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Biology subjects

Martin, N.

Publications and source records attributed to Martin, N..

At least 19 recordsLinked to original sources

Senescent cells are more susceptible to reductive stress-induced cell death: implications for senolytic research.

Proliferating cells can enter an irreversible state of cell-cycle arrest known as cellular senescence. The accumulation of senescent cells contributes to organismal ageing and age-related pathologies. Consequently, therapeutic strategies have emerged to selectively eliminate senescent cells (senolytics). Our previous work suggested that senescent mouse myoblasts are more susceptible to reductive stress-induced cell death than proliferating cells. Here, we replicated these findings in human LHCN-M2 myoblasts, demonstrating a biphasic dose-response relationship with cell death, wherein low concentrations were associated with reduced cell death in both proliferating and senescent cells, whereas higher concentrations selectively induced cytotoxicity in senescent cells. We propose that many identified natural senolytic compounds may exert their in vitro activity, at least in part, through the induction of reductive stress due to their antioxidant properties. These findings have important implications for understanding senolytic mechanisms and guiding the future development of senescence-targeting therapies.

cell biology↗

Single-nucleus profiling reveals age-associated remodeling opposed by parity in the postmenopausal human ovary

The postmenopausal ovary is commonly viewed as a passive organ, and its biology and cell composition remain incompletely characterized. Here, we generated a single-nucleus atlas of the aging postmenopausal human ovary comprising 439,011 nuclei across 64 ovarian samples from 28 donors. We resolved 37 fine cell states, revealing extensive stromal, vascular, and immune heterogeneity in the postmenopausal ovary. Aging was associated with stromal stress-state expansion, vascular and immune depletion, and enrichment of steroidogenic programs consistent with ovarian androgenization. Several major age-associated compositional shifts were supported in an independent GTEx ovary bulk RNA-seq cohort. Notably, the number of live births broadly opposed age-associated transcriptional and compositional remodeling. Together, our findings show that the postmenopausal ovary remains an actively remodeled aging tissue and that reproductive history leaves durable molecular and cellular imprints on ovarian aging.

genomics↗

Proteogenomic Profiling Reveals a Distinct Endogenous p16INK4a-Associated Senescence Signature in the Human Ovary.

The tumor suppressor and cell cycle regulator, p16INK4a (p16), has been extensively linked to cellular senescence, and its accumulation can reflect endogenous senescence within ovarian tissue. However, gene and protein signatures associated with p16 have not been well defined in human tissue. We utilized immunohistochemical (IHC) staining for P16 to identify distinct positive (P16+) and negative (P16-) regions within the ovarian cortex and employed the GeoMx Digital Spatial Profiler for simultaneous proteomic and transcriptomic analyses on cortical tissue cores. Differential expression and translation between p16-positive and p16-negative cores identified genes and proteins that are cellular senescence related (e.g., CDKN1A, GADD45B, GADD45G, and MYC) or key regulators of the extracellular matrix (e.g., collagen I, ADAMTS4, and MMP11). Additionally, the transcriptomic signature identified here was significantly enriched for the spatially derived ovarian p16-associated signature, BuckSenOvary, but not for other senescence gene sets. Lastly, given the association between changes to the extracellular matrix in aged ovaries and ovarian cancer, we compared genes upregulated and downregulated in p16-positive regions relative to p16-negative regions against multiple ovarian cancer transcriptomic datasets. These findings provide new insight into the molecular landscape of naturally occurring ovarian senescence and its possible relationship to age-associated disease processes, including cancer development.

