Biology subjects

Ganguly, A.

Publications and source records attributed to Ganguly, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Histotripsy-induced vascular remodeling in the tumor microenvironment enhances local and off-target intratumoral drug delivery

Solid tumors are known to be refractory to treatment due to a poorly perfused microenvironment that blocks immune cell infiltration and effective drug delivery. Histotripsy is a non-invasive focused ultrasound modality that generates cavitation microbubbles to mechanically disrupt solid tumors, resulting in decreased hypoxia and stimulation of tumor-targeted adaptive immune responses. In this study, we aim to investigate whether post-histotripsy hypoxia reduction and cytotoxic immune cell infiltration are associated with normalization of tumor vasculature and enhanced perfusion. Structural analysis of both treated and contralateral off-target tumors following partial histotripsy revealed significant vascular remodeling, enhanced vascular integrity, and decreased vascular leakage indicative of vascular normalization in multiple in vivo models of melanoma, hepatocellular carcinoma, and pancreatic adenocarcinoma. These effects appeared antigen-specific, as no remodeling was observed in contralateral off-target tumors of discordant pathology. Mechanistically, CXCR3+CD8+ T cells played a role in mediating these vascular changes, as genetic knockout of CD8 and pharmacological antagonism of CXCR3 impaired both remodeling and normalization. Additionally, significant changes in endothelial CXCR4 and Angiopoietin-1 and -2 expressions were observed following histotripsy, indicating their potential involvement in promoting vascular normalization and remodeling. Significant vascular remodeling was accompanied by enhanced tumor perfusion and intratumoral delivery of chemotherapeutic agents and therapeutic monoclonal antibodies. These findings suggest that histotripsy not only creates a more favorable microenvironment for immunotherapy, but also optimizes drug delivery into solid tumors. Combinatorial approaches using histotripsy with chemotherapy or immunotherapy may be a novel therapeutic strategy to overcome current limitations of conventional solid tumor therapies.

immunology↗

bioRxiv2025

3-Mercaptopyruvate Sulfurtransferase (MPST) Regulates Mitochondrial Metabolism and Epithelial Differentiation in Neonatal Patient-derived Airway Cells

Early-life airway epithelial development relies on tightly coordinated mitochondrial metabolic programs, yet the pathways that govern normal epithelial maturation during this vulnerable developmental window remain poorly defined. Hyperoxia disrupts airway epithelial maturation, contributing to lung injury and airway remodeling in infants with bronchopulmonary dysplasia (BPD), underscoring the need to identify mitochondrial pathways that regulate early epithelial differentiation. 3-Mercaptopyruvate sulfurtransferase (MPST), a mitochondrial sulfur metabolism enzyme, supports mitochondrial metabolic and bioenergetic function, but its role in human airway epithelial development is unknown. In this study, we used neonatal patient-derived tracheal airway epithelial cells (nTAECs) in a three-dimensional air-liquid interface (ALI) model to show that hyperoxia reduces MPST protein abundance. To determine how MPST loss alters early epithelial differentiation and metabolic homeostasis we used RNAi to knock down MPST during ALI differentiation. MPST loss in nTAECs induced early (ALI day 3) transcriptomic shifts involving mitochondrial metabolic pathways, epithelial differentiation programs, and stress-response signature corresponding with decreased ciliated cell numbers during mid-differentiation phase (ALI day 7). Metabolic flux analysis revealed significantly reduced mitochondrial respiration without compensatory increase in glycolysis, indicative of disrupted metabolic flexibility. Together, these data show that MPST is essential for maintaining mitochondrial metabolic integrity necessary for normal airway epithelial development. Loss of MPST creates a developmental vulnerability that may contribute to hyperoxia-induced airway injury in neonates. Targeting MPST-dependent pathways could represent a new strategy to preserve airway health in infants at risk for BPD airway remodeling. NEW & NOTEWORTHYThis study identifies MPST as a previously unrecognized regulator of neonatal airway epithelial development. In our neonatal patient-derived three-dimensional organotypic model, hyperoxia reduces MPST, and MPST loss alters mitochondrial metabolism and epithelial differentiation programs. These findings indicate that MPST deficiency contributes to mitochondrial dysfunction under hyperoxic conditions and highlight MPST-linked pathways as potential therapeutic targets to mitigate early-life airway injury and remodeling relevant to infants with bronchopulmonary dysplasia.

