Biology subjects

Stout, M.

Publications and source records attributed to Stout, M..

11 recordsLinked to original sources

bioRxiv2026

Multimodal profiling establishes ovarian fibrosis as a measurable and targetable hallmark of human reproductive aging

ABSTRACT Ovarian aging underpins infertility, systemic morbidity, and mortality in women. Stromal fibrosis is implicated in ovarian aging but has not been defined in the human ovary in situ. We integrated shear wave elastography (SWE), extracellular matrix (ECM) neoepitope fingerprinting, and singlecell RNA sequencing of follicular fluid aspirates within the same individual to comprehensively profile ovarian fibrosis. In an age-stratified cohort (<33 and >37 years; N=32), age predicted ovarian stiffness, while mean stiffness was independently associated with reduced oocyte yield and follicular efficiency. ECM profiling revealed a dynamic fibrotic index favoring formation over degradation products. Single-cell transcriptomics demonstrated an age-associated fibroinflammatory stromal program enriched in pro-fibrotic pathways with stromal-immune crosstalk. In a larger validation cohort (25-45 years; N=100), age was similarly associated with ovarian stiffness. Thus, ovarian fibrosis is a quantifiable hallmark of human reproductive aging and represents a robust potential non-invasive biomarker and target for therapeutic intervention.

cell biology↗

bioRxiv2026

Development and Function of Ovarian Lymphatic Vasculature

Lymphatic vessels play essential roles in interstitial fluid clearance and immune cell trafficking. Recent studies have uncovered previously unrecognized, organ-specific functions of the lymphatic vasculature in the meninges, heart, kidney, and lungs. However, the development and physiological significance of the ovarian lymphatic network remain poorly defined. To address this gap, we performed high-resolution three-dimensional imaging of ovarian lymphatic vasculature in mice. Our results reveal that the ovarian lymphatic network comprises lymphatic capillaries and valve-containing pre-collectors and the ovarian lymphatic vasculature arises from pre-existing lymphatic vessels in the broad ligament starting at postnatal day 5. Furthermore, we demonstrate that the VEGF-C/VEGFR-3 signaling is essential for ovarian lymphatic development and Vegfr3 insufficiency impairs ovarian lymphangiogenesis, leading to fibrosis and premature ovarian aging. Together, these findings identify the lymphatic vasculature as a critical component of the ovarian microenvironment and establish a causal link between lymphatic insufficiency and accelerated ovarian aging.

developmental biology↗

bioRxiv2025

Cell type-specific intronic RNAs shape genome architecture during neuronal lineage specification

Cell differentiation towards neurons is accompanied by widespread changes in three-dimensional (3D) genome organization and gene expression. Chromatin-associated RNAs have been proposed to be important regulators of such changes; however, the type, abundance, and role of these RNAs during neuronal differentiation remain largely unexplored. Here, we integrate multi-omic data generated in the frame of the Functional ANnoTation Of the Mammalian genome (FANTOM6) to chart 3D genome, RNA-DNA contactome, and transcriptome changes occurring during in vitro differentiation of human induced pluripotent stem cells to neural stem cells and neurons. We reveal a previously unreported phenomenon, in which intronic RNAs engage in long-distance contacts with DNA loci distributed all over the genome. These trans-contacting intronic RNAs (TIRs) are produced from exceptionally long (mean length: 750 kilobases, kb) protein-coding genes that carry ultra-long introns and are selectively expressed in neurons. We show that TIRs do not undergo rapid co-transcriptional degradation but rather accumulate in the nucleus of neuronal cells, forming large dot clouds around their source loci and spreading across the nucleus, as visualized by single-molecule RNA fluorescence in situ hybridization. TIRs engage in contacts with a set of genomic regions (TIR-contacted regions or TIRCs) that carry much shorter (mean length: [~]30 kb) neuronally expressed genes forming high-connectivity hubs. We also show that the expression of genes within TIRCs contacted by the same set of TIRs is highly co-varied, and that TIR source genes, especially their introns, are enriched in genetic risk loci for neurodevelopmental and neuropsychiatric disorders. Our findings point to a functional role of the persistence of long intronic RNAs in the nucleus of neuronal cells and might contribute to explain why neurons uniquely express many ultra-long genes. We propose a model in which TIRs form pan-nuclear scaffolds--which we propose to name introsomes--that constitute a dynamically self-renewing regulatory layer, where transcription itself continuously regenerates the very scaffold that organizes genome function in neurons, and that might be involved in the pathogenesis of neurodevelopmental and neuropsychiatric disorders.

