Biology subjects

Nair, R. V.

Publications and source records attributed to Nair, R. V..

14 recordsLinked to original sources

bioRxiv2026

Gene therapy targeting of AKAP6β-CaMKII signalosomes improves myocardial inflammation and heart failure in a swine model of cardiometabolic syndrome

BackgroundCardiometabolic heart failure with preserved ejection fraction (HFpEF) is associated with systemic and cardiac inflammation and diastolic dysfunction. A-kinase anchoring protein 6{beta} (AKAP6{beta}) is a scaffold protein located at the cardiomyocyte outer nuclear membrane that promotes pathological cardiac remodeling via the recruitment of multiple regulatory proteins including protein kinases. In mice, adeno-associated virus (AAV) mediated expression of a peptide based upon a kinase binding domain (KBD) within AKAP6{beta} inhibited the development of heart failure due to chronic pressure overload. Whether KBD expression can also inhibit the development of cardiometabolic heart failure is unknown, and if so, the mechanism of KBD action in HFpEF has yet to be explored. MethodsThe efficacy of a cardiotropic self-complementary AAV gene therapy that expresses the AKAP6{beta} KBD peptide (AAV9sc.KBD) was tested in a female Ossabaw swine model of cardiometabolic syndrome and HFpEF. Single nucleus and bulk RNA sequencing of swine heart tissue and immunoprecipitation-mass spectrometry, live cell imaging, and biochemical assays using primary rat cardiomyocytes were employed to study KBD mechanism of action. ResultsAAV9sc.KBD inhibited the development of diastolic dysfunction and heart failure in the Ossabaw model, without negatively impacting systolic function. The improvement in cardiac phenotype was associated with decreased T-cell myocardial infiltrates and partial reversal of pathological gene expression. An unbiased interactome study revealed that the KBD peptide binds Ca2+/calmodulin-dependent protein kinase II (CaMKII), identifying CaMKII as a new AKAP6{beta} binding partner. Perinuclear CaMKII activity detected by live cell imaging required AKAP6{beta} expression and was inhibited by KBD expression. In addition, the CaMKII substrate Inhibitor of NF-{kappa}B Kinase {beta} (IKK{beta}) bound AKAP6{beta}. IKK phosphorylation in the Ossabaw model and in myocytes was inhibited by KBD expression, and NF-{kappa}B nuclear translocation in myocytes was dependent upon AKAP6{beta}-CaMKII protein complex formation. AAV9sc.KBD treatment inhibited cardiomyocyte NF-{kappa}B-dependent gene expression in the Ossabaw model. ConclusionsRegulated by perinuclear AKAP6{beta}-CaMKII signalosomes, NF-{kappa}B pro-inflammatory gene expression in cardiomyocytes participates in a positive feedback loop with cardiac inflammation promoting HFpEF. Proof-of-concept is provided in a large animal model that gene therapy-based cardiomyocyte expression of the KBD peptide will prevent cardiac dysfunction in cardiometabolic syndrome. Clinical PerspectiveO_ST_ABSWhat is newC_ST_ABSO_LIThe cardiomyocyte-selective gene therapy AAV9sc.KBD, which targets signalosomes organized by the scaffold protein AKAP6{beta}, is shown to inhibit myocardial T-cell infiltration and improve cardiac structure and function in a large animal model of cardiometabolic HFpEF. C_LIO_LIThe AKAP6{beta} KBD peptide is shown to bind and inhibit the function of CaMKII. C_LIO_LICaMKII and IKK{beta} are shown to participate in perinuclear AKAP6{beta} signalosomes, where they regulate activation of the NF-{kappa}B pro-inflammatory gene regulatory pathway. C_LI Clinical implicationsO_LIProof-of-concept for a novel strategy for the treatment of HFpEF is provided, intracellular expression by a cardiomyocyte-selective gene therapy vector of an inhibitory peptide, which will inhibit compartmentalized intracellular signal transduction. C_LIO_LIIn conjunction with previous studies in small rodents, the new data obtained in Ossabaw swine support clinical translation of the AAV9sc.KBD gene therapy. C_LI

physiology↗

bioRxiv2026

Plasma proteomics reveals divergent sex-specific senescence and bone biology signatures across neurodegenerative diseases