cell biology↗

SCALPEL: A pipeline for processing large-scale spatial transcriptomics data

Spatial transcriptomics enables the precise mapping of gene expression patterns within tissue architecture, offering unprecedented insights into cellular interactions, tissue heterogeneity, and disease pathology that are unattainable with traditional transcriptomic approaches. We present a tool for processing spatial transcriptomics data, SCALPEL (Spatial Cell Analysis, Labeling, Processing, and Expression Linking). SCALPEL is specifically designed to support the analysis of large, atlas-level datasets. Our new workflow features advanced 3D segmentation optimized for dense and heterogeneous tissues, refined filtering criteria, and transcriptome-based doublet detection to remove low-quality or artifactual cells. Cell type label transfer from existing taxonomies is further improved through updated filtering thresholds. Spatial domain detection is incorporated to capture local transcriptomic organization, and tissue sections are registered to the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3) for precise anatomical alignment. Genome-wide expression imputation from single-cell RNA-sequencing (scRNAseq) further enriches the dataset. Crucially, we benchmark the performance of this updated pipeline against a previously published version of our whole-mouse-brain (WMB) dataset (Yao et al., 2023b), demonstrating substantial improvements in cell number, expression profile clarity, and spatial registration. These advances provide a robust foundation for downstream spatial analyses and set a new standard for large-scale spatial transcriptomics studies.

bioinformatics↗

The Caudate Nucleus Exhibits Distinct Pathology and Cell Type-Specific Responses Across Alzheimer's Disease

A{beta} presence in the caudate nucleus (Ca) partially defines Thal stage III in Alzheimers disease (AD), but little is known about ADs cellular impact on the region. Leveraging a public basal ganglia taxonomy of cellular populations, we generated a cellular resolution atlas of AD-associated pathological changes in Ca. Unlike cortex, we found that Ca AD pathology is dominated by two key features: phosphorylated tau (pTau)-containing neuropil threads enriched near oligodendrocytes in white matter tracts and amyloid-{beta} diffuse plaques enriched in gray matter. Although AD pathology in affected cortical regions results in neuronal loss, we find no AD-driven reductions in neuron proportions in Ca. However, there were observable changes in multiple cellular populations. Protoplasmic astrocytes and FLT1+/IL1B+ microglia increased in abundance with global pTau levels. We also observe gene expression changes in fast-spiking PTHLH-PVALB interneurons indicative of disrupted signaling pathways and altered intrinsic physiological properties. This work provides a cellular-resolution framework for understanding AD pathology in Ca.

neuroscience↗

Genome-Environment Associations reveal shared and unique adaptive loci across multiple pollutants and populations of the eastern mosquitofish Gambusia holbrooki

Rapid adaptation to human-induced stressors is commonplace in the context of global change, including during biological invasions. Identifying the genomic bases and associated biological functions underlying such adaptation is hence crucial to understand and anticipate the response of populations and species to changing conditions. In particular, the extent to which genetic responses to multiple anthropogenic stressors vary between populations in the wild has been relatively unexplored. We addressed this question by leveraging whole-genome sequence data (both PoolSeq and IndSeq) in invasive populations of Gambusia holbrooki - a widespread invasive fish species - collected from 14 locations with different multi-pollutants exposure. We sought to identify adaptive loci associated with pollution tolerance by conducting Genome-Environment Association (GEA) analyses. Additionally, we investigated the degree of adaptive loci reuse between pollutants and their combinations as well as across populations. We found strong signals of association between allele frequency changes and pollutant exposure at several genomic locations, often overlapping with genes known for their functions in detoxification and immune response. We further showed that most adaptive loci are not shared among all populations, suggesting heterogeneous genomic response to each local selection. Interestingly, multiple tests looking for footprints of selection and association to pollutants yielded consistent results. Our results shed new light on the extent of genetic convergence in the genomic bases of rapid adaptation to different cocktails of human-induced pollution, and are important to our understanding of the fate of wild populations facing increasingly complex and stressful environments.

genomics↗

The Pioneer Transcription Factor Oct4 Differentially Co-opts Bcl11a and Bcl11b to Regulate Reprogramming to Pluripotency

Pioneer transcription factors (TFs) orchestrate development, reprogramming, and cancer. Yet, the molecular mechanisms by which they cooperate with endogenous TFs and chromatin to trigger cell fate conversions remain largely unknown. Here, we identified antagonistic functions in reprogramming to pluripotency for the two paralogous somatic zinc finger TFs Bcl11a and Bcl11b. We reveal that Bcl11a and Bcl11b are initially co-expressed in mouse embryonic fibroblasts and then segregate in cellular intermediates respectively prone or refractory to reprogramming, transdifferentiation, and oncogenic transformation. They exert opposite functions - with Bcl11a promoting and Bcl11b hindering - the efficacy of induced pluripotent stem cells generation. During reprogramming, we uncover that Bcl11b safeguards cellular identity by persistently binding to differentiation genes with Runx1 in refractory intermediates. In contrast, in reprogramming intermediates, Bcl11a interacts with Oct4 and is initially displaced from MEF enhancers. Bcl11a then binds transiently and contributes to activate the E3 ubiquitin ligase Pja1 that regulates Smad3, thus promoting mesenchymal-epithelial transition and constraining senescence. Collectively, our work unveils how the differential repurposing of paralogous TFs by Oct4 orchestrates reprogramming to pluripotency.