genomics↗

bioRxiv2024

Multinucleated giant cells are hallmarks of ovarian aging with unique immune and degradation-associated molecular signatures

The ovary is one of the first organs to exhibit signs of aging, characterized by reduced tissue function, chronic inflammation, and fibrosis. Multinucleated giant cells (MNGCs), formed by macrophage fusion, typically occur in chronic immune pathologies, including infectious and non-infectious granulomas and the foreign body response1, but are also observed in the aging ovary2-4. The function and consequence of ovarian MNGCs remain unknown as their biological activity is highly context-dependent, and their large size has limited their isolation and analysis through technologies such as single-cell RNA sequencing. In this study, we define ovarian MNGCs through a deep analysis of their presence across age and species using advanced imaging technologies as well as their unique transcriptome using laser capture microdissection. MNGCs form complex interconnected networks that increase with age in both mouse and nonhuman primate ovaries. MNGCs are characterized by high Gpnmb expression, a putative marker of ovarian and non-ovarian MNGCs5,6. Pathway analysis highlighted functions in apoptotic cell clearance, lipid metabolism, proteolysis, immune processes, and increased oxidative phosphorylation and antioxidant activity. Thus, MNGCs have signatures related to degradative processes, immune function, and high metabolic activity. These processes were enriched in MNGCs compared to primary ovarian macrophages, suggesting discrete functionality. MNGCs express CD4 and colocalize with T-cells, which were enriched in regions of MNGCs, indicative of a close interaction between these immune cell types. These findings implicate MNGCs in modulation of the ovarian immune landscape during aging given their high penetrance and unique molecular signature that supports degradative and immune functions.

cell biology↗

bioRxiv2024

Aged mice exhibit faster acquisition of intravenous opioid self-administration with variable effects on intake

Although opioid abuse is more prevalent in young individuals, opioid use, overdose, and use disorders continue to climb at a rapid rate among the elderly. Little is known about abuse potential in a healthy aged population, in part due to technical and logistical difficulties testing intravenous self-administration in aged rodents. The goal of this study was to address the critical gap in the literature regarding age-dependent differences in opioid (remifentanil and fentanyl) self-administration between old and young mice. Male and female mice were grouped into young (mean: 19 weeks) and old (mean: 101 weeks), and were trained to self-administer intravenous fentanyl or remifentanil in daily sessions. In both old and young mice, acquisition, intake, and cue-responding after forced abstinence were measured for both drugs, and a dose-response curve (remifentanil) and dose-escalation (fentanyl) were conducted. Surprisingly, old mice learned to self-administer both remifentanil and fentanyl faster and more accurately than young mice. Baseline intake of remifentanil was also substantially greater in old mice compared to their young counterparts; however, we did not see increased intake of fentanyl with age at either dose tested. Further, compared to young mice, the old mice showed a greater incubation of responding for cues previously associated with remifentanil after a forced abstinence, but again this was not observed with fentanyl. Together these data suggest that an aged population may have an increased drug-abuse vulnerability for opioids compared to young counterparts and underscore the importance of future work on mechanisms responsible for this increased vulnerability.

animal behavior and cognition↗

bioRxiv2024

Two retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity

The human genome contains 24 gag-like capsid genes derived from deactivated retrotransposons conserved among eutherians. Although some of their encoded proteins retain the ability to form capsids and even transfer cargo, their fitness benefit has remained elusive. Here we show that the gag-like genes PNMA1 and PNMA4 support reproductive capacity. Six-week-old mice lacking either Pnma1 or Pnma4 are indistinguishable from wild-type littermates, but by six months the mutant mice become prematurely subfertile, with precipitous drops in sex hormone levels, gonadal atrophy, and abdominal obesity; overall they produce markedly fewer offspring than controls. Analysis of donated human ovaries shows that expression of both genes declines normally with aging, while several PNMA1 and PNMA4 variants identified in genome-wide association studies are causally associated with low testosterone, altered puberty onset, or obesity. These findings expand our understanding of factors that maintain human reproductive health and lend insight into the domestication of retrotransposon-derived genes.

genetics↗

bioRxiv2023

The Fanconi anemia core complex promotes CtIP-dependent end-resection to drive homologous recombination at DNA double-strand breaks