Neurodegenerative diseases are often accompanied by systemic comorbidities, including changes in bone health, but the molecular relationship between neurodegeneration, skeletal decline, and cellular senescence remains poorly understood. In this study, we investigated sex-specific changes in circulating bone- and senescence-related proteins across the spectrum of Alzheimers disease(AD), Lewbody dementia(LB) and Parkinsons disease(PD). Plasma proteomic profiling was performed on samples from 408 participants deeply phenotyped for neurodegenerative diseases, followed by differential protein and pathway analyses. This study reveals sex-dependent alterations in bone and senescence-related circulating proteins in AD-related, PD and LB-related neurodegenerative diseases, providing insights into the complex relationship between neurodegeneration and bone health. Several candidate proteins were also associated with established plasma neurodegeneration biomarkers, particularly pTau181. Pathway analyses revealed shared mitochondrial and metabolic dysfunction across neurodegenerative diseases, with disease-specific features including vesicle trafficking disruption in AD and inflammatory-senescence pathways in LB, plus sex-divergent patterns in inflammatory signaling and bone-related pathways.

neuroscience↗

bioRxiv2026

Organoid modeling of tumor-associated macrophages reveals phagocytosis checkpoint blockade-induced conversion to an immunosuppressive SPP1+ phenotype

Tumor-associated macrophages (TAM) exert essential functions during the immune response to cancer. However, investigations of TAM within a native human tumor microenvironment (TME) have been impeded by a lack of appropriate model systems. Here, patient-derived organoids (PDO) from air-liquid interface (ALI)-grown tumor fragments, containing a human TME that encompassed stroma and immune subsets, robustly preserved TAM that were maintained by endogenous CSF-1 and appropriately responded to polarization signals. Antibody blockade of the CD47 regulatory checkpoint in organoids stimulated phagocytosis and remodeled TAM cytokine secretion profiles that were confirmed in anti-CD47 phase I trial patients. Amongst PDO histologies screened, anti-CD47 tumor killing was notable in clear cell renal cell carcinoma (ccRCC) which was associated with increased TAM infiltration. PDO contained diverse previously described TAM subsets; however, anti-CD47 reprogrammed organoid TAM toward an immunosuppressive SPP1+ phenotype, highlighting a negative feedback mechanism. Our findings uncover a resistance circuit engaged by macrophage checkpoint blockade and position ALI PDO as a robust translational platform for dissecting human macrophage biology and informing precision immunotherapy.

