic variation interpretation and trait-associated gene identification, exemplified by discovering KLF1 as a novel causal gene for red blood cell traits. This expanded Registry is a valuable resource for studying the regulatory genome and its impact on health and disease.

genomics↗

bioRxiv2024

Long-read sequencing transcriptome quantification with lr-kallisto

RNA abundance quantification has become routine and affordable thanks to high-throughput "short-read" technologies that provide accurate molecule counts at the gene level. Similarly accurate and affordable quantification of definitive fulllength, transcript isoforms has remained a stubborn challenge, despite its obvious biological significance across a wide range of problems. "Long-read" sequencing platforms now produce data-types that can, in principle, drive routine definitive isoform quantification. However some particulars of contemporary long-read datatypes, together with isoform complexity and genetic variation, present bioinformatic challenges. We show here, using ONT data, that fast and accurate quantification of long-read data is possible and that it is improved by exome capture. To perform quantifications we developed lr-kallisto, which adapts the kallisto bulk and single-cell RNA-seq quantification methods for long-read technologies.

bioinformatics↗

bioRxiv2024

The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states

Postnatal genomic regulation significantly influences tissue and organ maturation but is under-studied relative to existing genomic catalogs of adult tissues or prenatal development in mouse. The ENCODE4 consortium generated the first comprehensive single-nucleus resource of postnatal regulatory events across a diverse set of mouse tissues. The collection spans seven postnatal time points, mirroring human development from childhood to adulthood, and encompasses five core tissues. We identified 30 cell types, further subdivided into 69 subtypes and cell states across adrenal gland, left cerebral cortex, hippocampus, heart, and gastrocnemius muscle. Our annotations cover both known and novel cell differentiation dynamics ranging from early hippocampal neurogenesis to a new sex-specific adrenal gland population during puberty. We used an ensemble Latent Dirichlet Allocation strategy with a curated vocabulary of 2,701 regulatory genes to identify regulatory "topics," each of which is a gene vector, linked to cell type differentiation, subtype specialization, and transitions between cell states. We find recurrent regulatory topics in tissue-resident macrophages, neural cell types, endothelial cells across multiple tissues, and cycling cells of the adrenal gland and heart. Cell-type-specific topics are enriched in transcription factors and microRNA host genes, while chromatin regulators dominate mitosis topics. Corresponding chromatin accessibility data reveal dynamic and sex-specific regulatory elements, with enriched motifs matching transcription factors in regulatory topics. Together, these analyses identify both tissue-specific and common regulatory programs in postnatal development across multiple tissues through the lens of the factors regulating transcription.

genomics↗

bioRxiv2024

Hijacked Immune Cells Traverse Microenvironmental Barriers by Positioning and Pushing their Intracellular Parasite Cargo

Cell migration is fundamental to development, homeostasis, and immunity, and requires cells to traverse space-limited microenvironments by deforming intracellular organelles such as the nucleus. Although nuclear mechanics are established as a rate-limiting factor during confined migration, how cells transport bulky foreign cargo remains unclear. Here, using Toxoplasma gondii, a disease-causing parasite that hijacks motile immune cells for dissemination while replicating into large intracellular assemblies, we discover that parasitic cargoes exceed the size and stiffness of host nuclei, and therefore constitute a primary bottleneck for migration. We uncover a mechanoadaptive response to parasite size, characterized by size-dependent intracellular repositioning, myosin-II contractility, and bleb-based protrusions. This reprogramming of forces and subcellular architecture enables the transport of oversized, mechanically rigid cargo through space-limited microenvironments. These findings establish a mechanobiological principle of how cells size-dependently adapt forces and their subcellular architecture to accommodate intracellular objects that challenge the physical limits of cell migration.