developmental biology↗

bioRxiv2025

BAG3 modulates clathrin-mediated endocytosis and tau uptake in astrocytes

In a healthy brain, astrocytes maintain neuronal homeostasis by removing proteins like tau from the extracellular space, preventing their uptake by neurons. In Alzheimers disease (AD), this function is impaired, contributing to tau accumulation. Many AD risk genes are linked to endocytosis pathways, suggesting their role in AD pathogenesis. Astrocytes can internalize, degrade, and release tau, but the mechanisms remain unclear. BAG3, a multifunctional protein, regulates vacuolar processes and interacts with clathrin-mediated endocytosis (CME) components. However, its role in astrocytic CME and tau processing is not fully understood. We show BAG3 depletion in astrocytes reduces clathrin-AP-2 interaction, inhibits CME-dependent epidermal growth factor receptor internalization, and decreases tau uptake. Live-cell imaging reveals BAG3 depletion impairs CME dynamics, increasing clathrin particle lifetimes. BAG3 depletion also alters endolysosomal compartments, increasing Lamp1+ puncta and tau co-localization. These findings highlight BAG3s role in CME, tau trafficking, and vacuolar processes, suggesting its dysfunction may contribute to AD pathogenesis.

neuroscience↗

bioRxiv2025

Quantitative Proteomics Links Mitochondrial Dysfunction to Metabolic Changes and Epithelial Differentiation Defects in Hyperoxia-Exposed Neonatal Airway Cells

Premature infants often require supplemental oxygen therapy, however, exposure to supraphysiological oxygen (hyperoxia) can disrupt normal lung development and contribute to bronchopulmonary dysplasia (BPD). Mitochondrial dysfunction is increasingly recognized as a contributor to hyperoxia-induced BPD. However, the effects of hyperoxia on mitochondrial function and mucociliary differentiation in the developing upper airway epithelium remain poorly understood. This study tested the hypothesis that hyperoxia impairs neonatal airway mucociliary differentiation by disrupting mitochondrial bioenergetic function. Neonatal tracheal airway epithelial cells (nTAECs) from term infants (n=5) were cultured in a 3D air-liquid interface (ALI) model and exposed to 60% O2 during the mid-phase of differentiation (ALI day 7-14). Cellular phenotype was assessed using immunofluorescence staining and gene expression analyses. Mitochondrial function was evaluated through Seahorse metabolic flux analysis, and global protein changes were characterized by quantitative proteomics. Hyperoxia exposure significantly impaired terminal epithelial differentiation, characterized by reductions in ciliated and goblet cells. Seahorse assay revealed a decrease in baseline oxygen consumption and mitochondrial ATP production, accompanied by a compensatory increase in glycolytic ATP production. Quantitative proteomics identified disruption of mitochondrial Complex I as a central feature of the hyperoxic response. Downstream proteomic pathway analyses further confirmed the metabolic shift from mitochondrial to glycolytic ATP production and demonstrated altered epithelial differentiation pathways, including NOTCH and TGF-{beta} signaling. These findings reveal that moderate hyperoxia impairs mitochondrial bioenergetics and alters metabolic programming, leading to disrupted mucociliary differentiation. Future in vivo studies should evaluate mitochondrial oxidative fitness as a therapeutic target in neonatal lung disease. NEW & NOTEWORTHYWe report that moderate hyperoxia during a critical window of mucociliary differentiation disrupts terminal maturation in neonatal airway epithelial cells cultured in a 3D model. Hyperoxia induced mitochondrial bioenergetic dysfunction and metabolic reprogramming, with proteomic analysis identifying Complex I disruption as a key driver of impaired differentiation. Overall, these findings reveal a previously underrecognized link between mitochondrial bioenergetics and airway epithelial development, positioning metabolic dysfunction as an early trigger of hyperoxia-induced neonatal airway injury.