Homologous Recombination (HR) is a high-fidelity repair mechanism of DNA Double-Strand Breaks (DSBs), which are induced by irradiation, genotoxic chemicals or physiological DNA damaging processes. DSBs are also generated as intermediates during the repair of interstrand crosslinks (ICLs). In this context, the Fanconi anemia (FA) core complex, which is effectively recruited to ICLs, promotes HR-mediated DSB-repair. However, whether the FA core complex also promotes HR at ICL-independent DSBs remains controversial. Here, we identified the FA core complex members FANCL and Ube2T as HR-promoting factors in a CRISPR/Cas9-based screen with cells carrying the DSB-repair reporter DSB-Spectrum. Using isogenic cell-line models, we validated the HR-function of FANCL and Ube2T, and demonstrated a similar function for their ubiquitination-substrate FANCD2. We further show that FANCL and Ube2T are directly recruited to DSBs and are required for the accumulation of FANCD2 at these break sites. Mechanistically, we demonstrate that FANCL ubiquitin ligase activity is required for the accumulation of the nuclease CtIP at DSBs, and consequently for optimal end-resection and Rad51 loading. CtIP overexpression rescues HR in FANCL-deficient cells, validating that FANCL primarily regulates HR by promoting CtIP recruitment. Together, these data demonstrate that the FA core complex and FANCD2 have a dual genome maintenance function by promoting repair of DSBs as well as the repair of ICLs.

molecular biology↗

bioRxiv2023

A single-cell atlas of the aging murine ovary

Ovarian aging leads to diminished fertility, dysregulated endocrine signaling, and increased chronic disease burden. These effects begin to emerge long before follicular exhaustion. Around 35 years old, women experience a sharp decline in fertility, corresponding to declines in oocyte quality. Despite a growing body of work, the field lacks a comprehensive cellular map of the transcriptomic changes in the aging ovary to identify early drivers of ovarian decline. To fill this gap, we performed single-cell RNA sequencing on ovarian tissue from young (3-month-old) and reproductively aged (9-month-old) mice. Our analysis revealed a doubling of immune cells in the aged ovary, with lymphocyte proportions increasing the most, which was confirmed by flow cytometry. We also found an age-related downregulation of collagenase pathways in stromal fibroblasts, which corresponds to rises in ovarian fibrosis. Follicular cells displayed stress response, immunogenic, and fibrotic signaling pathway inductions with aging. This report raises provides critical insights into mechanisms responsible for ovarian aging phenotypes.

cell biology↗

bioRxiv2023

Metabolic benefits of 17α-estradiol in liver are partially mediated by ERβ in male mice

Metabolic dysfunction underlies several chronic diseases. Dietary interventions can reverse metabolic declines and slow aging but remaining compliant is difficult. 17-estradiol (17-E2) treatment improves metabolic parameters and slows aging in male mice without inducing significant feminization. We recently reported that estrogen receptor is required for the majority of 17-E2-mediated benefits in male mice, but that 17-E2 also attenuates fibrogenesis in liver, which is regulated by estrogen receptor {beta} (ER{beta})-expressing hepatic stellate cells (HSC). The current studies sought to determine if 17-E2-mediated benefits on systemic and hepatic metabolism are ER{beta}-dependent. We found that 17-E2 treatment reversed obesity and related systemic metabolic sequela in both male and female mice, but this was partially blocked in female, but not male, ER{beta}KO mice. ER{beta} ablation in male mice attenuated 17-E2-mediated benefits on hepatic stearoyl-coenyzme A desaturase 1 (SCD1) and transforming growth factor {beta}1 (TGF-{beta}1) production, which play critical roles in HSC activation and liver fibrosis. We also found that 17-E2 treatment suppresses SCD1 production in cultured hepatocytes and hepatic stellate cells, indicating that 17-E2 directly signals in both cell-types to suppress drivers of steatosis and fibrosis. We conclude that ER{beta} partially controls 17-E2-mediated benefits on systemic metabolic regulation in female, but not male, mice, and that 17-E2 likely signals through ER{beta} in HSCs to attenuate pro-fibrotic mechanisms.

physiology↗

bioRxiv2022

17α-estradiol, a lifespan-extending compound, attenuates liver fibrosis by modulating collagen turnover rates in male mice