cell biology↗

Senescence-Linked Fibrosis in the Aging Human Ovary Revealed by p16-Based Histological Profiling and Spatial Transcriptomics

Cellular senescence is implicated as a driver of ovarian aging, but senescent cells in the human postmenopausal ovary remain poorly defined. Using spatially resolved p16INK4a protein expression, a canonical senescence marker, we identified and mapped senescent cells in postmenopausal ovaries. We integrated p16 immunohistochemistry, multiplexed immunofluorescence, spatial transcriptomics, and AI-guided digital pathology to map senescent microenvironments. p16-positive cells formed discrete stromal, vascular, and cyst-associated clusters that increased with age and were enriched for macrophages and myofibroblast-like cells. Wholetranscriptome profiling of 92 spatial regions uncovered a 32-gene p16-associated signature, BuckSenOvary, that distinguished p16-positive regions across cortex and medulla. BuckSenOvary is characterized by suppression of cell-cycle regulators and activation of inflammatory and extracellular-matrix remodelling genes. AI-based collagen matrix analysis confirmed that p16-positive regions exhibit more architecturally complex collagen, demonstrating that focal senescent microenvironments are fibro-inflammatory. These findings position senescent ovarian niches as therapeutic targets to preserve ovarian function.

cell biology↗

A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia

The basal ganglia are interconnected subcortical nuclei with complex topographical organization that orchestrate goal-directed behaviors and are implicated in neurodegenerative movement disorders. We generated a cellular-resolution, spatial transcriptomic atlas of the basal ganglia in human, rhesus macaque, and common marmoset, sampling over one million cells in each species. By integrating spatial data with a cross-species, consensus snRNA-seq cell type taxonomy, this atlas reveals conserved principles of molecular organization within and across structures. The cellular architecture is complex but highly stereotyped, with gene expression gradients superimposed onto discrete compartments. Extensive spatial sampling illuminates 3D gradients of molecular organization in the striatum and reveals cell type-specific core and shell compartments in the primate internal globus pallidus, which is conserved with mouse. This unified, cross-species spatial transcriptomic atlas will be a foundational resource for characterizing the molecular and functional organization of the basal ganglia and their roles in health and disease.

neuroscience↗

Spatial patterning of transcriptional and regulatory programs in the primate subcortex

Mammalian brain cell identity is shaped by intrinsic factors and external context. We present a spatially resolved transcriptomic and gene regulatory atlas of cell types across all subcortical regions in a primate, the common marmoset. Dense sampling and cross-species integration revealed spatially precise neuronal assemblies, including in complex midbrain and diencephalic structures. Chromatin accessibility and transcriptional identity are spatially tuned within and across subcortical structures; spatial gradients within hippocampal subfields are orchestrated by graded transcription factors acting through graded enhancers. The primate-expanded thalamic GABAergic population shares transcriptional and regulatory syntax with conserved midbrain populations, reflecting an evolutionary adaptation compared with rodents. Similar regional expression across cell types can arise by distinct regulatory architectures, as for telencephalic astrocytes and neurons. Conversely, distant cell types can share regulatory programs despite divergent identities: striatal GABAergic medium spiny neurons and telencephalic glutamatergic neurons share a postsynaptic regulatory program despite divergent lineage, region, and neurotransmitter identity.

neuroscience↗

Trans-acting mutations reveal non-nuclear modulators of both intrinsic and extrinsic gene expression noise in a eukaryote.

