Biology subjects

Habib, N.

Publications and source records attributed to Habib, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Concurrent cognitive, behavioral and systemic physiological features mark preclinical Alzheimer's disease

Alzheimer's disease (AD) pathology accumulates years before overt cognitive impairment, yet its multidomain phenotype remains poorly defined. To limit confounding by uncontrolled comorbidities, we assembled a cohort of 644 older adults self-reporting intact cognition, free of systemic or neurological diseases and managed medically for risk factors. Plasma p-tau217 was elevated in 20%, and 93 of these were cognitively unimpaired. This biomarker-defined, risk factor -controlled preclinical AD subgroup showed subtle, concurrent cognitive and behavioral differences, accompanied by modest differences in physiological measures within clinical reference ranges, and alongside higher biomarkers of astrogliosis (GFAP) and neurodegeneration (NfL). Reported modifiable risk factor histories were not associated with p-tau217 when effectively managed. A proof-of-concept AI classifier integrating routine multidomain clinical data improved identification of p-tau217-high individuals relative to cognitive screening alone. These findings indicate preclinical AD is not phenotypically silent at the group level and support multidomain-based screening for biomarker testing and early-detection.

neuroscience↗

bioRxiv2026

Altered microglial communication in brains with Alzheimers Disease pathology

Microglia are the resident immune cells of the central nervous system and are highly versatile, continuously monitoring the brain microenvironment with their motile processes and responding to perturbations in diverse ways. Recent studies have revealed substantial functional heterogeneity among microglial states, suggesting that analyzing individual subpopulations is essential to capture specialized signaling programs and disease-associated interactions that would otherwise be obscured in bulk analyses. To better understand how these cells interact, we performed a ligand-receptor communication analysis using single-nucleus RNA sequencing data from the dorsolateral prefrontal cortex, comprising 16 microglial subpopulations together with other myeloid cells identified in brain tissue, including macrophages and monocytes. We characterized the signaling roles of these cell populations, compared individuals with and without neuropathologically defined Alzheimers disease, and associated cell-pair interactions with AD-related clinical and neuropathological traits. We found that AD was characterized by altered microglial composition and rewiring of intercellular communication, including disease-specific signaling pathways and distinct interaction hubs. Lipid-associated microglia were associated with tau pathology, whereas nuclear receptor signaling microglia were linked to hippocampal sclerosis. These findings were replicated in three independent datasets. Overall, this work provides an initial but comprehensive map of microglial communication in the aging human brain and identifies candidate signaling interactions for future functional validation.

neuroscience↗

bioRxiv2026

Disruption of the Brain-Spleen Axis Impairs Monocyte-Microglia Communication and Accelerates Disease Progression in a Model of Amyloidosis

Alzheimers disease (AD) is characterized by a prolonged asymptomatic phase before cognitive decline emerges, yet the mechanisms driving symptom onset remain unclear. Here, we hypothesized that the transition from asymptomatic to symptomatic disease is linked to dysfunction of brain-immune communication. Retrograde neuronal tracing in the 5xFAD mouse model of amyloidosis revealed reduced brain-spleen connectivity at advanced disease stages. To probe the functional role of the brain-spleen axis in coping with disease, we denervated the splenic nerve at an early presymptomatic stage. This intervention accelerated cognitive decline, impaired splenic hematopoiesis, diminished monocyte recruitment to the brain, disrupted monocyte-microglia signaling networks, and reduced the transition of microglia from a homeostatic to the disease-associated (DAM) state. Conversely, enhancing splenic noradrenergic input increased hematopoiesis, restored monocyte homing to the brain, and delayed cognitive impairment. The protective role of splenic monocytes was independently validated in a retinal cytotoxic injury model, in which splenic denervation impaired post-insult retinal ganglion cell survival. Together, these findings identify an active brain-spleen circuit in regulating monocyte recruitment and establish peripheral monocytes as key drivers of microglial state transitions and disease progression.

neuroscience↗

bioRxiv2026

Adult human ex vivo brain slices for dissecting glial biology and multicellular communication