developmental biology↗

bioRxiv2025

Precision Breathing: Asthma Phenotyping via Machine Learning

Asthma is a complex condition characterized by chronic airway inflammation, with varying severity, symptoms, triggers, and treatment responses. Traditional classification relies on clinical attributes, but the growing understanding of asthmas heterogeneity highlights the need for phenotyping. Effective management requires regular monitoring, medication, and prevention of exacerbations, but current diagnostic methods face challenges such as the lack of definitive tests and reliance on subjective measures. Implementing precision medicine, especially for severe cases, necessitates identifying measurable markers in biofluids. This study explores machine learning methods to identify biomarkers differentiating various asthma phenotypic states. We measured inflammatory markers in both plasma and saliva samples and used machine learning algorithms to determine their efficacy in reflecting airway inflammation. Our findings indicate that saliva markers provide a more accurate representation of localized inflammation compared to plasma markers, which reflect a systemic response. Using MRMR (Minimum Redundancy Maximum Relevance) ranking, we enhanced model efficacy. The K-Nearest Neighbor (KNN) classifier achieved 75% accuracy with the first 12 saliva markers, while the Random Forest (RF) classifier performed best for plasma models, though with lower accuracy. Our results suggest machine learning can effectively identify key markers for asthma phenotyping, aiding personalized treatment strategies. Customizable point-of-care devices could validate these models and improve their accuracy, advancing asthma treatment and management.

bioengineering↗

bioRxiv2025

Granzyme-targeting quenched activity-based probes for assessing tumor response to immunotherapy

Molecular imaging of immune activation holds tremendous potential for the development of novel immunotherapy. In particular, chemical probes capable of detecting immune responses before changes in tumor size occur can guide early therapeutic strategies. Here, we present quenched activity-based probes targeting granzymes as a biomarker of antitumor immunity. Through optimization of peptide recognition element and functional chemical warhead, we have developed an optical imaging probe Cy5-IEPCyaPhP-QSY21, which rapidly reacts with GzmB at substoichiometric concentrations and enables efficient, selective labeling of the active enzyme in a complex proteome. With high specificity and minimal background signal, this probe produces GzmB-induced near-infrared fluorescence signals in the tumors of living mice shortly after injection. Both in vivo and ex vivo fluorescence signals correlate with GzmB expression and activity, and the population of CD8+ cells in tumor tissues. Moreover, it demonstrates the potential to track tumor response to immunotherapy. Thus, this study offers a chemical tool for assessing immune-mediated anticancer activity using noninvasive optical imaging. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/643086v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1bff748org.highwire.dtl.DTLVardef@3c80dorg.highwire.dtl.DTLVardef@4301ceorg.highwire.dtl.DTLVardef@12b7c8a_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

METTL3 shapes m6A epitranscriptomic landscape for successful human placentation

Methyltransferase-like 3 (METTL3), the catalytic enzyme of methyltransferase complex for m6A methylation of RNA, is essential for mammalian development. However, the importance of METTL3 in human placentation remains largely unexplored. Here, we show that a fine balance of METTL3 function in trophoblast cells is essential for successful human placentation. Both loss-of and gain-in METTL3 functions are associated with adverse human pregnancies. A subset of recurrent pregnancy losses and preterm pregnancies are often associated with loss of METTL3 expression in trophoblast progenitors. In contrast, METTL3 is induced in pregnancies associated with fetal growth restriction (FGR). Our loss of function analyses showed that METTL3 is essential for the maintenance of human TSC self-renewal and their differentiation to extravillous trophoblast cells (EVTs). In contrast, loss of METTL3 in human TSCs promotes syncytiotrophoblast (STB) development. Global analyses of RNA m6A modification and METTL3-RNA interaction in human TSCs showed that METTL3 regulates m6A modifications on the mRNA molecules of critical trophoblast regulators, including GATA2, GATA3, TEAD1, TEAD4, WWTR1, YAP1, TFAP2C and ASCL2, and loss of METTL3 leads to depletion of mRNA molecules of these critical regulators. Importantly, conditional deletion of Mettl3 in trophoblast progenitors of an early post-implantation mouse embryo also leads to arrested self-renewal. Hence, our findings indicate that METLL3 is a conserved epitranscriptomic governor in trophoblast progenitors and ensures successful placentation by regulating their self-renewal and dictating their differentiation fate.

developmental biology↗

bioRxiv2024

CELL CYCLE STATE PREDICTION USING GRAPH NEURAL NETWORKS

Mitosis is a crucial process ensuring the faithful transmission of the genetic information stored in the cell nucleus. Aberrations in this intricate process pose a significant threat to an organisms health, leading to conditions like cancer and various diseases. Hence, the study of mitosis holds paramount importance. Recent investigations have involved manual and semiautomated analyses of time-lapse microscopy images to understand mitosis better. This paper introduces an approach for predicting mitosis stages, employing a Convolutional Neural Network (CNN) as the initial feature extractor, followed by a Graph Neural Network (GNN) for predicting cell cycle states. A distinctive timestamp is incorporated into the feature vectors, treating this information as a graph to leverage internal interactions for predicting the subsequent cell state. To assess performance, experiments were conducted on three datasets, demonstrating that our method exhibits comparable efficacy to state-of-the-art techniques.