Gene expression regulation is a stochastic process that can be modified by mutations not only in a deterministic manner but also in a probabilistic way, for example by changing the extent of cell-to-cell variability in gene expression (also called "gene expression noise"). Although systematic studies have successfully analyzed the properties of cis-acting mutations that modulate expression noise at their own locus, less is known about the type of genetic changes that alter expression noise in trans (at loci distant from the mutation). Here, we applied genetic mapping on yeast strains (Saccharomyces cerevisiae) generated by random mutagenesis and identified three mutations (in chs1, yme2 and msh1 genes) that changed the expression noise of a reporter gene in the nuclear genome regulated by the yeast TDH3 promoter. These mutations affected either extrinsic noise (variability due to cell-specific factors), intrinsic noise (inherent variability within each cell) or both, and their effects were found to not be specific to the TDH3 promoter. Surprisingly, all three mutations targeted proteins located outside of the nucleus: Yme2 and Msh1 being involved in the maintenance of mitochondrial genome integrity, and Chs1 being necessary for the repair of cell-wall defects in freshly-born daughter cells. Our results reveal that mitochondrial state can modulate the extent of intrinsic expression noise of eukaryotic nuclear genes.

genetics↗

Expression and localization of NMDA receptor GluN2 subunits in dorsal horn pain circuits across sex, species, and late postnatal development

Despite being essential mediators of pain processing, the molecular identity of N-methyl-D-aspartate receptor (NMDAR) subtypes in nociceptive dorsal horn circuits is poorly understood, especially between sexes and in humans. Given the importance of GluN2 subunits in shaping NMDAR function and plasticity, we investigated the expression and localization of specific GluN2 NMDAR variants in the dorsal horn of viable spinal cord tissue from male and female rodents and human organ donors. Analysis of single-cell/nuclei sequencing datasets and quantitative reverse transcriptase polymerase chain reactions (qRT-PCR) revealed that the GluN2A (GRIN2A) and GluN2B (GRIN2B) subunits are robustly expressed in dorsal horn neurons of mice, rats and humans, with moderate expression of GluN2D (GRIN2D). Immunohistochemistry (IHC) with antigen retrieval demonstrated that GluN2A, GluN2B, and GluN2D proteins are all preferentially localized to the superficial dorsal horn of both adult rats and humans, which is conserved between males and females. Surprisingly, we found that these GluN2 NMDAR subunits are enriched in the lateral superficial dorsal horn in rats but not in humans, while presynaptic and neuronal markers are symmetrically distributed across the rat mediolateral axis. A dramatic shift in localization of GluN2A to the lateral superficial dorsal horn was observed across later postnatal development (PD21-PD90) in both male and female rats, with a corresponding change in synaptic NMDAR currents. This discovery of changes in NMDAR subunit distribution during maturation and between species will shed light on the physiological roles of NMDARs and their potential as therapeutic targets for pain. SIGNIFICANCE STATEMENTWe used complementary single-cell/nuclei analysis, immunostaining, quantitative reverse transcriptase polymerase chain reactions, RNAscope in situ hybridization, and electrophysiological approaches to compare the relative expression of N-methyl-D-aspartate receptor (NMDAR) GluN2 subunits in dorsal horn spinal cord pain circuits of mouse, rat, and human spinal cord tissue. Through these comparisons, we find that the transcripts and proteins of the GluN2A, GluN2B, and GluN2D NMDAR subunits are robustly expressed in superficial dorsal horn neurons, with conserved expression across sex but important differences in expression and localization patterns across late development and between species. These discoveries shed light on the physiological roles of NMDARs and their utility as potential therapeutic targets for pain.

neuroscience↗

Transitions in human gut viral communities from ancient to industrialized societies

The composition and function of the human gut microbial community (the microbiome) have changed substantially over millennia, with implications for human health. While microbiome research has focused primarily on bacterial dynamics, the long-term history of gut viral communities (the virome) remains largely unexplored, despite their crucial role in shaping bacterial populations. We analyzed gut viromes from 14 pre-modern human coprolites (1301 BCE-1400s CE), as well as 502 non-industrialized and 492 industrialized contemporary human fecal samples. We found that, from pre-modern to contemporary and industrialized populations, human gut viral communities have become more similar in gene content, increasingly dominated by temperate lifestyles, and more supportive of bacterial pathogenicity. These synergistic ecological shifts suggest that long-term changes, especially with industrialization, have fundamentally altered the gut virome, likely affecting human health. These insights into historical shifts in gut viral community and function open potential avenues for ecologically grounded therapeutics to enhance gut microbiome resilience.