Glial cells are critical modulators of brain function in health, aging, and disease, emerging as promising therapeutic targets. However, exploring their roles and therapeutic potential is limited by the lack of experimental systems that faithfully capture the repertoire of mature human glial cells while permitting controlled perturbations. Here, we establish a robust ex vivo platform for cell-type specific interrogation of glial responses and multicellular crosstalk, based on adult human organotypic brain slice cultures, obtained from neurosurgical resections. We show that slice cultures preserve tissue architecture, maintain all major cell types and mature cellular identities over weeks in culture. These cultures elicit robust, stimulus-specific transcriptional programs to diverse stressors and inflammatory stimuli, demonstrating sensitivity to distinguish closely related signals and reproducibility despite biological and technical variation. Moreover, we resolved coordinated glial cell type-specific responses to TNF, a key mediator of neuroinflammation, uncovering distinct and physiologically relevant functional roles validated in postmortem human brains. Network analyses discovered balanced pro- and anti-inflammatory loops among microglia and astrocyte cells, which notably also involved oligodendrocyte precursor cells (OPCs), confirming their suggested role in regulation of the tissue level inflammatory response in human brains. We experimentally validated that glial activation in slice cultures is orchestrated not only by direct stimulation but also through intercellular signaling across cell types, mirroring natural multicellular dynamics in brain tissue. Together, organotypic brain slice cultures emerge as a sensitive and robust platform for dissecting adult human glial biology, paving the way for deeper mechanistic insights and advanced drug-screening applications.

neuroscience↗

bioRxiv2025

DeepDynamics resolves cell-subtype and clinicopathological dynamics from bulk RNA-seq to identify mediators of Alzheimer's disease risk

Processes such as Alzheimers disease and aging are shaped by dynamic cascades of cellular and molecular changes. Mapping how genetic and environmental risk factors alter these cascades is critical for pinpointing disease susceptibility and guiding therapeutic intervention, yet this task requires dense sampling of cell-subtype and -subpopulation changes throughout the full course of disease. Bulk measurements provide scale but obscure cell-type and subpopulation resolution, whereas single-cell assays offer resolution but lack sufficient sample size and temporal coverage. We present DeepDynamics, a deep-learning framework that combines a smaller reference sc/snRNA-seq atlas with a larger bulk RNA-seq cohorts to infer cell-subpopulation and clinicopathological dynamics along annotated trajectories. Applied to Alzheimers disease (AD), DeepDynamics mapped 1,092 cortical bulk profiles onto aging and disease trajectories, revealing faster accumulation of AD clinicopathologies, disease-associated glia, and specific neuronal subpopulations in APOE4 carriers. These changes, stronger in females, were accompanied by upregulation of cell-type-specific molecular pathways and early downregulation of heat-shock proteins across cell types. By unifying genetic risk, pathology, and cell-subpopulation dynamics, DeepDynamics provides a scalable approach to prioritize putative mediators of risk and resilience amid the myriad changes along the cascade, thus informing targeted therapies.

bioinformatics↗

bioRxiv2025

Early neuronal reprogramming and cell cycle reentry shape Alzheimer's disease progression

Alzheimers disease (AD) is a progressive neurodegenerative disorder characterized by hallmark pathologies, synaptic dysfunction, neuronal loss, gliosis and cognitive decline-dementia. Recent large-scale cell atlases of human AD brains exposed vulnerability of specific neuronal subtypes and highlighted early, coordinated glial responses, suggesting glial involvement in disease progression. However, the timing and nature of neuronal changes, differences between neuronal subtypes, and their coordination with glia remain unclear. Here, we used non-negative matrix factorization to identify co-expression gene programs in single-nucleus RNA profiles from the prefrontal cortex of 437 samples from donors whose clinical symptoms ranged between no cognitive impairment and AD dementia. This approach identified early coordinated transcriptional changes across all neuronal subtypes, preceding clinical symptoms of cognitive decline, and validated in independent snRNA-seq, proteomics, and ELISA datasets. We found neurons in AD undergo rapid modulation of synaptic genes, accompanied by convergence of neurons into two distinct programs: An oxidative stress and apoptosis program abundant in vulnerable neuronal subtypes, and a DNA damage and cell-cycle reentry program associated with resilient subtypes. Moreover, neuronal reprogramming was closely tied to glial responses, and diverged between AD to non-AD brain aging, suggesting neuro-glial coordinated reprogramming shapes the AD cascade and influences disease outcomes.