cancer biology↗

bioRxiv2026

Small molecule ensembles reshape amyloid aggregation landscapes

Proteins in living systems are highly dynamic, continuously populating heterogeneous ensembles of functionally distinct conformational and aggregation states whose relative populations and interconversion rates are governed by an underlying free-energy landscape. Perturbations such as ligand binding, chemical modification, or changes in the environment remodel these assemblies, thereby reshaping protein behavior and function. Understanding how such protein networks are dynamically remodeled is a fundamental challenge in biophysics. Here, we utilize the A{beta}42 aggregation landscape as a model to demonstrate that remodeling can occur without detectable changes in the apparent activation free-energy barrier, instead arising from system-level redistribution of species along a conserved kinetic pathway. Using EPPS (4-(2-Hydroxyethyl)-1-piperazinepropanesulfonic acid) as a model modulator, temperature-dependent kinetic analysis reveals an invariant apparent activation free energy, suggesting that the underlying energetic framework remains unchanged even as the system is reshaped. We find that EPPS modulates A{beta}42 disaggregation in a concentration-dependent manner. At intermediate concentrations, enhanced redistribution toward soluble species is observed, whereas at higher concentrations, modulator self-association into supramolecular clusters is associated with reduced net disaggregation and partial recovery of aggregation signatures. Thermal disruption of these assemblies restores activity, consistent with a role of modulator self-association in governing the observed behavior. Furthermore, our experiments indicate that this disaggregation process is reduced in crowded environments compared to dilute conditions. Together, these results support a biophysical framework in which amyloid remodeling is driven by species redistribution along a conserved kinetic landscape, where the extent of disaggregation is determined by modulator concentration-dependent partitioning of protein species, modulator self-association, and environmental constraints. SignificanceAn emerging view of protein function recognizes that proteins exist as dynamic networks of interconverting conformational and aggregation states. Binding interactions and environmental perturbations remodel these networks, thereby altering protein behavior. Amyloid aggregates associated with Alzheimers disease exemplify such dynamic systems, yet how small molecules remodel them remains poorly understood. Using A{beta}42 as a model, we show that small molecules remodel amyloid networks by redistributing protein populations in a concentration-dependent manner. This redistribution is modulated by self-association of the small molecule, molecular crowding, and temperature. These findings establish population redistribution within dynamic amyloid networks as a mechanism for remodeling protein assemblies, offering new insights into controlling pathological aggregation.

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↗

bioRxiv2026

Species Identification and Antimicrobial Susceptibility of Mycobacterial Isolates from Dogs and Cats

Nontuberculous Mycobacterium (NTM) species are increasingly recognized as opportunistic pathogens in companion animals, yet data on species distribution and antimicrobial resistance remain limited. The goal of this study was to evaluate species identification methods and determine antimicrobial susceptibility profiles of NTM isolates from cats and dogs submitted to the University of Tennessee veterinary diagnostic laboratory. Twenty-nine NTM isolates (25 feline, 4 canine) collected between 2016 and 2022 were cultured and identified using MALDI-TOF MS and 16S rRNA sequencing. Antimicrobial susceptibility testing (AST) was performed by broth microdilution. Most isolates (27/29) were rapidly growing mycobacteria from skin or wound samples. Combined MALDI-TOF and sequencing identified 11 isolates within the Mycobacterium fortuitum complex, 10 as M. smegmatis, 4 within the M. abscessus group, and one each as M. mucogenicum and M. farcinogenes. MALDI-TOF failed to identify four isolates, including two slow-growing strains. AST revealed consistent susceptibility to amikacin and moxifloxacin, while resistance was highest to doxycycline (44%), clarithromycin (37%), and tobramycin (33%). Rapidly growing NTM predominates in feline cutaneous infections, with species-specific resistance patterns underscoring the need for accurate identification and AST to guide therapy. Importance StatementNontuberculous mycobacteria (NTM) are emerging causes of skin infections in cats and dogs, yet little is known about which species are involved or how they respond to treatment. Knowing the specific species and their resistance patterns is critical for choosing effective treatments and improving outcomes for affected animals. This study provides critical baseline data by identifying NTM species and their antimicrobial resistance patterns in companion animals. These findings highlight the need for accurate diagnostic methods and targeted therapy to improve clinical outcomes. Understanding these trends is essential for guiding veterinary care and informing future research on antimicrobial resistance in animal health.

microbiology↗

bioRxiv2025

LOSS OF ROR2 TYROSINE KINASE RECEPTOR IS ASSOCIATED WITH ENDOTHELIAL DYSFUNCTION IN PAH VIA INAPPROPRIATE INTEGRIN BETA 1 ACTIVATION

