Biology subjects

Rosenfeld, M. G.

Publications and source records attributed to Rosenfeld, M. G..

13 recordsLinked to original sources

bioRxiv2026

Stress-Induced PTBP1 Reprograms Neuronal Function and Activates Cellular Senescence

Chronic oxidative stress is a major contributor to neuronal aging. Due to the lack of homologous recombination (HR) DNA damage repair, high oxygen consumption in neurons causes DNA damage accumulation with age, resulting in a decline in neuronal function, senescence-like phenotypes and onset of neurodegenerative diseases. Here, we identify increased PTBP1 as a stress-inducible negative regulator of neuronal gene expression and senescence-protectant genes. Oxidative stress robustly increases PTBP1 expression in ShSY-5Y differentiated neurons and primary mouse cortical neurons, coinciding with the loss of neuronal genes, including neuronal PTBP2, and activation of stress-responsive genes. Knockdown of PTBP1 in fibroblasts reduces the expression of key senescence genes. Transcriptomic analyses revealed that PTBP1 overexpression results in coordinated shift in gene expression characterized by repression of neuronal commitment genes and activation of stress and senescence genes. Mechanistically, PTBP1 induction is regulated by stress induced CTCF binding at the PTBP1 promoter. Together, our findings suggest that alteration in levels of PTBP1 acts as a molecular switch between neuronal function and survival, providing insight into transcriptional adaptations associated with aging. SUMMARYO_LILoss of PTBP1 in fibroblasts acts as a senescence protective gene C_LIO_LIxidative stress induces expression of PTBP1, reducing neuronal function gene expression and activating stress and cell cycle genes C_LIO_LIEctopic PTBP1 expression reprograms neuronal transcription, down-regulating cell fate commitment genes and activating a cell senescence program C_LIO_LIxidative stress induces PTBP1 and suppresses neuronal specific PTBP2 expression in primary cortical neurons C_LI

molecular biology↗

bioRxiv2026

Regulation of the Balance between Concentric and Eccentric Cardiac Hypertrophy by a CDC14A-KMT5A Signaling Pathway

BackgroundDepending upon the type of pathological stress, the heart undergoes concentric or eccentric remodeling. This structural change is associated with diastolic and/or systolic ventricular dysfunction reflecting differentially altered cardiomyocyte morphology, ultrastructure, metabolism, contractility, and survival, as well as interstitial myocardial fibrosis. Despite an association of both concentric and eccentric remodeling with heart failure and sudden death, the molecular mechanisms resulting in abnormal cardiac geometry remain poorly understood. A better understanding of the basic mechanisms conferring these contrasting forms of remodeling should inform novel approaches to preserve normal cardiac structure and function in cardiovascular disease. The protein phosphatase Cell Division Cycle 14A (CDC14A) and its substrate the lysine methyltransferase KMT5A are identified herein as key regulators of the balance between concentric and eccentric pathological cardiac remodeling. MethodsThe regulation of adult rat ventricular myocyte morphology by CDC14A and KMT5A was studied in vitro following gain and loss of function by expression of wild-type and mutant proteins and RNA interference (RNAi). Epigenomic regulation by KMT5A was studied by mapping histone 4 lysine 20 mono-methylation (H4K20me1) modified chromatin sites and correlating them with gene transcription. Regulation of pathological cardiac remodeling in vivo was demonstrated by CDC14A and KMT5A RNAi using adeno-associated virus (AAV) mediated cardiomyocyte-specific small hairpin RNA (shRNA) expression in mice. ResultsCDC14A inhibited the growth in width of cultured adult myocytes stimulated by -adrenergic receptor activation or by serum response factor. KMT5A was downregulated by CDC14A in cardiomyocytes and was required for myocyte growth in width. -adrenergic stimulation of KMT5A-dependent H4K20 mono-methylation across transcription units correlated with regulation of gene transcription. Accordingly, AAV-expressed KMT5A shRNA induced eccentric remodeling and cardiac dysfunction in wild-type mice. Conversely, expression of Cdc14A shRNA improved systolic function and cardiac structure and inhibited pathological gene expression in the Tpm1 E54K mouse with Dilated Cardiomyopathy. ConclusionsCDC14A-KMT5A-dependent epigenomic regulation of gene transcription constitutes a molecular switch that determines concentric versus eccentric cardiac remodeling. These findings identify CDC14A as a potential therapeutic target for the treatment of dilated cardiomyopathy and other forms of heart failure with reduced ejection fraction. Clinical PerspectiveO_ST_ABSWhat is newC_ST_ABSO_LIA function is identified for the first time for the protein phosphatase CDC14A in the heart, regulation of cardiomyocyte morphology and overall cardiac geometry in pathological cardiac remodeling. C_LIO_LIThe lysine methyltransferase KMT5A is shown to mediate the effects of CDC14A in the adult cardiomyocyte by regulating H4K20 mono-methylation, such that reduced KMT5A expression promotes a phenotype resembling Dilated Cardiomyopathy. C_LIO_LIH4K20me1 epigenomic modification is identified as a regulator of cardiac structure and function. C_LI Clinical implicationsO_LICDC14A loss of function experimentation in vivo, resulting in improved cardiac structure and function in a mouse model of Dilated Cardiomyopathy, suggests that CDC14A is a novel therapeutic target for heart failure with reduced ejection fraction. C_LI