cell biology↗

bioRxiv2023

A single pair of pharyngeal neurons functions as a commander to reject high salt in Drosophila melanogaster

Salt is an essential nutrient for survival, while excessive NaCl can be detrimental. In the fruit fly, Drosophila melanogaster, internal taste organs in the pharynx are critical gatekeepers impacting the decision to accept or reject a food. Currently, our understanding of the mechanism through which pharyngeal gustatory receptor neurons (GRNs) sense high salt are rudimentary. Here, we found that a member of the ionotropic receptor family, Ir60b, is expressed exclusively in a pair of GRNs activated by high salt. Using a two-way choice assay (DrosoX) to measure ingestion volume, we demonstrate that IR60b and two coreceptors IR25a and IR76b, are required to prevent high salt consumption. Mutants lacking external taste organs but retaining the internal taste organs in the pharynx exhibit much higher salt avoidance than flies with all taste organs but missing the three IRs. Our findings highlight the vital role for IRs in a pharyngeal GRN to control ingestion of high salt.

neuroscience↗

bioRxiv2023

PP1β opposes classic PP1 function, inhibiting spine maturation and promoting LTP

Protein phosphatase 1 (PP1) regulates synaptic plasticity and has been described as a molecular constraint on learning and memory. There are three neuronal isoforms, PP1, PP1{beta}, and PP1{gamma}, but little is known about their individual functions. PP1 and PP1{gamma} are assumed to mediate the effects of PP1 on learning and memory based on their enrichment at dendritic spines and their preferential binding to neurabin and spinophilin, major PP1 synaptic scaffolding proteins. However, it was recently discovered that human de novo PP1{beta} mutations cause intellectual disability, suggesting an important but ill-defined role for PP1{beta}. In this study, we investigated the functions of each PP1 isoform in hippocampal synaptic physiology using conditional CA1-specific knockout mice. In stark contrast to classic PP1 function, we found that PP1{beta} promotes synaptic plasticity as well as spatial memory. These changes in synaptic plasticity and memory are accompanied by changes in GluA1 phosphorylation, GluN2A levels, and dendritic spine density and morphology, including silent synapse number. These functions of PP1{beta} reveal a previously unidentified signaling pathway regulating spine maturation and plasticity, broadening our understanding of the complex role of PP1 in synaptic physiology.

neuroscience↗

bioRxiv2022

Nuclear inhibitor of protein phosphatase 1 (NIPP1) regulates CNS tau phosphorylation and myelination during development

Nuclear inhibitor of protein phosphatase 1 (NIPP1) is a known regulator of gene expression and has been shown to play roles in many physiological or pathological processes such as stem cell proliferation and skin inflammation. While NIPP1 has many regulatory roles in proliferating cells, its function in the central nervous system (CNS) has not been directly investigated. In the present study, we examined NIPP1 CNS function using a conditional knockout (cKO) mouse model, in which the nipp1 gene is excised from neural precursor cells. These mice demonstrate severe developmental impairments that lead to premature lethality within the first few postnatal weeks. To delineate some of the neurological changes occurring in these animals, we first assessed microtubule associated protein tau, a known target of NIPP1 activity. Furthermore, observed tremors prompted exploration of myelin integrity, an integral structure for CNS function, whose disruption is associated with various neurological disorders and neurodegenerative diseases. First, immunoblotting demonstrated increased phospho-tau and altered AKT and PP1 activity in NIPP1 cKO mice, suggesting increased tau phosphorylation likely results from a shift in kinase/phosphatase activity. Second, immunoblots, electron microscopy, and electrophysiology demonstrated a myelin deficit within the brain and optic nerve. Our study suggests that NIPP1 in neural precursors regulates phosphorylation of tau and CNS myelination and may represent a novel therapeutic target for neurodegenerative diseases.