RationaleEndothelial dysfunction is a key feature of pulmonary arterial hypertension (PAH). We previously identified Wnt7a, a ligand of the Wnt planar cell polarity (PCP) pathway, as essential for pulmonary angiogenesis, with its loss linked to PAH. Given the importance of Wnt/PCP to lung endothelial function and angiogenesis, our goal is to elucidate how Wnt/PCP regulates angiogenic responses in pulmonary microvascular endothelial cells (PMVECs). ROR2, a tyrosine kinase receptor specific to Wnt/PCP, is crucial for cardiovascular development, but its role in PAH is unclear. We hypothesized that ROR2 supports endothelial homeostasis, and its loss would impair angiogenesis, contributing to PAH. MethodsEndothelial-specific ROR2 knockout (ROR2 ECKO) and wild-type (WT) mice were studied under normoxia and chronic hypoxia using echocardiography, hemodynamics, and lung morphometry. PMVECs from healthy and PAH lungs were transfected with ROR2 siRNA/constructs for functional and molecular studies. Focal adhesion (FA) activation and force generation were assessed via FRET-based methods. Bulk and single-cell transcriptomic analyses were performed on siROR2 PMVECs and ROR2 ECKO lungs. ResultsROR2 ECKO mice exhibited worsened pulmonary hypertension, right ventricular remodeling, microvascular loss, and muscularization in hypoxia. Single-cell RNA sequencing of lung endothelial cells showed dysregulation of pathways involved in barrier formation and angiogenesis. Evans blue dye extravasation confirmed reduced endothelial barrier integrity in ROR2 ECKO mice. ROR2-deficient PAH PMVECs displayed increased adhesion, permeability, and FA numbers, with reduced VE-cadherin at cell junctions. Confocal imaging revealed ROR2 localization in FAs, interacting with integrin {beta}1 (ITGB1). FRET analysis showed that ITGB1 remained in an active, adhesion-promoting state in ROR2-deficient cells. Restoring ROR2 in PAH PMVECs normalized adhesion, barrier function, and FA abundance. Transcriptomic analysis identified Rab12 as a key mediator of ROR2-ITGB1 crosstalk, with Rab12 knockdown mimicking ROR2 deficiency in PMVECs. ConclusionsROR2 regulates pulmonary angiogenesis by maintaining endothelial barrier integrity and facilitating integrin recycling. Restoring ROR2 signaling could be a potential therapeutic approach for PAH.

cell biology↗

bioRxiv2025

CES1 DEFICIENCY IS ASSOCIATED WITH METABOLIC REPROGRAMING AND ENDOTHELIAL DYSFUNCTION IN PULMONARY ARTERIAL HYPERTENSION

BackgroundPulmonary arterial hypertension (PAH) is a progressive disease characterized by pulmonary microvascular loss and obliterative remodeling, driven by metabolic reprogramming, oxidative stress, and endothelial dysfunction. While BMPR2 mutations contribute to metabolic shifts in pulmonary microvascular endothelial cells (PMVECs), their low penetrance suggests additional genetic modifiers play a role. A genetic screen of PAH PMVECs identified carboxylesterase 1 (CES1)--an endoplasmic reticulum (ER) enzyme involved in lipid metabolism and detoxification--as a candidate regulator of endothelial metabolism and angiogenesis. We hypothesize that CES1 loss promotes endothelial dysfunction via metabolic reprogramming, lipotoxicity, and oxidative stress. MethodsPAH and healthy PMVECs and lung tissues were obtained from transplant donors and commercial sources. CES1 expression was modulated in PMVECs using siRNA knockdown and plasmid overexpression. Mitochondrial and ER function were assessed via confocal microscopy and proteomics. CES1 heterozygous knockout (HET KO) and endothelial-specific knockout (ECKO) mice were exposed to normoxia or hypoxia, with lung tissues analyzed by single-cell RNA sequencing (scRNA-seq) and histopathology. ResultsCES1 expression was significantly reduced in PAH PMVECs and vascular lesions. CES1-deficient PMVECs exhibited increased apoptosis, reactive oxygen species (ROS) production, mitochondrial fragmentation, ER stress, and impaired angiogenesis. Confocal imaging and metabolic studies revealed lipid droplet accumulation, reduced fatty acid oxidation, and a glycolytic shift-- phenotypes reversed by CES1 restoration. Mechanistically, CES1 transcription was induced by BMPR2 via NRF2 activation, a key regulator of redox and metabolic homeostasis. In vivo, CES1-deficient mice developed severe pulmonary hypertension (PH) under hypoxia, with extensive vascular remodeling, right ventricular dysfunction, and dysregulated angiogenesis and lipid metabolism pathways, as confirmed by lung scRNA-seq. ConclusionsCES1 is essential for pulmonary endothelial homeostasis and serves as a critical modifier of BMPR2 signaling. Given the limited efficacy of current PAH therapies in reversing endothelial dysfunction and small-vessel loss, restoring CES1 expression represents a promising therapeutic strategy.