cell biology↗

bioRxiv2025

Endogenous Real Time Imaging Reveals Dynamic Chromosomal Mobility During Ligand-Mediated Transcriptional Burst Events

Enhancers serve as the major genomic elements regulating mammalian signal-dependent transcriptional programs, characterized by alternating periods of target gene "bursting" and "non-busting" that require investigation of induced enhancer condensates and locus motility in real time to provide dynamic insights into signal/ligand-dependent regulatory events. Here, endogenous live cell imaging has revealed the altered chromosomal dynamics/condensate formation occurring during estrogen receptor (ER)-dependent target gene bursting/post-bursting and chronic activation events. Simultaneous DNA/RNA endogenous live imaging reveals that an increased mobility of acutely ER-stimulated loci observed during the bursting phase is, unexpectedly, further increased in the subsequent non-burst phase. Single molecule tracking (SMT) of ER shows that the relatively high-burst, lower-mobility acute state was indeed enriched for high-viscosity, 1,6-hexanediol-sensative ER molecules in a low sub-diffusive confined state with enhanced condensate formation during burst activation. Consistent with this, blocking transcription with flavopiridol shifts DNA tracks into a non-confined state. Differential DNA kinetics during burst vs non-burst has provided a strategy to assess altered condensate formation during gene activation events. (165)

molecular biology↗

bioRxiv2025

Liquid-liquid phase separation mediated immune evasion of RSV against OAS-RNase L pathway

Respiratory syncytial virus (RSV) infection is the major cause of severe respiratory illnesses in infants and older adults. RSV forms phase-separated biomolecular condensates called inclusion bodies (IBs), which serve as hubs for viral replication. However, the contribution of IBs to host immune response evasion remains elusive. We report that RSV IBs protect viral RNA from the 2'-5' oligoadenylate synthetase (OAS)-RNase L pathway, a critical antiviral defense mechanism that cleaves viral and cellular RNAs. RSV infection did not activate the OAS-RNase L pathway, and ectopically activated RNase L did not suppress viral replication. In RSV-infected cells, double-stranded RNA (dsRNA) was efficiently sequestered within liquid-liquid phase separation (LLPS)-mediated IBs, rendering its detection challenging. LLPS perturbation caused dsRNA release from IBs into the cytosol. dsRNA extracted from infected cells, which lacked LLPS shielding, triggered OAS-RNase L pathway activation. Thus, LLPS-driven IBs structurally sequester viral RNA, facilitating RSV to evade RNase-dependent genomic RNA degradation mediated by the OAS-RNase L antiviral pathway.

microbiology↗

bioRxiv2024

Recruitment of CTCF to the SIRT1 promoter after Oxidative Stress mediates Cardioprotective Transcription

Because most DNA-binding transcription factors (dbTFs), including the architectural regulator CTCF, bind RNA and exhibit di-/multimerization, a central conundrum is whether these distinct properties are regulated post-transcriptionally to modulate transcriptional programs. Here, investigating stress-dependent activation of SIRT1, encoding an evolutionarily-conserved protein deacetylase, we show that induced phosphorylation of CTCF acts as a rheostat to permit CTCF occupancy of low-affinity promoter DNA sites to precisely the levels necessary. This CTCF recruitment to the SIRT1 promoter is eliciting a cardioprotective cardiomyocyte transcriptional activation program and provides resilience against the stress of the beating heart in vivo. Mice harboring a mutation in the conserved low-affinity CTCF promoter binding site exhibit an altered, cardiomyocyte-specific transcriptional program and a systolic heart failure phenotype. This transcriptional role for CTCF reveals that a covalent dbTF modification regulating signal-dependent transcription serves as a previously unsuspected component of the oxidative stress response.