neuroscience↗

bioRxiv2025

Gene module-trait network analysis uncovers cell type specific systems and genes relevant to Alzheimers Disease

Alzheimers Disease (AD) is marked by the accumulation of pathology, neuronal loss, and gliosis and frequently accompanied by cognitive decline. Understanding brain cell interactions is key to identifying new therapeutic targets to slow its progression. Here, we used systems biology methods to analyze single-nucleus RNA sequencing (snRNASeq) data generated from dorsolateral prefrontal cortex (DLPFC) tissues of 424 participants in the Religious Orders Study or the Rush Memory and Aging Project (ROSMAP). We identified modules of co-regulated genes in seven major cell types, assigned them to coherent cellular processes, and assessed which modules were associated with AD traits such as cognitive decline, tangle density, and amyloid-{beta} deposition. Coexpression network structure was conserved in the majority of modules across cell types, but we also found distinct communities with altered connectivity, especially when compared to bulk RNASeq, suggesting cell-specific gene co-regulation. These coexpression modules can also capture signatures of cell subpopulations and be influenced by cell proportions. Using a Bayesian network framework, we modeled the direction of relationships between the modules and AD progression. We highlight two key modules, a microglia module (mic_M46), associated with tangles; and an astrocyte module (ast_M19), associated with cognitive decline. Our work provides cell-specific molecular networks modeling the molecular events leading to AD.

systems biology↗

bioRxiv2023

Molecular Connectomics Reveals a Glucagon-Like Peptide 1 Sensitive Neural Circuit for Satiety

Liraglutide and other agonists of the glucagon-like peptide 1 receptor (GLP-1RAs) are effective weight loss drugs, but how they suppress appetite remains unclear. One potential mechanism is by activating neurons which inhibit hunger-promoting Agouti-related peptide (AgRP) neurons of the arcuate hypothalamus (Arc). To identify these afferents, we developed a method combining rabies-based connectomics with single-nuclei transcriptomics. Applying this method to AgRP neurons predicted at least 21 afferent subtypes in the mouse mediobasal and paraventricular hypothalamus. Among these are Trh+ Arc neurons (TrhArc), inhibitory neurons which express the Glp1r gene and are activated by the GLP-1RA liraglutide. Activating TrhArc neurons inhibits AgRP neurons and feeding in an AgRP neuron-dependent manner. Silencing TrhArc neurons causes over-eating and weight gain and attenuates liraglutides effect on body weight. Our results demonstrate a widely applicable method for molecular connectomics, comprehensively identify local inputs to AgRP neurons, and reveal a circuit through which GLP-1RAs suppress appetite.

neuroscience↗

bioRxiv2023

Human subcutaneous and visceral adipocyte atlases uncover classical and specialized adipocytes and depot-specific patterns

Human adipose depots are functionally distinct. Yet, recent single-nucleus RNA-sequencing (snRNA-seq) analyses largely uncovered overlapping/similar cell-type landscapes. We hypothesized that adipocytes subtypes, differentiation trajectories, and/or intercellular communication patterns could illuminate this depot similarity-difference gap. For this, we performed snRNA-seq of human subcutaneous and visceral adipose tissue. Whereas the majority of adipocytes in both depots were classical, namely enriched in lipid metabolism pathways, we also observed specialized adipocyte subtypes that were enriched in immune-related, extracellular matrix deposition (fibrosis), vascularization/angiogenesis, or ribosomal processes. Pseudo-temporal analysis suggested a developmental trajectory from adipose progenitor cells to classical adipocytes via specialized adipocytes, suggesting that the classical state stems from loss, rather than gain, of specialized functions. Lastly, intercellular communication routes were consistent with the different inflammatory tone of the two depots. Jointly, these findings provide a high-resolution view into the contribution of cellular composition, differentiation, and intercellular communication patterns to human fat depot differences.