biochemistry↗

bioRxiv2025

Single Cell RNA Sequencing Analysis of Human Melanoma Reveals A Distinct Prognostic Myeloid Cell

Abstract/SummaryMyeloid-derived cells and tumor-associated macrophages (TAMs) represent an emerging field in melanoma research. Single-cell sequencing has enhanced our understanding of interactions within the tumor microenvironment (TME). Although there is no current consensus, several solid-tumor associated TAM subtypes have been identified by single-cell RNA sequencing (scRNA-seq). Due to the lack of agreement across models and tumor types, we aimed to characterize the myeloid sub-compartment in melanoma by analyzing compiled public scRNA-seq datasets. In this study, we identified six myeloid cell clusters, designated M_C1 through M_C6, with distinct gene expression profiles indicating differences in structure and function. The frequency of the M_C1 subtype was found to be predictive of overall survival (OS) in brain metastatic melanoma. This finding was externally validated by deconvolution of publicly available bulk RNA sequencing data from a clinical trial of advanced melanoma patients treated with nivolumab, as well as data from The Cancer Genome Atlas (TCGA) for melanoma stages I-IV. The M_C1 cell type appears to be a hybrid of dendritic cells and macrophages, demonstrating prognostic relevance across all melanoma stages and predictive potential for immunotherapy response. These data suggest that M_C1 may have utility as a prognostic biomarker in melanoma and as a target for future cell-based therapies.

immunology↗

bioRxiv2024

Genome-Wide Transcription Response of Staphylococcus epidermidis to Heat Shock and Medically Relevant Glucose Levels

Skin serves as both barrier and interface between body and environment. Skin microbes are intermediaries evolved to respond, transduce, or act in response to changing environmental or physiological conditions. Here, we quantify genome-wide changes in gene expression levels for one abundant skin commensal, Staphylococcus epidermidis, in response to an internal physiological signal, glucose levels, and an external environmental signal, temperature. We find 85 of 2354 genes change up to[~] 34-fold in response to medically relevant changes in glucose concentration (0 mM to 17 mM; adj P value [≤] 0.05). We observed carbon catabolite repression in response to a range of glucose spikes, as well as upregulation of genes involved in glucose utilization in response to persistent glucose. We observed 366 differentially expressed genes in response to a physiologically relevant change in temperature (37{degrees}C to 45{degrees}C; adj P value [≤] 0.05) and an S. epidermidis heat-shock response that mostly resembles the heat-shock response of related staphylococcal species. DNA motif analysis also revealed CtsR and CIRCE operator sequences arranged in tandem upstream of dnaK and groESL operons. We further identified 38 glucose-responsive genes as candidate ON or OFF switches for use in controlling synthetic genetic systems. Such systems might be used to instrument the in-situ skin microbiome or help control microbes bioengineered to serve as embedded diagnostics, monitoring, or treatment platforms.

microbiology↗

bioRxiv2022

Newly repopulated spinal cord microglia exhibit a unique transcriptome and coincide with sex-independent pain resolution

