Biology subjects

Cain, A.

Publications and source records attributed to Cain, A..

6 recordsLinked to original sources

bioRxiv2026

D-Mannose treats obesity by increasing adipose Treg cells and suppressing gut Firmicutes

Early-life microbiota represent an indispensable factor for the proper development and function of host metabolism and the immune system. We have demonstrated that neonatal exposure to antibiotics for the first 3 weeks (NeoATB) leads to obesity in adulthood, characterized by gut microbiota dysbiosis and dysregulated immune responses. Here, we demonstrate that feeding D-mannose suppresses NeoATB-induced obesity, accompanied by improved glucose tolerance and decreased insulin resistance. Mechanistically, D-mannose feeding decreased hypoxia and increased oxygenation and recovery of metabolic activity of adipocytes. D-mannose restored CD4+Foxp3+ST2+ Tregs, leading to a reduction of Th1 pro-inflammatory cells in the adipose tissue of NeoATB mice. Significantly, we revealed that D-mannose treatment reversed the dysregulated ratios of phylum Firmicutes to phylum Bacteroidetes in obese NeoATB mice, which was surprisingly attributed to D-mannose-mediated suppression of the growth of Firmicutes rather than an increase in the growth of Bacteroidetes. These findings should have therapeutic implications for the treatment of obesity in human patients.

immunology↗

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↗

bioRxiv2023

The 3'UTR of vigR is required for virulence in Staphylococcus aureus and has expanded through STAR sequence repeat insertions

Staphylococcus aureus is an adaptable human pathogen causing life-threatening endocarditis and bacteraemia. Methicillin-resistant S. aureus (MRSA) is alarmingly common, and treatment is confined to last-line antibiotics. Vancomycin is the treatment of choice for MRSA bacteraemia and vancomycin treatment failure is often associated with vancomycin-intermediate S. aureus strains termed VISA. The regulatory 3 UTR of vigR mRNA contributes to vancomycin tolerance in the clinical VISA isolate JKD6008 and upregulates the lytic transglycosylase IsaA. Using MS2-affinity purification coupled with RNA sequencing (MAPS), we find that the vigR 3 UTR also interacts with mRNAs involved in carbon metabolism, amino acid biogenesis, cell wall biogenesis, and virulence. The vigR 3 UTR was found to repress dapE, a succinyl-diaminopimelate desuccinylase required for lysine and cell wall peptidoglycan synthesis, suggesting a broader role in controlling cell wall metabolism and vancomycin tolerance. Deletion of the vigR 3 UTR increased VISA virulence in a wax moth larvae model, and we find that an isaA mutant is completely attenuated in the larvae model. Sequence and structural analysis of the vigR 3 UTR indicates that the UTR has expanded through the acquisition of Staphylococcus aureus repeat insertions (STAR repeats) that partly contribute sequence for the isaA interaction seed and may functionalise the 3 UTR. Our findings reveal an extended regulatory network for vigR, uncovering a novel mechanism of regulation of cell wall metabolism and virulence in a clinical S. aureus isolate.

microbiology↗

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↗

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↗