cell biology↗

bioRxiv2023

Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16INK4a

Glaucoma is a leading cause of irreversible blindness, with advanced age being the single most significant risk factor. However, the mechanisms underlying the relationship between aging and glaucoma remain unclear. Genome-wide association studies (GWAS) have successfully identified genetic variants strongly associated with increased glaucoma risk. Understanding how these variants function in pathogenesis is crucial for translating genetic associations into molecular mechanisms and, ultimately, clinical applications. The chromosome 9p21.3 locus is among the most replicated glaucoma risk loci discovered by GWAS. Nonetheless, the absence of protein-coding genes in the locus makes interpreting the disease association challenging, leaving the causal variant and molecular mechanism elusive. In this study, we report the identification of a functional glaucoma risk variant, rs6475604. By employing computational and experimental methods, we demonstrated that rs6475604 resides in a repressive regulatory element. Risk allele of rs6475604 disrupts the binding of YY1, a transcription factor known to repress the expression of a neighboring gene in 9p21.3, p16INK4A, which plays a crucial role in cellular senescence and aging. These findings suggest that the glaucoma disease variant contributes to accelerated senescence, providing a molecular link between glaucoma risk and an essential cellular mechanism for human aging.

genetics↗

bioRxiv2022

The regulatory landscapes of human ovarian ageing

Summary paragraphThe ovary is the first organ to age in the human body, affecting both fertility and overall health in women1-8. However, the biological mechanisms underlying human ovarian ageing remain poorly understood. Here we performed single-nuclei multi-omics analysis of young and reproductively aged human ovaries to understand the molecular and cellular basis of ovarian ageing in humans. Our analysis reveals coordinated changes in transcriptomic output and chromatin accessibility across cell types during ageing, including elevated mTOR and MAPK signaling, decreased activity of the oxidative phosphorylation and DNA damage repair pathways, and an increased signature of cellular senescence. By constructing cell type-specific regulatory networks, we uncover enhanced activity of the transcription factor CEBPD across cell types in the aged ovary, with a corresponding significant loss of activity of most cell identity-associated transcription factors. Moreover, by performing integrative analyses of our single-nuclei multi-omics data with common genetic variants associated with age at natural menopause (ANM) from genome-wide association studies, we demonstrate a global impact of functional variants on changes in gene regulatory networks across ovarian cell types. Finally, we nominate about a dozen of functional non-coding variants, their target genes and cell types and regulatory mechanisms that underlie genetic association with ANM. This work provides a comprehensive multimodal landscape of human ovarian ageing and mechanistic insights into inherited variation of ANM.

genomics↗

bioRxiv2021

The epigenetic eraser LSD1 lies at the apex of a reversible erythroid to myeloid cell fate decision

H3K4Me demethylase KDM1a/LSD1 is a therapeutic target for multiple diseases, including the {beta}-globinopathies (sickle cell disease and {beta}-thalassemia) since its inactivation has been shown to lead to robust induction of the fetal globin genes. Here we examined the consequences of conditional inactivation of Lsd1 in adult red blood cells using a new Gata1creERT2 BAC transgene. Loss of Lsd1 activity in mice blocked erythroid differentiation and expanded GMP-like cells, converting hematopoietic differentiation potential from an erythroid to a myeloid fate. The analogous phenotype was also observed in human HSPC, coincident with induction of myeloid transcription factors (e.g. PU.1 and CEBP). Finally, blocking the activity of myeloid transcription factors PU.1 or RUNX1 at the same time as LSD1 reverted myeloid lineage conversion to an erythroid phenotype. The data show that LSD1 promotes erythropoiesis by repressing myeloid cell fate, and that inhibition of myeloid differentiation reverses the lineage switch caused by LSD1 inactivation.

developmental biology↗

bioRxiv2020

Aberrant gliogenesis and excitation in MEF2C autism patient hiPSC-neurons and cerebral organoids

MEF2C has been shown to be a critical transcription factor for neurodevelopment, whose loss-of-function mutation in humans results in MEF2C haploinsufficiency syndrome (MHS), a severe form of autism spectrum disorder (ASD)/intellectual disability (ID). Here, we use patient hiPSC-derived cerebrocortical neurons and cerebral organoids to characterize MHS deficits. Unexpectedly, we found an aberrant micro-RNA-mediated gliogenesis pathway that contributes to decreased neurogenesis. We also demonstrate network-level hyperexcitability in neurons, as evidenced by excessive synaptic and extrasynaptic activity contributing to excitatory/inhibitory (E/I) imbalance. Notably, the extrasynaptic NMDA receptor antagonist, NitroSynapsin, corrects this aberrant electrical activity associated with abnormal phenotypes. During neurodevelopment, MEF2C regulates many ASD-associated gene networks suggesting that our approach may lead to personalized therapy for multiple forms of ASD. One sentence summaryAutism-like MEF2C+/- patient hiPSC models show miRNA-mediated overproduction of astrocytes and hyperactivity of neurons.