microbiology↗

Decoding Cellular Stress States for Toxicology Using Single-Cell Transcriptomics

We applied the TempO-LINC(R) platform to generate single-cell transcriptomic (SCTr) profiles of [~]40,000 HepaRG cells exposed to etoposide, brefeldin A, cycloheximide, rotenone, tBHQ, troglitazone, and tunicamycin at three concentrations for 24 hours. SCTr enabled a detailed analysis of adaptive stress response pathways (SRPs), including the unfolded protein response (UPR), oxidative stress response (OSR), heat shock response (HSR), and DNA damage response (DDR). Troglitazone upregulated lipid metabolism genes (PLIN2, ACOX1) along with HSR and UPR activation, with co-expression of DNAJA1, HSP90AA1, and DDIT3 in subsets of cells. Brefeldin A and tunicamycin strongly induced UPR markers (HSPA5, SYVN1, LMF2, PDIA4) in subsets of cells, with some also expressing apoptotic (DDIT3, CASP8) and autophagic (SQSTM1) genes, indicating diverse stress responses. Rotenone activated GDF15, TRIB3, and DDIT3 in a fraction of cells, accompanied by PLIN2 and mild UPR induction, reflecting heterogeneous mitochondrial stress responses. We scored individual cells using literature-derived SRP gene signatures to characterize overall stress phenotypes and clustered them using a generalized Jaccard metric. The clustering revealed five phenotypic groups spanning cell states associated with homeostasis, adaptive responses, terminal outcomes, autophagy, and apoptosis. By systematically analyzing the distributions of cells in different states across treatments, we visualized dynamic shifts in cellular subpopulations responding to chemicals, revealing early stress responses and potential transitions to cell death. Our findings suggest the utility of SCTr in decoding stress states that could provide possible insights into transitions between cellular adaptive and terminal transitions involved in toxicity.

pharmacology and toxicology↗

Different cellular and molecular mechanisms of chitin deposition contribute to the specificity of the two chitin synthases in D. melanogaster.

Chitin is a major component of arthropod extracellular matrices, including the exoskeleton and the midgut peritrophic matrix. It plays a key role in the development, growth and viability of insects. Besides the biological importance of this aminopolysaccharide, chitin also receives a lot of attention for its practical applications in medicine and biotechnology as a superior biopolymer with excellent physicochemical and mechanical properties. Chitin is produced and deposited extracellularly by chitin synthases. Most insects encode two types of chitin synthases, presumably with type A being required for exoskeletons and type B to produce the peritrophic matrix. It is not fully understood, however, which factors contribute to the specificity of each type of chitin synthase. Here we leverage the advantages of Drosophila melanogaster for functional manipulations to evaluate the mechanisms of activity and functional requirements of Kkv (Chitin synthase A) and Chs2 (Chitin synthase B). We first demonstrate that Chs2 is expressed and required in a region in the larval proventriculus that produces the chitin deposited in the peritrophic matrix. We then analyse whether the two chitin synthases can replace each other. We also investigate the subcellular localisation of these chitin synthases in different tissues and their ability to deposit chitin in combination with known auxiliary proteins. Our results indicate that the two different chitin synthases are not functionally equivalent, and that they use specific cellular and molecular mechanisms to deposit chitin. We suggest that the specificity of the different insect chitin synthases may underly the production of chitin polymers with different properties, conferring different physiological activities to the extracellular matrices.

developmental biology↗

A Novel C. elegans Model for Tau spreading Reveals Genes Critical for Endolysosomal Integrity and Seeded Tau Aggregation