neuroscience↗

bioRxiv2021

Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign

DNA polymerases have evolved to feature a highly conserved activity across the tree of life: formation of, without exception, phosphodiester linkages that create the repeating sugarphosphate backbone of DNA. Can this linkage selectivity observed in nature be overcome by design to produce non-natural nucleic acids? Here, we report that structure-guided redesign of an archaeal DNA polymerase (9{degrees}N) enables a new polymerase activity that is undetectable in the wild type enzyme: catalyzing the formation of N3[->]P5 phosphoramidate linkages in the presence of 3-amino-2,3-dideoxynucleoside 5-triphosphate (3-NH2-ddNTP) building blocks. Replacing a highly conserved metal-binding aspartate in the 9{degrees}N active site (Asp-404) with asparagine was key to the emergence of this unnatural enzyme activity. Molecular dynamics simulations provided insights into how a single substitution could enhance the productive positioning of the 3-amino nucleophile in the active site. Further remodeling of the protein-nucleic acid interface with substitutions in the finger subdomain led to a quadruple-mutant variant (9{degrees}N-NRQS) that incorporated 3-NH2-ddNTPs into a 3-amino-primer on various DNA templates. This work presents the first example of an active-site substitution of a metal-binding residue that leads to a novel activity in a DNA polymerase, and sheds light on the molecular basis of substrate fidelity and latent promiscuity in enzymes.

biochemistry↗

bioRxiv2021

Post-mating Refractoriness in Drosophila melanogaster Depends Upon Ecdysis Triggering Hormone Signaling

An individuals decision to engage in courtship depends on external cues from potential mates and internal cues related to maturation, health, and experience. Hormones allow such information to be conveyed to distal tissues in a coordinated fashion. Here, we show Ecdysis-Triggering Hormone (ETH) is a regulator of male courtship in Drosophila melanogaster, and critical for mate choice and courtship inhibition after the completion of copulation. Preventing ETH release increases male-male courtship and decreases post-copulation courtship inhibition (PCCI). Such aberrant male courtship behavior in ETH-deficient males appears to be the consequence of inabilityto integrate pheromone cues into decision making. Silencing of ETH receptor (ETHR) in GR32A-expressing neurons leads to reduced ligand sensitivity and elevated male-male courtship. We find OR67D is critical for suppression of courtship after mating, and ETHR silencing in OR67D-expressing neurons, and GR32A-expressing neurons to a lesser degree, elevates post-copulation courtship. Finally, ETHR silencing in the corpus allatum increases post-copulation courtship; treatment of with juvenile hormone analog partially restores normal post-mating behavior. ETH, a stress-sensitive reproductive hormone, appears to coordinate multiple sensory modalities to guide Drosophila male courtship behaviors, especially after mating.

neuroscience↗

bioRxiv2021

Structural and functional characterization of Rv0792c from Mycobacterium tuberculosis: identifying small molecule inhibitors against GntR protein.

In order to adapt in host tissues, microbial pathogens regulate their gene expression through an array of transcription factors. Here, we have functionally characterized Rv0792c, a GntR homolog from M. tuberculosis. In comparison to the parental strain, {Delta}Rv0792c mutant strain of M. tuberculosis was compromised for survival upon exposure to oxidative stress, cell wall agents and infection in guinea pigs. RNA-seq analysis revealed that Rv0792c regulates the expression of genes that are involved in stress adaptation and virulence of M. tuberculosis. Solution small angle X-ray scattering (SAXS) data steered model building confirmed that the C-terminal region plays a pivotal role in dimer formation. Systematic evolution of ligands by exponential enrichment resulted in identification of ssDNA aptamers that can be used as a tool to identify small molecule inhibitors targeting Rv0792c. Using SELEX and SAXS data based modelling, we identified residues essential for the DNA binding activity of Rv0792c and I-OMe-Tyrphostin as an inhibitor of Rv0792c aptamer binding activity. Taken together, we provide a detailed shape-function characterization of GntR family of transcription factors from M. tuberculosis. To the best of our knowledge, this is the first study that has resulted in the identification of small molecule inhibitors against GntR family of transcription factors from bacterial pathogens.

microbiology↗

bioRxiv2021

Mechanistic insight into light-dependent recognition of Timeless by Drosophila cryptochrome