Microglia contribute to the initiation of pain, however, a translationally viable approach addressing how or when to modulate these cells remains elusive. We used a targeted, inducible, genetic microglial depletion strategy at both acute and acute-to-chronic transition phases in the clinically-relevant tibial fracture/casting pain model to determine the contribution of microglia to the initiation and maintenance of pain. We observed complete resolution of pain after transient microglial depletion at the acute-to-chronic phase, which coincided with the timeframe of full repopulation of microglia. These repopulated microglia were morphologically distinct from control microglia, signifying they may exhibit a unique transcriptome. RNA sequencing of repopulated spinal cord microglia identified genes of interest using weighted gene co-expression network analysis (WGCNA). We intersected these genes with a newly-generated single nuclei microglial dataset from human spinal cord dorsal horn and identified human-relevant genes that may ultimately promote pain resolution after injury. This work presents a novel approach to gene discovery in pain and provides comprehensive datasets for the development of future microglial-targeted therapeutics.

neuroscience↗

bioRxiv2021

A microRNA cluster downstream of the selector gene Fezf2 coordinates fate specification with dendritic branching in cortical neurons

In the cerebral cortex, cortical projection neurons comprise classes of neurons project to distant regions of the central nervous system. These neurons develop from the same progenitor pool, but they acquire strikingly different inputs and outputs to underpin strikingly different functions. The question of how corticospinal projection neurons - involved in motor function and implicated in paralysis - and callosal projection neurons - involved in cognitive function and implicated in autism - develop represents a fundamental and clinically important question in neurodevelopment. A network of transcription factors, including the selector gene Fezf2, is central to specifying cortical projection neuron fates. Gene regulation up- and down-stream of these transcription factors, however, is not well understood, particularly as it relates to the development of the major inputs to cortical projection neurons. Here we show that the miR-193b~365 microRNA cluster downstream of Fezf2 cooperatively represses the signaling molecule Mapk8, and impacts dendritic branching of cortical projection neurons.

developmental biology↗

bioRxiv2018

Aged blood inhibits hippocampal neurogenesis and activates microglia through VCAM1 at the blood-brain barrier

An aged circulatory environment can promote brain dysfunction and we hypothesized that the blood-brain barrier (BBB) mediates at least some of these effects. We observe brain endothelial cells (BECs) in the aged mouse hippocampus express an inflammatory transcriptional profile with focal upregulation of Vascular Cell Adhesion Molecule 1 (VCAM1), a protein that facilitates vascular-immune cell interactions. Concomitantly, the shed, soluble form of VCAM1 is prominently increased in the aged circulation of humans and mice, and aged plasma is sufficient to increase VCAM1 expression in cultured BECs and young mouse hippocampi. Systemic anti-VCAM1 antibody or genetic ablation of VCAM1 in BECs counteracts the detrimental effects of aged plasma on young brains and reverses aging aspects in old mouse brains. Thus, VCAM1 is a negative regulator of adult neurogenesis and inducer of microglial reactivity, establishing VCAM1 and the luminal side of the BBB as possible targets to treat age-related neurodegeneration.

neuroscience↗

bioRxiv2017

NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells

NF90 and splice variant NF110 are DNA- and RNA-binding proteins encoded by the Interleukin enhancer-binding factor 3 (ILF3) gene that regulate RNA splicing, stabilization and export. The role of NF90 in regulating transcription as a DNA-binding protein has not been comprehensively characterized. Here, ENCODE ChIP-seq identified 9,081 genomic sites specifically bound by NF90/110 in K562 cells. One third of binding sites occurred at promoters of annotated genes. NF90/110 binding colocalized with chromatin marks associated with active promoters and strong enhancers. Comparison with 150 ENCODE ChIP-seq experiments revealed that NF90 clustered with transcription factors exhibiting preference for promoters over enhancers (POLR2A, MYC, YY1). Differential gene expression analysis following shRNA knockdown of NF90 in K562 cells revealed that NF90 directly activates transcription factors that drive growth and proliferation (EGR1, MYC), while attenuating differentiation along erythroid lineage (KLF1). NF90/110 binds chromatin to hierarchically regulate transcription factors to promote proliferation and suppress differentiation.

genetics↗