BackgroundEstrogen signaling is protective against chronic liver diseases, although men and a subset of women are contraindicated for chronic treatment with 17{beta}-estradiol (17{beta}-E2) or combination hormone replacement therapies. We sought to determine if 17-estradiol (17-E2), a naturally-occurring diastereomer of 17{beta}-E2, could attenuate liver fibrosis. MethodsWe evaluated the effects of 17-E2 treatment on collagen synthesis and degradation rates using tracer-based labeling approaches in male mice subjected to carbon tetrachloride (CCl4)-induced liver fibrosis. We also assessed the effects of 17-E2 on markers of hepatic stellate cell (HSC) activation, collagen crosslinking, collagen degradation, and liver macrophage content and polarity. FindingsWe found that 17-E2 significantly reduced collagen synthesis rates and increased collagen degradation rates, which was mirrored by declines in transforming growth factor {beta}1 (TGF-{beta}1) and lysyl oxidase-like 2 (LOXL2) protein content in liver. These improvements were associated with increased matrix metalloproteinase 2 (MMP2) activity and suppressed stearoyl-coenzyme A desaturase 1 (SCD1) protein levels, the latter of which has been linked to the resolution of liver fibrosis. We also found that 17-E2 increased liver fetuin-A protein, a strong inhibitor of TGF-{beta}1 signaling, and reduced pro-inflammatory macrophage activation and cytokines expression in the liver. InterpretationWe conclude that 17-E2 reduces fibrotic burden by suppressing HSC activation and enhancing collagen degradation mechanisms. Future studies will be needed to determine if 17-E2 acts directly in hepatocytes, HSCs, and/or immune cells to elicit these benefits. FundingThis work was supported by the US National Institutes of Health and US Department of Veterans Affairs. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe prevalence and severity of chronic liver diseases are greater in men than women and men are twice as likely to die from chronic liver diseases. However, the prevalence and severity of nonalcoholic fatty liver disease (NAFLD), nonalcoholic steatohepatitis (NASH), and liver fibrosis becomes comparable between the sexes following menopause, particularly when hormone replacement therapies (HRT) are not initiated. These observations suggest that estrogen signaling is protective against liver disease onset and progression, which is supported by studies in rodents demonstrating that 17{beta}-estradiol (17{beta}-E2) ameliorates hepatic steatosis and fibrogenesis. However, chronic administration of 17{beta}-E2 or combination HRTs are unrealistic in men due to feminization and increased risk for stroke and prostate cancer, and a subset of the female population are also at an increased risk for breast cancer and cardiovascular events when on HRTs. Therefore, we have begun exploring the therapeutic potential of 17-estradiol (17-E2), a naturally-occurring, nonfeminizing, diastereomer of 17{beta}-E2, for the treatment of liver diseases. Added value of this studyIn this study, using tracer-based labeling approaches in male mice subjected to CCl4-induced liver fibrosis, we show that 17-E2 reduces liver fibrosis by attenuating collagen synthesis and enhancing collagen degradation mechanisms. Both transforming growth factor {beta}1 (TGF-{beta}1) and lysyl oxidase-like 2 (LOXL2) protein content in liver were reduced by 17-E2. We also found that 17-E2 increased matrix metalloproteinase 2 (MMP2) activity and suppressed stearoyl-coenzyme A desaturase 1 (SCD1) protein levels, the latter of which has been linked to the resolution of liver fibrosis. We also found that 17-E2 increased liver fetuin-A protein, a strong inhibitor of TGF-{beta}1 signaling, and reduced pro-inflammatory macrophage activation and cytokine expression in the liver. Implications of all the available evidenceThis study supports the idea that estrogens are protective against chronic liver diseases and that 17-E2 may have therapeutic utility for the treatment of liver fibrosis.

physiology↗

bioRxiv2020

An Organoid for woven Bone

Bone formation (osteogenesis) is a complex process in which cellular differentiation and the generation of a mineralized organic matrix are synchronized to produce a hybrid hierarchical architecture. To study the mechanisms of osteogenesis in health and disease, there is a great need for functional model systems that capture in parallel both cellular and matrix formation processes. Stem cell-based organoids are promising as functional, self-organizing 3D in vitro models for studying the physiology and pathology of various tissues. However, for human bone, no such functional model system is yet available. This study reports the in vitro differentiation of human bone marrow stromal cells into a functional 3D self-organizing co-culture of osteoblasts and osteocytes, creating an organoid for early stage bone (woven bone) formation. It demonstrates the formation of an organoid where osteocytes are embedded within the collagen matrix that is produced by the osteoblasts and mineralized under biological control. Alike in vivo osteocytes the embedded osteocytes show network formation and communication via expression of sclerostin. The current system forms the most complete 3D living in vitro model system to investigate osteogenesis, both in physiological and pathological situations, as well as under influence of external triggers (mechanical stimulation, drug administration).

bioengineering↗