cell biology↗

bioRxiv2024

Traction Force Microscopy with DNA FluoroCubes

Mechanical forces at the cell-substrate interface govern processes from migration to differentiation, yet mapping these forces at high spatial resolution remains challenging. Traction force microscopy (TFM) addresses this by quantifying substrate deformations using fiducial markers, which are conventionally fluorescent beads. Here, we introduce fluorescently labeled DNA nanostructures (FluoroCubes) as alternative fiducials grafted onto polydimethylsiloxane (PDMS) substrates. Co-anchored with RGD peptides, FluoroCubes remain stably tethered, resist internalization, and enable dense, minimally perturbing labeling. This surface-functionalized platform is compatible with TIRF microscopy and leverages tunable biotin-NeutrAvidin chemistry for precise control of fiducial density. Using a modified multi-channel optical flow algorithm, we achieve improved displacement sensitivity and force reconstruction resolution compared to conventional algorithms. FluoroCube-functionalized substrates provide a reproducible, high-resolution method for traction force mapping and offer a versatile foundation for future integration with DNA-based molecular sensors to probe interfacial forces at biointerfaces.

biophysics↗

bioRxiv2024

Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD

The gene expression profiles of distinct cell types reflect complex genomic interactions among multiple simultaneous biological processes within each cell that can be altered by disease progression as well as genetic background. The identification of these active cellular programs is an open challenge in the analysis of single-cell RNA-seq data. Latent Dirichlet Allocation (LDA) is a generative method used to identify recurring patterns in counts data, commonly referred to as topics that can be used to interpret the state of each cell. However, LDAs interpretability is hindered by several key factors including the hyperparameter selection of the number of topics as well as the variability in topic definitions due to random initialization. We developed Topyfic, a Reproducible LDA (rLDA) package, to accurately infer the identity and activity of cellular programs in single-cell data, providing insights into the relative contributions of each program in individual cells. We apply Topyfic to brain single-cell and single-nucleus datasets of two 5xFAD mouse models of Alzheimers disease crossed with C57BL6/J or CAST/EiJ mice to identify distinct cell types and states in different cell types such as microglia. We find that 8-month 5xFAD/Cast F1 males show higher level of microglial activation than matching 5xFAD/BL6 F1 males, whereas female mice show similar levels of microglial activation. We show that regulatory genes such as TFs, microRNA host genes, and chromatin regulatory genes alone capture cell types and cell states. Our study highlights how topic modeling with a limited vocabulary of regulatory genes can identify gene expression programs in singlecell data in order to quantify similar and divergent cell states in distinct genotypes.

genomics↗

bioRxiv2023

Within-subject changes in DNA-methylome profile identify individual signatures of early-life adversity, with a potential to predict neuropsychiatric outcome.