systems biology↗

bioRxiv2023

Cellular dynamics across aged human brains uncover a multicellular cascade leading to Alzheimer's disease

Alzheimers Disease (AD) is a progressive neurodegenerative disease seen with advancing age. Recent studies have revealed diverse AD-associated cell states, yet when and how they impact the causal chain leading to AD remains unknown. To reconstruct the dynamics of the brains cellular environment along the disease cascade and to distinguish between AD and aging effects, we built a comprehensive cell atlas of the aged prefrontal cortex from 1.64 million single-nucleus RNA-seq profiles. We associated glial, vascular and neuronal subpopulations with AD-related traits for 424 aging individuals, and aligned them along the disease cascade using causal modeling. We identified two distinct lipid-associated microglial subpopulations, one contributed to amyloid-{beta} proteinopathy while the other mediated the effect of amyloid-{beta} in accelerating tau proteinopathy, as well as an astrocyte subpopulation that mediated the effect of tau on cognitive decline. To model the coordinated dynamics of the entire cellular environment we devised the BEYOND methodology which uncovered two distinct trajectories of brain aging that are defined by distinct sequences of changes in cellular communities. Older individuals are engaged in one of two possible trajectories, each associated with progressive changes in specific cellular communities that end with: (1) AD dementia or (2) alternative brain aging. Thus, we provide a cellular foundation for a new perspective of AD pathophysiology that could inform the development of new therapeutic interventions targeting cellular communities, while designing a different clinical management for those individuals on the path to AD or to alternative brain aging.

neuroscience↗

bioRxiv2022

Cell-subtype specific effects of genetic variation in the aging and Alzheimer cortex

The relationship between genetic variation and gene expression in individual brain cell types and subtypes has remained elusive. Here, we generated single-nucleus RNA sequencing data from the dorsolateral prefrontal cortex of 424 individuals of advanced age; analyzing 1.5 million nuclear transcriptomes, we assessed the effect of genetic variants on RNA expression in cis (cis-eQTL) for 7 cell types and 81 cell subtypes. This effort identified 10,004 eGenes at the cell type level and 8,138 eGenes at the cell subtype level. Many eGenes are only detected within cell subtypes. A new variant influences APOE expression only in microglia and is associated with greater cerebral amyloid angiopathy but not Alzheimer pathology, accounting for the effect of APOE{varepsilon}4, providing mechanistic insights into both pathologies. While eQTLs are readily detected, only a TMEM106B variant robustly affects the proportion of cell subtypes. Integration of these results with GWAS highlighted the targeted cell type and likely causal gene within susceptibility loci for Alzheimers, Parkinsons, schizophrenia, and educational attainment.

genomics↗

bioRxiv2022

A cross-disease human microglial framework identifies disease-enriched subsets and tool compounds for microglial polarization.

Human microglia play a pivotal role in neurological diseases, but few targeted therapies that directly modulate microglial state or function exist due to an incomplete understanding of microglial heterogeneity. We use single-cell RNA sequencing to profile live human microglia from autopsies or surgical resections across diverse neurological diseases and central nervous system regions. We observe a central divide between oxidative and heterocyclic metabolism and identify subsets associated with antigen presentation, motility, and proliferation. Specific subsets are enriched in susceptibility genes for neurodegenerative diseases or the disease-associated microglial signature. We validate subtypes in situ with an RNAscope-immunofluorescence pipeline and leverage our dataset as a classification resource, finding that iPSC model systems recapitulate substantial in vivo heterogeneity. Finally, we identify and validate candidates for chemically inducing subtype-specific states in vitro, showing that Camptothecin downregulates the transcriptional signature of disease-enriched subsets and upregulates a signature previously shown to be depleted in Alzheimers.

neuroscience↗

bioRxiv2022

Uncovering molecular iron compounds in the living human brain.