neuroscience↗

bioRxiv2020

A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease

In diseased organs, stress-activated signaling cascades alter chromatin, triggering broad shifts in transcription and cell state that exacerbate pathology. Fibroblast activation is a common stress response that worsens lung, liver, kidney and heart disease, yet its mechanistic basis remains poorly understood1,2. Pharmacologic inhibition of the BET family of transcriptional coactivators alleviates cardiac dysfunction and associated fibrosis, providing a tool to mechanistically interrogate maladaptive fibroblast states and modulate their plasticity as a potential therapeutic approach3-8. Here, we leverage dynamic single cell transcriptomic and epigenomic interrogation of heart tissue with and without BET inhibition to reveal a reversible transcriptional switch underlying stress-induced fibroblast activation. Transcriptomes of resident cardiac fibroblasts demonstrated robust and rapid toggling between the quiescent fibroblast and activated myofibroblast state in a manner that directly correlated with BET inhibitor exposure and cardiac function. Correlation of single cell chromatin accessibility with cardiac function revealed a novel set of reversibly accessible DNA elements that correlated with disease severity. Among the most dynamic elements was an enhancer regulating the transcription factor MEOX1, which was specifically expressed in activated myofibroblasts, occupied putative regulatory elements of a broad fibrotic gene program, and was required for TGF{beta}-induced myofibroblast activation. CRISPR interference of the most dynamic cis-element within the enhancer, marked by nascent transcription, prevented TGF{beta}-induced activation of Meox1. These findings identify MEOX1 as a central regulator of stress-induced myofibroblast activation associated with cardiac dysfunction. The plasticity and specificity of the BET-dependent regulation of MEOX1 in endogenous tissue fibroblasts provides new trans- and cis- targets for treating fibrotic disease.

molecular biology↗

bioRxiv2019

Cell type-specific enhancer-promoter connectivity maps in the human brain and disease risk association

Unique cell type-specific patterns of activated enhancers can be leveraged to interpret non-coding genetic variation associated with complex traits and diseases such as neurological and psychiatric disorders. Here, we have defined active promoters and enhancers for major cell types of the human brain. Whereas psychiatric disorders were primarily associated with regulatory regions in neurons, idiopathic Alzheimers disease (AD) variants were largely confined to microglia enhancers. Interactome maps connecting GWAS variants in cell type-specific enhancers to gene promoters revealed an extended microglia gene network in AD. Deletion of a microglia-specific enhancer harboring AD-risk variants ablated BIN1 expression in microglia but not in neurons or astrocytes. These findings revise and expand the genes likely to be influenced by non-coding variants in AD and suggest the probable brain cell types in which they function.\n\nOne Sentence SummaryIdentification of cell type-specific regulatory elements in the human brain enables interpretation of non-coding GWAS risk variants.

neuroscience↗

bioRxiv2019

LSD1-mediated enhancer silencing enables endocrine cell development through attenuation of retinoic acid signalling.

Developmental progression depends on temporally defined changes in gene expression mediated by transient exposure of lineage intermediates to signals in the progenitor niche. To identify a possible contribution of cell-intrinsic epigenetic mechanisms to signal-induced transcriptional responses, we manipulated the signalling environment and activity of the histone demethylase LSD1 during stepwise differentiation of gut tube intermediates into pancreatic endocrine cells. Analysis of enhancer and transcriptome landscapes revealed that lineage progression and endocrine cell differentiation requires LSD1-mediated silencing of transiently active retinoic acid (RA)-induced enhancers. In the absence of LSD1, early RA-responsive enhancers remain partially active despite RA removal, resulting in perduring expression of RA-induced genes, and failure to progress in development. Our findings identify LSD1-mediated enhancer silencing as a cell-intrinsic epigenetic feedback mechanism by which the duration of the transcriptional response to a developmental signal is limited. Given LSD1s requirement in numerous developmental contexts, the here-described mechanism would be broadly relevant.

developmental biology↗

bioRxiv2017

GPS2 regulates mitochondria biogenesis via mitochondrial retrograde signaling and chromatin remodeling of nuclear-encoded mitochondrial genes

As most of the mitochondrial proteome is encoded in the nucleus, mitochondrial functions critically depend on nuclear gene expression and bidirectional mito-nuclear communication. However, mitochondria-to-nucleus communication pathways are incompletely understood. Here, we identify G-Protein Pathway Suppressor 2 (GPS2) as a mediator of mitochondrial retrograde signaling and a key transcriptional activator of nuclear-encoded mitochondrial genes in mammals. GPS2 regulated translocation from mitochondria to nucleus is essential for the transcriptional activation of the nuclear stress response to mitochondrial depolarization and for supporting basal mitochondrial biogenesis in differentiating adipocytes and in brown adipose tissue from mice. In the nucleus, GPS2 recruitment to target gene promoters regulates histone H3K9 demethylation and RNA Polymerase II (POL2) activation through inhibition of Ubc13-mediated ubiquitination. Together, these findings reveal an unexpected layer of regulation of mitochondrial gene transcription as they uncover a novel mitochondria-nuclear communication pathway.

molecular biology↗