BackgroundAdverse early-life experiences (ELA), including poverty, trauma and neglect, affect a majority of the worlds children. Whereas the impact of ELA on cognitive and emotional health throughout the lifespan is well-established, it is not clear how distinct types of ELA influence child development, and there are no tools to predict for an individual child their vulnerability or resilience to the consequences of ELAs. Epigenetic markers including DNA-methylation profiles of peripheral cells may encode ELA and provide a predictive outcome marker. However, the rapid dynamic changes in DNA methylation in childhood and the inter-individual variance of the human genome pose barriers to identifying profiles predicting outcomes of ELA exposure. Here, we examined the relation of several dimensions of ELA to changes of DNA methylation, using a longitudinal within-subject design and a high threshold for methylation changes in the hope of mitigating the above challenges. MethodsWe analyzed DNA methylation in buccal swab samples collected twice for each of 110 infants: neonatally and at 12 months. We identified CpGs differentially methylated across time, calculated methylation changes for each child, and determined whether several indicators of ELA associated with changes of DNA methylation for individual infants. We then correlated select dimensions of ELA with methylation changes as well as with measures of executive function at age 5 years. We examined for sex differences, and derived a sex-dependent impact score based on sites that most contributed to the methylation changes. FindingsSetting a high threshold for methylation changes, we discovered that changes in methylation between two samples of an individual child reflected age-related trends towards augmented methylation, and also correlated with executive function years later. Among the tested factors and ELA dimensions, including income to needs ratios, maternal sensitivity, body mass index and sex, unpredictability of parental and household signals was the strongest predictor of executive function. In girls, an interaction was observed between a measure of high early-life unpredictability and methylation changes, in presaging executive function. InterpretationThese findings establish longitudinal, within-subject changes in methylation profiles as a signature of some types of ELA in an individual child. Notably, such changes are detectable beyond the age-associated DNA methylation dynamics. Future studies are required to determine if the methylation profile changes identified here provide a predictive marker of vulnerabilities to poorer cognitive and emotional outcomes. FundingSupported by NIH P50 MH096889, a Precision Medicine Initiative grant from the State of California (OPR20141) and the Bren Foundation. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSIdentification of individuals at risk for cognitive and emotional problems is required for targeted interventions. At the population level, experiencing early-life adversity has been consistently linked to an elevated susceptibility to various mental illnesses. However, recent studies have revealed a significant limitation in the ability of early-life adversity to predict individual-level risk, and there is presently no reliable tool available to determine whether a child experiencing adversity will develop future mental health problems. Promising efforts to discover predictive markers by examining DNA methylation in peripheral cells are challenged by extensive genetic and epigenetic population variability and the rapid methylation changes taking place during childhood, rendering the identification of clinically valuable predictive markers a complex endeavor. Added value of this studyThis study examined neurodevelopmental outcomes following several dimensions of ELA, including a recently identified dimension-unpredictability of parental and environmental signals to the child. It demonstrates changes in DNA methylation in children exposed to a spectrum of ELA dimensions and severity using alternative approaches to those used previously: It employs a longitudinal within-subject design, enabling assessment of DNA changes within an individual over time rather than a cross section comparison of different groups, and focuses on the first year of life, an understudied epoch of development. The study uses reduced representation bisulfite sequencing to measure methylation, an approach compromising between targeted sequencing and a whole genome approach, and sets a high threshold for methylation changes, in consideration of the large changes of DNA methylation during childhood. Finally, in accord with emerging discoveries of the differential effects of ELA on males and females, the study uncovers sex-effects arising already before puberty. Implications of all the available evidenceCollectively, our study, together with a robust existing literature (1) identifies early-life unpredictability as an additional determinant of DNA methylation changes, (2) indicates that within-subject changes in methylation profiles of peripheral cells hold promise as precision medicine tools for predicting risk and resilience to the adverse consequences of early-life hardships on mental health, and (3) suggests that sex-differences should be explored even prior to puberty. Our study contributes significantly to the important goal of early identification of predictive "epigenetic scars" caused by adverse early-life experiences. Such markers are required for targeting interventions to those most at need.

neuroscience↗

bioRxiv2023

C5aR1 antagonism suppresses inflammatory glial gene expression and alters cellular signaling in an aggressive Alzheimer's model

Alzheimers disease (AD) is the leading cause of dementia in older adults, and the need for effective, sustainable therapeutic targets is imperative. Pharmacologic inhibition of C5aR1 reduces plaque load, gliosis and memory deficits in animal models. However, the cellular basis underlying this neuroprotection and which processes were the consequence of amyloid reduction vs alteration of the response to amyloid were unclear. In the Arctic model, the C5aR1 antagonist PMX205 did not reduce plaque load, but deficits in short-term memory in female mice were prevented. Hippocampal single cell and single nucleus RNA-seq clusters revealed C5aR1 dependent and independent gene expression and cell-cell communication. Microglial clusters containing neurotoxic disease-associated microglial genes were robustly upregulated in Arctic mice and drastically reduced with PMX205 treatment, while genes in microglia clusters that were overrepresented in the Arctic-PMX205 vs Arctic group were associated with synapse organization and transmission and learning. PMX205 treatment also reduced some A-1 astrocyte genes. In spite of changes in transcript levels, overall protein levels of some reactive glial markers were relatively unchanged by C5aR1 antagonism, as were clusters associated with protective responses to injury. C5aR1 inhibition promoted signaling pathways associated with cell growth and repair, such as TGF{beta} and FGF, in Arctic mice, while suppressing inflammatory pathways including PROS, Pecam1, and EPHA. In conclusion, pharmacologic C5aR1 inhibition prevents cognitive loss, limits microglial polarization to a detrimental inflammatory state and permits neuroprotective responses, as well as leaving protective functions of complement intact, making C5aR1 antagonism an attractive therapeutic strategy for individuals with AD. One Sentence SummaryPharmacologic inhibition of C5aR1 suppresses disease-enhancing processes and promotes disease mitigating pathways in an aggressive model of Alzheimers disease.

neuroscience↗