Strict iron regulation is essential for normal brain function. The iron homeostasis, determined by the milieu of available iron compounds, is impaired in aging, neurodegenerative diseases and cancer. However, non-invasive assessment of different molecular iron environments implicating brain tissues iron homeostasis remains a challenge. We present a novel magnetic resonance imaging (MRI) technology sensitive to the iron homeostasis of the living brain (the r1-r2* relaxivity). In vitro, our MRI approach reveals the distinct paramagnetic properties of ferritin, transferrin and ferrous iron. In the in vivo human brain, we validate our approach against ex vivo iron compounds quantification and gene expression. Our approach varies with the iron mobilization capacity across brain regions and in aging. It reveals brain tumors iron homeostasis, and enhances the distinction between tumor tissue and non-pathological tissue without contrast agents. Therefore, our approach may allow for non-invasive research and diagnosis of iron homeostasis in living human brains. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/490254v2_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@17e2722org.highwire.dtl.DTLVardef@13b646aorg.highwire.dtl.DTLVardef@3d9bfeorg.highwire.dtl.DTLVardef@cc5b7d_HPS_FORMAT_FIGEXP M_FIG Non-invasive assessment of normal and impaired iron homeostasis in living human brains. C_FIG

neuroscience↗

bioRxiv2022

Accelerated cognitive decline in obese mouse model of Alzheimer's disease is linked to sialic acid-driven immune deregulation

Systemic immunity supports healthy brain homeostasis. Accordingly, conditions causing systemic immune deregulation may accelerate onset of neurodegeneration in predisposed individuals. Here we show that, in the 5xFAD mouse model of Alzheimers disease (AD), high-fat diet-induced obesity accelerated cognitive decline, which was associated with immune deviations comprising increased splenic frequencies of exhausted CD4+ T effector memory cells and CD4+FOXP3+ regulatory T cells (Tregs). Non-targeted plasma metabolomics identified N-acetylneuraminic acid (NANA), the predominant sialic acid, as the major obesity-induced metabolite in 5xFAD mice, the levels of which directly correlated with Tregs abundance and inversely correlated with cognitive performance. Visceral adipose tissue macrophages were identified by sNuc-Seq as one potential source of NANA. Exposure to NANA led to immune deregulation in middle-aged wild-type mice, and ex vivo in human T cells. Our study identified diet-induced immune deregulation, potentially via sialic acid, as a previously unrecognized link between obesity and AD.

neuroscience↗

bioRxiv2021

Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain

Development of effective vaccines against Coronavirus Disease 2019 (COVID-19) is a global imperative. Rapid immunization of the world human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and many different vaccine approaches are being pursued to meet this task. Engineered filamentous bacteriophage (phage) have unique potential in vaccine development due to their inherent immunogenicity, genetic plasticity, stability, cost-effectiveness for large-scale production, and proven safety profile in humans. Herein we report the design, development, and initial evaluation of targeted phage-based vaccination approaches against Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) by using dual ligand peptide-targeted phage and adeno-associated virus/phage (AAVP) particles. Towards a unique phage- and AAVP-based dual-display candidate approach, we first performed structure-guided antigen design to select six solvent-exposed epitopes of the SARS-CoV-2 spike (S) protein for display on the recombinant major capsid coat protein pVIII. Targeted phage particles carrying one of these epitopes induced a strong and specific humoral response. In an initial experimental approach, when these targeted phage particles were further genetically engineered to simultaneously display a ligand peptide (CAKSMGDIVC) on the minor capsid protein pIII, which enables receptor-mediated transport of phage particles from the lung epithelium into the systemic circulation (termed "dual-display"), they enhanced a systemic and specific spike (S) protein-specific antibody response upon aerosolization into the lungs of mice. In a second line of investigation, we engineered targeted AAVP particles to deliver the entire S protein gene under the control of a constitutive cytomegalovirus (CMV) promoter, which induced tissue-specific transgene expression stimulating a systemic S protein-specific antibody response. As proof-of-concept preclinical experiments, we show that targeted phage- and AAVP-based particles serve as robust yet versatile enabling platforms for ligand-directed immunization and promptly yield COVID-19 vaccine prototypes for further translational development. SignificanceThe ongoing COVID-19 global pandemic has accounted for over 2.5 million deaths and an unprecedented impact on the health of mankind worldwide. Over the past several months, while a few COVID-19 vaccines have received Emergency Use Authorization and are currently being administered to the entire human population, the demand for prompt global immunization has created enormous logistical challenges--including but not limited to supply, access, and distribution--that justify and reinforce the research for additional strategic alternatives. Phage are viruses that only infect bacteria and have been safely administered to humans as antibiotics for decades. As experimental proof-of-concept, we demonstrated that aerosol pulmonary vaccination with lung-targeted phage particles that display short epitopes of the S protein on the capsid as well as preclinical vaccination with targeted AAVP particles carrying the S protein gene elicit a systemic and specific immune response against SARS-CoV-2 in immunocompetent mice. Given that targeted phage- and AAVP-based viral particles are sturdy yet simple to genetically engineer, cost-effective for rapid large-scale production in clinical grade, and relatively stable at room temperature, such unique attributes might perhaps become additional tools towards COVID-19 vaccine design and development for immediate and future unmet needs.