The spreading of Tau pathology is closely associated with the progression of neurodegeneration and cognitive decline in Alzheimers disease and other tauopathies. A key event in this process is the rupture of endolysosomal vesicles following the intercellular transfer of Tau aggregates, releasing the transferred Tau species into the cytosol where they can promote the aggregation of endogenous Tau. However, understanding of the cellular pathways involved in this process remains limited. In this study, we investigated cellular pathways that prevent endolysosomal vesicle rupture. We established a new C. elegans model of Tau spreading by introducing an mCherry-labelled, disease-associated aggregation-prone fragment of human Tau (F3{Delta}K281::mCh) into the six touch receptor neurons. F3{Delta}K281::mCh transgenic animals exhibited significant neurotoxicity and mechanosensory deficits due to the accumulation of this Tau fragment. In addition, its intercellular transmission compromised the endolysosomal system in receiving hypodermal cells. Using this model, we conducted an unbiased genome-wide RNAi screen and identified 59 genes critical for maintaining endolysosomal integrity. GO-term analysis revealed an enrichment of genes related to the ESCRT complex, the ubiquitin-proteasome system, mRNA splicing, and fatty acid metabolism. Silencing of selected conserved genes exacerbated seeded Tau aggregation in a human induced pluripotent stem cell (hiPSC)-derived cortical neuron model and triggered endolysosomal rupture in HEK293T cells, confirming the crucial role of endolysosomal damage in seeded Tau aggregation. Overall, this study discovered novel cellular pathways that safeguard endolysosomal integrity. These findings may guide the development of therapeutics that improve endolysosomal integrity to halt the progression of Tau pathology.

cell biology↗

Sphingolipid imbalance aggravates fibrillar Tau-induced endomembrane rigidification and rupture

Endolysosomal dysfunction is a hallmark of Alzheimers disease (AD) and related tauopathies, yet underlying mechanisms remain poorly understood. This study investigates the role of sphingolipid metabolism in maintaining endolysosomal membrane integrity and its impact on tau aggregation and toxicity in Caenorhabditis elegans and human cell culture models. Fluorescence recovery after photobleaching and C-Laurdan dye imaging revealed that silencing sphingolipid metabolism genes reduced endolysosomal vesicle membrane fluidity, increasing their rupture. The accumulation of aggregated tau in endolysosomal vesicles further aggravated endomembrane rigidification and damage and promoted seeded tau aggregation, potentially by facilitating the escape of tau seeds from the endolysosomal system. Supplementation with unsaturated fatty acids improved membrane fluidity, suppressing endolysosomal rupture and seeded tau aggregation in cell models, and alleviating tau-associated neurotoxicity in C. elegans. Together, this study provides mechanistic insight into how perturbation of sphingolipid metabolism promotes endolysosomal membrane damage and contributes to the escape of aggregated tau from this compartment, suggesting that restoration of membrane fluidity may represent a strategy to limit tau propagation and toxicity.

cell biology↗

A comprehensive multi-omics signature of doxorubicin-induced cellular senescence in the postmenopausal human ovary.

A major aging hallmark is the accumulation of cellular senescence burden. Over time senescent cells contribute to tissue deterioration through chronic inflammation and fibrosis driven by the Senescence-Associated Secretory Phenotype (SASP). The human ovary is one of the first organs to age, and prominent age-related fibroinflammation within the ovarian microenvironment is consistent with the presence of senescent cells, but these cells have not been characterized in the human ovary. We thus established a doxorubicin-induced model of cellular senescence to establish a "senotype" (gene/protein signature of a senescence cell state) for ovarian senescent cells. Explants of human postmenopausal ovarian cortex and medulla were treated with doxorubicin for 24 hours followed by culture for up to 10 days in a doxorubicin-free medium. Tissue viability was confirmed by histology, lack of apoptosis, and continued glucose consumption by explants. Single nuclei sequencing and proteomics revealed an unbiased signature of ovarian senescence. We identified distinct senescence profiles for the cortex and medulla, driven predominantly by epithelial and stromal cells. Proteomics uncovered subregional differences in addition to 120 proteins common to the cortex and medulla SASP. Integration of transcriptomic and proteomic analyses revealed 26 shared markers, defining a senotype of doxorubicin-induced senescence unique to the postmenopausal ovary. A subset of these proteins: Lumican, SOD2, MYH9, and Periostin were mapped onto native tissue to reveal compartment-specific localization. This senotype will help determine the role of cellular senescence in ovarian aging, inform biomarker development to identify, and therapeutic applications to slow or reverse ovarian aging, senescence, and cancer.

molecular biology↗