Cryptochrome (CRY) entrains the fly circadian clock by binding to Timeless (TIM) in light and triggering its degradation. Undocking of a helical C-terminal tail (CTT) in response to photoreduction of the CRY flavin cofactor gates TIM binding. A generally-applicable Select Western-blot-Free Tagged-protein Interaction (SWFTI) assay enables quantification of CRY binding to TIM in dark and light. The assay is utilized to study CRY variants with residue substitutions in the flavin pocket and correlate their TIM affinities with CTT undocking, as measured by pulse-dipolar ESR spectroscopy and evaluated by molecular dynamics simulations. CRY variants with the CTT removed or undocked bind TIM constitutively, whereas those incapable of photoreduction bind TIM weakly. In response to flavin redox state, two conserved histidine residues contribute to a robust on/off switch by mediating CTT interactions with the flavin pocket and TIM. Our approach provides an expeditious means to quantify protein-protein interactions and photoreceptor targeting.

biochemistry↗

bioRxiv2021

Requirement for an Otopetrin-Like protein for acid taste in Drosophila

Many of the Drosophila receptors required for bitter, sugar and other tastes have been identified. However, the receptor required for the taste of acid has been elusive. In Drosophila, the major families of taste receptors, such as "Gustatory Receptors" and "Ionotropic Receptors" are unrelated to taste receptors in mammals. Previous work indicated that members of these major families do not appear to be broadly required acid sensors. Here, to identify the enigmatic acid taste receptor, we interrogated three genes encoding proteins distantly related the mammalian Otopertrin1 proton channel. We found that RNAi knockdown or mutation of Otopetrin-Like A (OtopLA) by CRISPR/Cas9, severely impairs the behavioral rejection of sugary foods laced with HCl or carboxylic acids. Mutation of OtopLA also greatly reduces acid-induced action potentials. We identified an isoform of OtopLA that was expressed in the proboscis and was sufficient to restore acid sensitivity to OtopLA mutant flies. OtopLA functioned in acid taste in a subset of bitter-activated gustatory receptor neurons that senses protons. This work highlights an unusual functional conservation of a receptor required for a taste modality in flies and mammals.

neuroscience↗

bioRxiv2021

Anti-allergic and anti-inflammatory activities of black cumin extracts in in vitro and in vivo model systems

Black cumin (Nigella sativa) is a widely used ingredient of traditional medicine for its broad-spectrum pharmacological actions, including anti-allergic, bronchial asthma, and anti-inflammatory properties. We sought to evaluate BC extracts efficacy for their anti-allergic and anti-inflammatory properties using a comprehensive in vitro, in vivo, and silico experimental setup. To investigate whether BC extract has anti-inflammatory, anti-allergic, and analgesic therapeutic potentials in vitro and in vivo. The activity of BC was assessed through anti-allergic activity on rat basophilic leukemia-2H3 cell line, anti-inflammatory activity on J774.1A cell line, anti-inflammatory activity by carrageenan-induced rat paw edema, analgesic activity by acetic acid-induced writhing test, and ingenuity analysis of the BC extracts in inflammation control. BC exerted potent anti-allergic activity by inhibiting antigen-induced degranulation. An anti-inflammatory effect is shown by inhibiting TNF- production. The acetic acid-induced writhing test shown a dose-dependent reduction of writhing number following BC administration. Rat paw edema test shown the dose-dependent reduction of paw edema volume following BC administration. Ingenuity Pathway Analysis (IPA) suggested BC extracts containing ferulic acid, p-coumaric acid, kaempferol, and quercetin can inhibit inflammation. This study suggests that bioactive compounds in BC extract act as an anti-allergic and anti-inflammatory agent by regulating several downstream and upstream inflammation pathways.

plant biology↗

bioRxiv2020

Aberrant RNA methylation triggers recruitment of an alkylation repair complex

A critical question in genome stability is the nature of the chemical damage responsible for repair activation. We previously reported a novel pathway specifically activated during alkylation damage in human cells, where the E3 ubiquitin ligase RNF113A mediates the recruitment of the ASCC repair complex. Yet the mechanistic basis for the alkylation damage selectivity of this pathway remains unclear. Here, we demonstrate that RNA but not DNA alkylation is the initiating signal for this process. Aberrantly methylated RNA is sufficient to recruit ASCC, while an RNA dealkylase suppresses ASCC recruitment during chemical alkylation. This aberrant RNA methylation causes transcriptional repression in a manner dependent on the ASCC complex. We show that an alkylated pre-mRNA, or an RNA containing a single damaged base, is sufficient to activate RNF113A E3 activity in a phosphorylation-dependent manner. Together, our work identifies an unexpected role for RNA damage in eliciting a DNA repair response, and suggests that RNA may serve as the "canary in the coal mine" for sensing alkylation damage.

molecular biology↗