microbiology↗

bioRxiv2020

Multi-cellular communities are perturbed in the aging human brain and with Alzheimer's disease

The role of different cell types and their interactions in Alzheimers disease (AD) is an open question. Here we pursued it by assembling a high-resolution cellular map of the aging frontal cortex by single nucleus RNA-seq of 24 individuals with different clinicopathologic characteristics. We used the map to infer the neocortical cellular architecture of 638 individuals profiled by bulk RNA-seq, providing the sample size necessary for identifying statistically robust associations. We uncovered diverse cell populations associated with AD, including inhibitory neuronal subtypes and oligodendroglial states. We further recovered a network of multicellular communities, each composed of coordinated subpopulations of neuronal, glial and endothelial cells, and found that two of these communities are altered in AD. Finally, we used mediation analyses to prioritize cellular changes that might contribute to cognitive decline. Thus, our deconstruction of the aging neocortex provides a roadmap for evaluating the cellular microenvironments underlying AD and dementia.

neuroscience↗

bioRxiv2019

A cellular and spatial map of the choroid plexus across brain ventricles and ages

The choroid plexus (ChP), located in each brain ventricle, produces cerebrospinal fluid (CSF) and forms the blood-CSF barrier, but is under-characterized. Here, we combine single cell RNA-Seq and spatial mapping of RNA and proteins to construct an atlas of each ChP in the developing and adult mouse brain. Each ChP comprises of epithelial, endothelial, mesenchymal, immune, neuronal, and glial cells, with distinct subtypes, differentiation states and anatomical locations. Epithelial, fibroblast, and macrophage populations had ventricle-specific, regionalized gene expression programs across the developing brain. Key cell types are retained in adult, with loss of developmental signatures and maturation of ventricle-specific regionalization in the epithelial cells. Expression of cognate ligand-receptor pairs across cell subtypes suggests substantial cell-cell interactions within the ChP. Our atlas sheds new light on the development and function of the ChP brain barrier system, and will facilitate future studies on its role in brain development, homeostasis and disease.

neuroscience↗

bioRxiv2018

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

Single-nucleus RNA-Seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate, including frozen clinical samples. This opens the way, in principle, to large studies, such as those required for human genetics, clinical trials, or precise cell atlases of large organs. However, such applications are currently limited by batch effects, sequential processing, and costs. To address these challenges, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies against the nuclear pore complex to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled in multiplex with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter the recovered transcriptome profiles. We further developed demuxEM, a novel computational tool that robustly detects inter-sample nucleus multiplets and assigns singlets to their samples of origin by antibody barcodes, and validated its accuracy using gender-specific gene expression, species-mixing and natural genetic variation. Nucleus hashing significantly reduces cost per nucleus, recovering up to about 5 times as many single nuclei per microfluidc channel. Our approach provides a robust technique for diverse studies including tissue atlases of isogenic model organisms or from a single larger human organ, multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.

genomics↗